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A LARGE MARGIN APPROACH
A DISSERTATION
SUBMITTED TO THE DEPARTMENT OF COMPUTER SCIENCE
AND THE COMMITTEE ON GRADUATE STUDIES
OF STANFORD UNIVERSITY
IN PARTIAL FULFILLMENT OF THE REQUIREMENTS
FOR THE DEGREE OF
DOCTOR OF PHILOSOPHY
Ben Taskar
December 2004
c _Copyright by Ben Taskar 2005
All Rights Reserved
ii
I certify that I have read this dissertation and that, in my opin
ion, it is fully adequate in scope and quality as a dissertation
for the degree of Doctor of Philosophy.
Daphne Koller
Computer Science Department
Stanford University
(Principal Advisor)
I certify that I have read this dissertation and that, in my opin
ion, it is fully adequate in scope and quality as a dissertation
for the degree of Doctor of Philosophy.
Andrew Y. Ng
Computer Science Department
Stanford University
I certify that I have read this dissertation and that, in my opin
ion, it is fully adequate in scope and quality as a dissertation
for the degree of Doctor of Philosophy.
Fernando Pereira
Computer Science Department
University of Pennsylvania
Approved for the University Committee on Graduate Stud
ies:
iii
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To my parents, Mark and Tsilya, and my love, Anat.
Abstract
Most questions require more than just truefalse or multiplechoice answers. Yet super
vised learning, like standardized testing, has placed the heaviest emphasis on complex
questions with simple answers. The acquired expertise must now be used to address tasks
that demand answers as complex as the questions. Such complex answers may consist of
multiple interrelated decisions that must be weighed against each other to arrive at a glob
ally satisfactory and consistent solution to the question. In natural language processing, we
often need to construct a global, coherent analysis of a sentence, such as its corresponding
partofspeech sequence, parse tree, or translation into another language. In computational
biology, we analyze genetic sequences to predict 3D structure of proteins, ﬁnd global align
ment of related DNA strings, and recognize functional portions of a genome. In computer
vision, we segment complex objects in cluttered scenes, reconstruct 3D shapes from stereo
and video, and track motion of articulated bodies.
We typically handle the exponential explosion of possible answers by building mod
els that compactly capture the structural properties of the problem: sequential, grammat
ical, chemical, temporal, spatial constraints and correlations. Such structured models in
clude graphical models such as Markov networks (Markov random ﬁelds), recursive lan
guage models such as context free grammars, combinatorial optimization problems such as
weighted matchings and graphcuts. This thesis presents a discriminative estimation frame
work for structured models based on the large margin principle underlying support vector
machines. Intuitively, the largemargin criterion provides an alternative to probabilistic,
likelihoodbased estimation methods by concentrating directly on the robustness of the de
cision boundary of a model. Our framework deﬁnes a suite of efﬁcient learning algorithms
that rely on the expressive power of convex optimization to compactly capture inference or
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solution optimality in structured models. For some of these models, alternative estimation
methods are intractable.
The largest portion of the thesis is devoted to Markov networks, which are undirected
probabilistic graphical models widely used to efﬁciently represent and reason about joint
multivariate distributions. We use graph decomposition to derive an exact, compact, con
vex formulation for largemargin estimation of Markov networks with sequence and other
lowtreewidth structure. Seamless integration of kernels with graphical models allows ef
ﬁcient, accurate prediction in realworld tasks. We analyze the theoretical generalization
properties of maxmargin estimation in Markov networks and derive a novel type of bound
on structured error. Using an efﬁcient onlinestyle algorithm that exploits inference in the
model and analytic updates, we solve very large estimation problems.
We deﬁne an important subclass of Markov networks, associative Markov networks
(AMNs), which captures positive correlations between variables and permits exact infer
ence which scales up to tens of millions of nodes and edges. While likelihoodbased meth
ods are believed to be intractable for AMNs over binary variables, our framework allows
exact estimation of such networks of arbitrary connectivity and topology. We also intro
duce relational Markov networks (RMNs), which compactly deﬁne templates for Markov
networks for domains with relational structure: objects, attributes, relations.
In addition to graphical models, our framework applies to a wide range of other models:
We exploit context free grammar structure to derive a compact maxmargin formulation that
allows highaccuracy parsing in cubic time by using novel kinds of lexical information. We
use combinatorial properties of weighted matchings to develop an exact, efﬁcient formu
lation for learning to match and apply it to prediction of disulﬁde connectivity in proteins.
Finally, we derive a maxmargin formulation for learning the scoring metric for clustering
from clustered training data, which tightly integrates metric learning with the clustering
algorithm, tuning one to the other in a joint optimization.
We describe experimental applications to a diverse range of tasks, including handwrit
ing recognition, 3D terrain classiﬁcation, disulﬁde connectivity prediction in proteins, hy
pertext categorization, natural language parsing, email organization and image segmen
tation. These empirical evaluations show signiﬁcant improvements over stateoftheart
methods and promise wide practical use for our framework.
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Acknowledgements
I am profoundly grateful to my advisor, Daphne Koller. Her tireless pursuit of excellence in
research, teaching, advising, and every other aspect of her academic work is truly inspira
tional. I am indebted to Daphne for priceless and copious advice about selecting interesting
problems, making progress on difﬁcult ones, pushing ideas to their full development, writ
ing and presenting results in an engaging manner.
I would like to thank my thesis committee, Andrew Ng and Fernando Pereira, as well
as my defense committee members, Stephen Boyd and Sebastian Thrun, for their excellent
suggestions and thoughtprovoking questions. I have learned a great deal from their work
and their inﬂuence on this thesis is immense. In particular, Fernando’s work on Markov
networks has inspired my focus on this subject. Andrew’s research on clustering and clas
siﬁcation has informed many of the practical problems addressed in the thesis. Sebastian
introduced me to the fascinating problems in 3D vision and robotics. Finally, Stephen’s
book on convex optimization is the primary source of many of the insights and derivations
in this thesis.
Daphne’s research group is an institution in itself. I am very lucky to have been a part
of it and shared the company, the ideas, the questions and the expertise of Pieter Abbeel,
Drago Anguelov, Alexis Battle, Luke Biewald, Xavier Boyen, Vassil Chatalbashev, Gal
Chechik, Lise Getoor, Carlos Guestrin, Uri Lerner, Uri Nodelman, Dirk Ormoneit, Ron
Parr, Eran Segal, Christian Shelton, Simon Tong, David Vickrey, Haidong Wang and Ming
Fai Wong.
JeanClaude Latombe was my ﬁrst research advisor when I was still an undergraduate
at Stanford. His thoughtful guidance and quick wit were a great welcome and inspiration
to continue my studies. When I started my research in machine learning with Daphne, I
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had the privilege and pleasure to work with Nir Friedman, Lise Getoor and Eran Segal.
They have taught me to remain steadfast when elegant theories meet the ragged edge of
real problems. Lise has been a great friend and my other big sister throughout my graduate
life. I could not wish for more caring advice and encouragement than she has given me all
these years.
I was lucky to meet Michael Collins, Michael Littman and David McAllester all in
one place, while I was a summer intern at AT&T. Collins’ work on learning largemargin
tagging and parsing models motivated me to look at such methods for other structured
models. I am very glad I had the chance to work with him on the maxmargin parsing
project. Michael Littman, with his endearing combination of humor and warmth, lightness
and depth, has been a constant source of encouragement and inspiration. David’s wide
ranging research on probability and logic, languages and generalization bounds, to mention
a few, enlightened much of my work.
(Almost) everything I know about natural language processing I learned from Chris
Manning and Dan Klein. Chris’ healthy scepticism and emphasis on the practical has kept
me from going down many deadend paths. Dan has an incredible gift of making ideas
work, and better yet, explaining why other ideas do not work.
I would like to express my appreciation and gratitude to all my collaborators for their
excellent ideas, hard work and dedication: Pieter Abbeel, Drago Anguelov, Peter Bartlett,
Luke Biewald, Vassil Chatalbashev, Michael Collins, Nir Friedman, Audrey Gasch, Lise
Getoor, Carlos Guestrin, Geremy Heitz, Dan Klein, Daphne Koller, Chris Manning, David
McAllester, Eran Segal, David Vickrey and Ming Fai Wong.
Merci beaucoup to Pieter Abbeel, my sounding board for many ideas in convex opti
mization and learning, for numerous enlightening discussions that we have had anytime,
anywhere: gym, tennis court, biking to EV, over cheap Thai food. Ogromnoye spasibo to
my ofﬁcemate, sportsmate, always late, everready to checkmate, Drago Anguelov, who
is always willing to share with me everything from research problems to music and back
packing treks to Russian books and Belgian beer. Blagodarya vi mnogo for another great
Bulgarian I have the good luck to know, Vasco Chatalbashev, for his company and ideas,
good cheer and the great knack for always coming through. Muchas gracias to Carlos
Guestrin, my personal climbing instructor, fellow photography fanatic, avid grillmaster
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and exploiterofstructure extraordinaire, for opening his ear and heart to me when it mat
ters most. Mhgoisaai to Ming Fai Wong, for his sense of humor, kind heart and excellent
work.
Many thanks to my friends who have had nothing to do with work in this thesis, but
worked hard to keep my relative sanity throughout. I will not list all of you here, but my
gratitude to you is immense.
My parents, Mark and Tsilya, have given me unbending support and constant encour
agement. I thank them for all the sacriﬁces they have made to ensure that their children
would have freedom and opportunities they never had in Soviet Union. To my sister, Anna,
my brotherinlaw, Ilya, and my sweet niece, Talia, I am grateful for bringing me so much
joy and love. To my tireless partner in work and play, tears and laughter, hardship and love,
Anat Caspi, thank you for making me happy next to you.
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Contents
Abstract vii
Acknowledgements ix
1 Introduction 1
1.1 Supervised learning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 Complex prediction problems . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 Structured models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.4 Contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.5 Thesis outline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.6 Previously published work . . . . . . . . . . . . . . . . . . . . . . . . . . 13
I Models and methods 15
2 Supervised learning 16
2.1 Classiﬁcation with generalized linear models . . . . . . . . . . . . . . . . 19
2.2 Logistic regression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.3 Logistic dual and maximum entropy . . . . . . . . . . . . . . . . . . . . . 21
2.4 Support vector machines . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.5 SVM dual and kernels . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3 Structured models 24
3.1 Probabilistic models: generative and conditional . . . . . . . . . . . . . . . 25
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3.2 Prediction models: normalized and unnormalized . . . . . . . . . . . . . . 27
3.3 Markov networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.3.1 Representation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.3.2 Inference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.3.3 Linear programming MAP inference . . . . . . . . . . . . . . . . . 34
3.4 Context free grammars . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.5 Combinatorial problems . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
4 Structured maximum margin estimation 42
4.1 Maxmargin estimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.1.1 Minmax formulation . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.1.2 Certiﬁcate formulation . . . . . . . . . . . . . . . . . . . . . . . . 48
4.2 Approximations: upper and lower bounds . . . . . . . . . . . . . . . . . . 50
4.2.1 Constraint generation . . . . . . . . . . . . . . . . . . . . . . . . . 50
4.2.2 Constraint strengthening . . . . . . . . . . . . . . . . . . . . . . . 52
4.3 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
4.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
II Markov networks 57
5 Markov networks 58
5.1 Maximum likelihood estimation . . . . . . . . . . . . . . . . . . . . . . . 59
5.2 Maximum margin estimation . . . . . . . . . . . . . . . . . . . . . . . . . 61
5.3 M
3
N dual and kernels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
5.4 Untriangulated models . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
5.5 Generalization bound . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
5.6 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
5.7 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
6 M
3
N algorithms and experiments 75
6.1 Solving the M
3
N QP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
6.1.1 SMO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
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6.1.2 Selecting SMO pairs . . . . . . . . . . . . . . . . . . . . . . . . . 79
6.1.3 Structured SMO . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
6.2 Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
6.3 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
6.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
7 Associative Markov networks 89
7.1 Associative networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
7.2 LP Inference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
7.3 Mincut inference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
7.3.1 Graph construction . . . . . . . . . . . . . . . . . . . . . . . . . . 93
7.3.2 Multiclass case . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
7.4 Maxmargin estimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
7.5 Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
7.6 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
7.7 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
8 Relational Markov networks 109
8.1 Relational classiﬁcation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
8.2 Relational Markov networks . . . . . . . . . . . . . . . . . . . . . . . . . 113
8.3 Approximate inference and learning . . . . . . . . . . . . . . . . . . . . . 116
8.4 Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
8.4.1 Flat models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
8.4.2 Link model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
8.4.3 Cocite model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
8.5 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
8.6 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
III Broader applications: parsing, matching, clustering 127
9 Context free grammars 128
9.1 Context free grammar model . . . . . . . . . . . . . . . . . . . . . . . . . 128
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9.2 Context free parsing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
9.3 Discriminative parsing models . . . . . . . . . . . . . . . . . . . . . . . . 133
9.3.1 Maximum likelihood estimation . . . . . . . . . . . . . . . . . . . 134
9.3.2 Maximum margin estimation . . . . . . . . . . . . . . . . . . . . . 135
9.4 Structured SMO for CFGs . . . . . . . . . . . . . . . . . . . . . . . . . . 138
9.5 Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
9.6 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
9.7 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
10 Matchings 144
10.1 Disulﬁde connectivity prediction . . . . . . . . . . . . . . . . . . . . . . . 145
10.2 Learning to match . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
10.3 Minmax formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
10.4 Certiﬁcate formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
10.5 Kernels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
10.6 Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
10.7 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
10.8 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
11 Correlation clustering 160
11.1 Clustering formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
11.1.1 Linear programming relaxation . . . . . . . . . . . . . . . . . . . 162
11.1.2 Semideﬁnite programming relaxation . . . . . . . . . . . . . . . . 163
11.2 Learning formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
11.3 Dual formulation and kernels . . . . . . . . . . . . . . . . . . . . . . . . . 167
11.4 Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
11.4.1 Irrelevant features . . . . . . . . . . . . . . . . . . . . . . . . . . 168
11.4.2 Email clustering . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
11.4.3 Image segmentation . . . . . . . . . . . . . . . . . . . . . . . . . 170
11.5 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
11.6 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
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IV Conclusions and future directions 175
12 Conclusions and future directions 176
12.1 Summary of contributions . . . . . . . . . . . . . . . . . . . . . . . . . . 176
12.1.1 Structured maximum margin estimation . . . . . . . . . . . . . . . 177
12.1.2 Markov networks: maxmargin, associative, relational . . . . . . . 180
12.1.3 Broader applications: parsing, matching, clustering . . . . . . . . . 182
12.2 Extensions and open problems . . . . . . . . . . . . . . . . . . . . . . . . 183
12.2.1 Theoretical analysis and optimization algorithms . . . . . . . . . . 183
12.2.2 Novel prediction tasks . . . . . . . . . . . . . . . . . . . . . . . . 184
12.2.3 More general learning settings . . . . . . . . . . . . . . . . . . . . 185
12.3 Future . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
A Proofs and derivations 188
A.1 Proof of Theorem 5.5.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
A.1.1 Binary classiﬁcation . . . . . . . . . . . . . . . . . . . . . . . . . 189
A.1.2 Structured classiﬁcation . . . . . . . . . . . . . . . . . . . . . . . 190
A.2 AMN proofs and derivations . . . . . . . . . . . . . . . . . . . . . . . . . 195
A.2.1 Binary AMNs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
A.2.2 Multiclass AMNs . . . . . . . . . . . . . . . . . . . . . . . . . . 197
A.2.3 Derivation of the factored primal and dual maxmargin QP . . . . . 199
Bibliography 202
xvii
List of Tables
9.1 Parsing results on development set . . . . . . . . . . . . . . . . . . . . . . 140
9.2 Parsing results on test set . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
10.1 Bond connectivity prediction results . . . . . . . . . . . . . . . . . . . . . 156
xviii
List of Figures
1.1 Supervised learning setting . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 Examples of complex prediction problems . . . . . . . . . . . . . . . . . . 4
2.1 Handwritten character recognition . . . . . . . . . . . . . . . . . . . . . . 19
2.2 Classiﬁcation loss and upper bounds . . . . . . . . . . . . . . . . . . . . . 20
3.1 Handwritten word recognition . . . . . . . . . . . . . . . . . . . . . . . . 25
3.2 Chain Markov network . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3.3 Diamond Markov network . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3.4 Diamond network junction tree . . . . . . . . . . . . . . . . . . . . . . . . 34
3.5 Marginal agreement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.6 Example parse tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
4.1 Exact and approximate constraints for maxmargin estimation . . . . . . . 51
4.2 A constraint generation algorithm. . . . . . . . . . . . . . . . . . . . . . . 52
5.1 Chain M
3
N example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
5.2 Diamond Markov network . . . . . . . . . . . . . . . . . . . . . . . . . . 69
6.1 Blockcoordinate ascent . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
6.2 SMO subproblem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
6.3 SMO pair selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
6.4 Structured SMO diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
6.5 Structured SMO pair selection . . . . . . . . . . . . . . . . . . . . . . . . 85
6.6 OCR results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
xix
7.1 Mincut graph construction . . . . . . . . . . . . . . . . . . . . . . . . . . 94
7.2 αexpansion algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
7.3 Segbot: roving robot equipped with SICK2 laser sensors. . . . . . . . . . . 100
7.4 3D laser scan range map of the Stanford Quad. . . . . . . . . . . . . . . . 101
7.5 Comparison of terrain classiﬁcation models (detail) . . . . . . . . . . . . . 102
7.6 Mincut inference running times . . . . . . . . . . . . . . . . . . . . . . . 103
7.7 Comparison of terrain classiﬁcation models (zoomedout) . . . . . . . . . . 106
7.8 Labeled portion of the test terrain dataset (Ground truth and SVMpredictions)107
7.9 Labeled portion of the test terrain dataset (VotedSVM and AMN predictions)108
8.1 Link model for document classiﬁcation . . . . . . . . . . . . . . . . . . . 113
8.2 WebKB results: ﬂat models . . . . . . . . . . . . . . . . . . . . . . . . . . 120
8.3 WebKB results: link model . . . . . . . . . . . . . . . . . . . . . . . . . . 121
8.4 WebKB results: cocite model . . . . . . . . . . . . . . . . . . . . . . . . . 122
9.1 Two representations of a binary parse tree . . . . . . . . . . . . . . . . . . 130
10.1 PDB protein 1ANS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
10.2 Number of constraints vs. number of bonds . . . . . . . . . . . . . . . . . 150
10.3 Learning curve for bond connectivity prediction . . . . . . . . . . . . . . . 157
11.1 Learning to cluster with irrelevant features . . . . . . . . . . . . . . . . . . 169
11.2 Learning to organize email . . . . . . . . . . . . . . . . . . . . . . . . . . 170
11.3 Two segmentations by different users . . . . . . . . . . . . . . . . . . . . . 171
11.4 Two segmentations by different models . . . . . . . . . . . . . . . . . . . 172
xx
Chapter 1
Introduction
The breadth of tasks addressed by machine learning is rapidly expanding. Major appli
cations include medical diagnosis, scientiﬁc discovery, ﬁnancial analysis, fraud detection,
DNA sequence analysis, speech and handwriting recognition, game playing, image analy
sis, robot locomotion and many more. Of course, the list of things we would like a computer
to learn to do is much, much longer. As we work our way down that list, we encounter the
need for very sophisticated decision making from our programs.
Some tasks, for example, handwriting recognition, are performed almost effortlessly
by a person, but remain difﬁcult and errorprone for computers. The complex synthesis
of many levels of signal processing a person executes when confronted by a line of hand
written text is daunting. The reconstruction of an entire sentence from the photons hitting
the retina off of each tiny patch of an image undoubtedly requires an elaborate interplay of
recognition and representation of the penstrokes, the individual letters, whole words and
constituent phrases.
Computer scientists, as opposed to, say, neuroscientists, are primarily concerned with
achieving acceptable speed and accuracy of recognition rather than modeling this compli
cated process with any biological verity. Computational models for handwriting recogni
tion aim to capture the salient properties of the problem: typical shapes of the letters, likely
letter combinations that make up words, common ways to combine words into phrases, fre
quent grammatical constructions of the phrases, etc. Machine learning offers an alternative
to encoding all the intricate details of such a model from scratch. One of its primary goals
1
2 CHAPTER 1. INTRODUCTION
is to devise efﬁcient algorithms for training computers to automatically acquire effective
and accurate models from experience.
In this thesis, we present a discriminative learning framework and a novel family of efﬁ
cient models and algorithms for complex recognition tasks in several disciplines, including
natural language processing, computer vision and computational biology. We develop the
oretical foundations for our approach and show a wide range of experimental applications,
including handwriting recognition, 3dimensional terrain classiﬁcation, disulﬁde connec
tivity in protein structure prediction, hypertext categorization, natural language parsing,
email organization and image segmentation.
1.1 Supervised learning
The most basic supervised learning task is classiﬁcation. Suppose we wish to learn to
recognize a handwritten character from a scanned image. This is a classiﬁcation task,
because we must assigns a class (an English letter from ‘a’ through ‘z’) to an observation of
an object (an image). Essentially, a classiﬁer is a function that maps an input (an image) to
an output (a letter). In the supervised learning setting, we construct a classiﬁer by observing
labeled training examples, in our case, sample images paired with appropriate letters. The
main problem addressed by supervised learning is generalization. The learning program is
allowed to observe only a small sample of labeled images to produce an accurate classiﬁer
on unseen images of letters.
More formally, let x denote an input. For example, a blackandwhite image x can be
represented as a vector of pixel intensities. We use A to denote the space of all possible
inputs. Let y denote the output, and ¸ be the discrete space of possible outcomes (e.g.,
26 letters ‘a’‘z’). A classiﬁer (or hypothesis) h is a function from A to ¸, h : A → ¸.
We denote the set of all classiﬁers that our learning program can produce as H (hypothesis
class). Then given a set of labeled examples ¦x
(i)
, y
(i)
¦, i = 1, . . . , m, a learning program
seeks to produce a classiﬁer h ∈ H that will work well on unseen examples x, usually by
ﬁnding h that accurately classiﬁes training data. The diagram in Fig. 1.1 summarizes the
supervised learning setting.
1.1. SUPERVISED LEARNING 3
Labeled data
Learning
Prediction
Hypotheses
New data
Figure 1.1: Supervised learning setting
The problem of classiﬁcation has a long history and highly developed theory and prac
tice (see for example, Mitchell [1997]; Vapnik [1995]; Duda et al. [2000]; Hastie et al.
[2001]). The two most important dimensions of variation of classiﬁcation algorithms is the
hypothesis class Hand the criterion for selection of a hypothesis h from Hgiven the train
ing data. In this thesis, we build upon the generalized linear model family, which underlies
standard classiﬁers such as logistic regression and support vector machines. Through the
use of kernels to implicitly deﬁne highdimensional and even inﬁnitedimensional input
representations, generalized linear models can approximate arbitrarily complex decision
boundaries.
The task of selecting a hypothesis h reduces to estimating model parameters. Broadly
speaking, probabilistic estimation methods associate a joint distribution p(x, y) or condi
tional distribution p(y [ x) with h and select a model based on the likelihood of the data
[Hastie et al., 2001]. Joint distribution models are often called generative, while condi
tional models are called discriminative. Large margin methods, by contrast, select a model
based on a more direct measure of conﬁdence of its predictions on the training data called
the margin [Vapnik, 1995]. The difference between these two methods is one of the key
4 CHAPTER 1. INTRODUCTION
Thescreenwas
aseaofred
RSCCPCYWGGCPW
GQNCYPEGCSGPKV
brace
(a) (b) (c) (d)
Figure 1.2: Examples of complex prediction problems (inputstop, outputsbottom):
(a) handwriting recognition [image →word];
(b) natural language parsing [sentence →parse tree];
(c) disulﬁde bond prediction in proteins [aminoacid sequence →bond structure (shown in yellow)];
(d) terrain segmentation [3D image →segmented objects (trees, bushes, buildings, ground)]
themes in this thesis.
Most of the research has focused on the analysis and classiﬁcation algorithms for the
case of binary outcomes [¸[ = 2, or a small number of classes. In this work, we focus
on prediction tasks that involve not a single decision with a small set of outcomes, but a
complex, interrelated collection of decisions.
1.2 Complex prediction problems
Consider once more the problem of character recognition. In fact, a more natural and useful
task is recognizing words and entire sentences. Fig. 1.2(a) shows an example handwritten
word “brace.” Distinguishing between the second letter and fourth letter (‘r’ and ‘c’) in iso
lation is actually far from trivial, but in the context of the surrounding letters that together
form a word, this task is much less errorprone for humans and should be for computers
as well. It is also more complicated, as different decisions must be weighed against each
other to arrive at the globally satisfactory prediction. The space of all possible outcomes
1.2. COMPLEX PREDICTION PROBLEMS 5
¸ is immense, usually exponential in the number of individual decisions, for example, the
number of 5 letter sequences (26
5
). However, most of these outcomes are unlikely given
the observed input. By capturing the most salient structure of the problem, for example the
strong local correlations between consecutive letters, we will construct compact models
that efﬁciently deal with this complexity. Below we list several examples from different
ﬁelds.
• Natural language processing
Vast amounts of electronically available text have spurred a tremendous amount of
research into automatic analysis and processing of natural language. We mention
some of the lowerlevel tasks that have received a lot of recent attention [Charniak,
1993; Manning & Sch¨ utze, 1999]. Partofspeech tagging involves assigning each
word in a sentence a partofspeech tag, such as noun, verb, pronoun, etc. As with
handwriting recognition, capturing sequential structure of correlations between con
secutive tags is key. In parsing, the goal is to recognize the recursive phrase structure
of a sentence, such as verbal, noun and prepositional phrases and their nesting in
relation to each other. Fig. 1.2(b) shows a parse tree corresponding to the sentence:
“The screen was a sea of red” (more on this in Ch. 9). Many other problems, such as
namedentity and relation extraction, text summarization, translation, involve com
plex global decision making.
• Computational biology
The last two decades have yielded a wealth of highthroughput experimental data,
including complete sequencing of many genomes, precise measurements of protein
3D structure, genomewide assays of mRNA levels and proteinprotein interactions.
Major research has been devoted to geneﬁnding, alignment of sequences, protein
structure prediction, molecular pathway discovery [Gusﬁeld, 1997; Durbin et al.,
1998]. Fig. 1.2(c) shows disulﬁde bond structure (shown in yellow) we would like to
predict from the aminoacid sequence of the protein (more on this in Ch. 10).
• Computer vision
As digital cameras and optical scanners become commonplace accessories, medical
imaging technology produces detailed physiological measurements, laser scanners
6 CHAPTER 1. INTRODUCTION
capture 3D environments, satellites and telescopes bring pictures of Earth and distant
stars, we are ﬂooded with images we would like our computer to analyze. Example
tasks include object detection and segmentation, motion tracking, 3D reconstruction
from stereo and video, and much more [Forsyth & Ponce, 2002]. Fig. 1.2(d) shows a
3D laser range data image of the Stanford campus collected by a roving robot which
we would like to segment into objects such as trees, bushes, buildings, ground, etc.
(more on this in Ch. 7).
1.3 Structured models
This wide range of problems have been tackled using various models and methods. We
focus on the models that compactly capture correlation and constraint structure inherent to
many tasks. Abstractly, a model assigns a score (or likelihood in probabilistic models) to
each possible input/output pair (x, y), typically through a compact, parameterized scoring
function. Inference in these models refers to computing the highest scoring output given
the input and usually involves dynamic programming or combinatorial optimization.
• Markov networks
Markov networks (a.k.a. Markov random ﬁelds) are extensively used to model com
plex sequential, spatial, and relational interactions in prediction problems arising in
many ﬁelds. These problems involve labeling a set of related objects that exhibit
local consistency. Markov networks compactly represent complex joint distributions
of the label variables by modeling their local interactions. Such models are encoded
by a graph, whose nodes represent the different object labels, and whose edges rep
resent and quantify direct dependencies between them. The graphical structure of
the models encodes the qualitative aspects of the distribution: direct dependencies as
well as conditional independencies. The quantitative aspect of the model is deﬁned
by the potentials that are associated with nodes and cliques of the graph. The graph
ical structure of the network (more precisely, the treewidth of the graph, which we
formally deﬁne in Ch. 3) is critical to efﬁcient inference and learning in the model.
• Context free grammars
1.3. STRUCTURED MODELS 7
Contextfree grammars are one of the primary formalisms for capturing the recur
sive structure of syntactic constructions [Manning & Sch¨ utze, 1999]. For example,
in Fig. 1.2, the nonterminal symbols (labels of internal nodes) correspond to syntac
tic categories such as noun phrase (NP), verbal phrase (VP) or prepositional phrase
(PP) and partofspeech tags like nouns (NN), verbs (VBD), determiners (DT) and
prepositions (IN). The terminal symbols (leaves) are the words of the sentence. A
CFG consists of recursive productions (e.g. V P → V P PP, DT → The) that
can be applied to derive a sentence of the language. The productions deﬁne the set
of syntactically allowed phrase structures (derivations). By compactly deﬁning a
probability distribution over individual productions, probabilistic CFGs construct a
distribution over parse trees and sentences, and the prediction task reduces to ﬁnding
the most likely tree given the sentence. The context free restriction allows efﬁcient
inference and learning in such models.
• Combinatorial structures
Many important computational tasks are formulated as combinatorial optimization
problems such as the maximum weight bipartite and perfect matching, spanning
tree, graphcut, edgecover, and many others [Lawler, 1976; Papadimitriou & Stei
glitz, 1982; Cormen et al., 2001]. Although the term ‘model’ is often reserved for
probabilistic models, we use the term model very broadly, to include any scheme
that assigns scores to the output space ¸ and has a procedure for ﬁnding the opti
mal scoring y. For example, the disulﬁde connectivity prediction in Fig. 1.2(c) can
be modeled by maximum weight perfect matchings, where the weights deﬁne po
tential bond strength based on the local aminoacid sequence properties. The other
combinatorial structures we consider and apply in this thesis include graph cuts and
partitions, bipartite matchings, and spanning trees.
The standard methods of estimation for Markov networks and context free grammars
are based on maximum likelihood, both joint and conditional. However, maximum like
lihood estimation of scoring function parameters for combinatorial structures is often in
tractable because of the problem of deﬁning a normalized distribution over an exponential
set of combinatorial structures.
8 CHAPTER 1. INTRODUCTION
1.4 Contributions
This thesis addresses the problemof efﬁcient learning of highaccuracy models for complex
prediction problems. We consider a very large class of structured models, from Markov
networks to context free grammars to combinatorial graph structures such as matchings
and cuts. We focus on those models where exact inference is tractable, or can be efﬁciently
approximated.
◦ Learning framework for structured models
We propose a general framework for efﬁcient estimation of models for structured
prediction. An alternative to likelihoodbased methods, this framework builds upon
the large margin estimation principle. Intuitively, we ﬁnd parameters such that in
ference in the model (dynamic programming, combinatorial optimization) predicts
the correct answers on the training data with maximum conﬁdence. We develop gen
eral conditions under which exact large margin estimation is tractable and present
two formulations for structured maxmargin estimation that deﬁne compact convex
optimization problems, taking advantage of prediction task structure. The ﬁrst for
mulation relies on the ability to express inference in the model as a compact convex
optimization problem. The second one only requires compactly expressing optimal
ity of a given assignment according to the model and applies to a broader range of
combinatorial problems. These two formulations form the foundation which the rest
of the thesis develops.
◦ Markov networks
The largest portion of the thesis is devoted to novel estimation algorithms, represen
tational extensions, generalization analysis and experimental validation for Markov
networks, a model class of choice in many structured prediction tasks in language,
vision and biology.
Lowtreewidth Markov networks
We use graph decomposition to derive an exact, compact, convex learning for
mulation for Markov networks with sequence and other lowtreewidth structure.
The seamless integration of kernels with graphical models allows us to create
1.4. CONTRIBUTIONS 9
very rich models that leverage the immense amount of research in kernel de
sign and graphical model decompositions for efﬁcient, accurate prediction in
realworld tasks. We also use approximate graph decomposition to derive a
compact approximate formulation for Markov networks in which inference is
intractable.
Scalable online algorithm
We present an efﬁcient algorithm for solving the estimation problem called
Structured SMO. Our onlinestyle algorithm uses inference in the model and
analytic updates to solve extremely large estimation problems.
Generalization analysis
We analyze the theoretical generalization properties of maxmargin estimation
in Markov networks and derive a novel marginbased bound for structured pre
diction. This bound is the ﬁrst to address structured error (e.g. proportion
of mislabeled pixels in an image) and uses a proof that exploits the graphical
model structure.
Learning associative Markov networks (AMNs)
We deﬁne an important subclass of Markov networks that captures positive cor
relations present in many domains. We show that for AMNs over binary vari
ables, our framework allows exact estimation of networks of arbitrary connec
tivity and topology, for which likelihood methods are believed to be intractable.
For the nonbinary case, we provide an approximation that works well in prac
tice. We present an AMNbased method for object segmentation from 3D range
data. By constraining the class of Markov networks to AMNs, our models are
learned efﬁciently and, at runtime, scale up to tens of millions of nodes and
edges.
Representation and learning of relational Markov networks
We introduce relational Markov networks (RMNs), which compactly deﬁne
templates for Markov networks for domains with relational structure objects,
10 CHAPTER 1. INTRODUCTION
attributes, relations. The graphical structure of an RMN is based on the rela
tional structure of the domain, and can easily model complex interaction pat
terns over related entities. We use approximate inference in these complex mod
els, in which exact inference is intractable, to derive an approximate learning
formulation. We apply this class of models to classiﬁcation of hypertext using
hyperlink structure to deﬁne relations between webpages.
◦ Broader applications: parsing, matching, clustering
The other large portion the thesis addresses a range of prediction tasks with very di
verse models: context free grammars for natural language parsing, perfect matchings
for disulﬁde connectivity in protein structure prediction, graph partitions for cluster
ing documents and segmenting images.
Learning to parse
We exploit context free grammar structure to derive a compact maxmargin
formulation and show highaccuracy parsing in cubic time by exploiting novel
kinds of lexical information. We show experimental evidence of the model’s
improved performance over several baseline models.
Learning to match
We use combinatorial properties of weighted matchings to develop an exact,
efﬁcient algorithm for learning to match. We apply our framework to predic
tion of disulﬁde connectivity in proteins using perfect nonbipartite matchings.
The algorithm we propose uses kernels, which makes it possible to efﬁciently
embed the features in very highdimensional spaces and achieve stateoftheart
accuracy.
Learning to cluster
We derive a maxmargin formulation for learning the afﬁnity metric for clus
tering from clustered training data. In contrast to algorithms that learn a metric
independently of the algorithm that will be used to cluster the data, we describe
a formulation that tightly integrates metric learning with the clustering algo
rithm, tuning one to the other in a joint optimization. Experiments on synthetic
and realworld data show the ability of the algorithm to learn an appropriate
1.5. THESIS OUTLINE 11
clustering metric for a variety of desired clusterings, including email folder or
ganization and image segmentation.
1.5 Thesis outline
Below is a summary of the rest of the chapters in the thesis:
Chapter 2. Supervised learning: We review basic deﬁnitions and statistical framework
for classiﬁcation. We deﬁne hypothesis classes, loss functions, risk. We consider
generalized linear models, including logistic regression and support vector machines,
and review estimation methods based on maximizing likelihood, conditional likeli
hood and margin. We describe the relationship between the dual estimation problems
and kernels.
Chapter 3. Structured models: In this chapter, we deﬁne the abstract class of structured
prediction problems and models addressed by the thesis. We compare probabilistic
models, generative and discriminative and unnormalized models. We describe repre
sentation and inference for Markov networks, including dynamic and linear program
ming inference. We also brieﬂy describe context free grammars and combinatorial
structures as models.
Chapter 4. Structured maximum margin estimation: This chapter outlines the main prin
ciples of maximum margin estimation for structured models. We address the expo
nential blowup of the naive problem formulation by deriving two general equivalent
convex formulation. These formulations, minmax and certiﬁcate, allow us to ex
ploit decomposition and combinatorial structure of the prediction task. They lead
to polynomial size programs for estimation of models where the prediction problem
is tractable. We also discuss approximations, in particular using upper and lower
bounds, for solving intractable or very large problems.
Chapter 5. Markov networks: We review maximum conditional likelihood estimation
and present maximum margin estimation for Markov networks. We use graphical
model decomposition to derive a convex, compact formulation that seamlessly in
tegrates kernels with graphical models. We analyze the theoretical generalization
12 CHAPTER 1. INTRODUCTION
properties of maxmargin estimation and derive a novel marginbased bound for
structured classiﬁcation.
Chapter 6. M
3
N algorithms and experiments: We present an efﬁcient algorithmfor solv
ing the estimation problem in graphical models, called Structured SMO. Our online
style algorithm uses inference in the model and analytic updates to solve extremely
large quadratic problems. We present experiments with handwriting recognition,
where our models signiﬁcantly outperform other approaches by effectively capturing
correlation between adjacent letters and incorporating highdimensional input repre
sentation via kernels.
Chapter 7. Associative Markov networks: We deﬁne an important subclass of Markov
networks, associative Markov networks (AMNs), that captures positive interactions
present in many domains. We show that for associative Markov networks of over bi
nary variables, maxmargin estimation allows exact training of networks of arbitrary
connectivity and topology, for which maximum likelihood methods are believed to
be intractable. For the nonbinary case, we provide an approximation that works
well in practice. We present an AMNbased method for object segmentation from
3D range data that scales to very large prediction tasks involving tens of millions of
points.
Chapter 8. Relational Markov networks: We introduce the framework of relational Mar
kov networks (RMNs), which compactly deﬁnes templates for Markov networks in
domains with rich structure modeled by objects, attributes and relations. The graph
ical structure of an RMN is based on the relational structure of the domain, and can
easily model complex patterns over related entities. As we show, the use of an undi
rected, discriminative graphical model avoids the difﬁculties of deﬁning a coherent
generative model for graph structures in directed models and allows us tremendous
ﬂexibility in representing complex patterns. We provide experimental results on a
webpage classiﬁcation task, showing that accuracy can be signiﬁcantly improved by
modeling relational dependencies.
Chapter 9. Context free grammars: We present maxmargin estimation for natural lan
guage parsing on the decomposition properties of context free grammars. We show
1.6. PREVIOUSLY PUBLISHED WORK 13
that this framework allows highaccuracy parsing in cubic time by exploiting novel
kinds of lexical information. We show experimental evidence of the model’s im
proved performance over several baseline models.
Chapter 10. Perfect matchings: We apply our framework to learning to predict disulﬁde
connectivity in proteins using perfect matchings. We use combinatorial properties of
weighted matchings to develop an exact, efﬁcient algorithm for learning the param
eters of the model. The algorithm we propose uses kernels, which makes it possible
to efﬁciently embed the features in very highdimensional spaces and achieve state
oftheart accuracy.
Chapter 11. Correlation clustering: In this chapter, we derive a maxmargin formula
tion for learning afﬁnity scores for correlation clustering from clustered training data.
We formulate the approximate learning problem as a compact convex program with
quadratic objective and linear or positivesemideﬁnite constraints. Experiments on
synthetic and realworld data show the ability of the algorithm to learn an appro
priate clustering metric for a variety of desired clusterings, including email folder
organization and image segmentation.
Chapter 12. Conclusions and future directions: We reviewthe main contributions of the
thesis and summarize their signiﬁcance, applicability and limitations. We discuss ex
tensions and future research directions not addressed in the thesis.
1.6 Previously published work
Some of the work described in this thesis has been published in conference proceedings.
The minmax and certiﬁcate formulations for structured maxmargin estimation have not
been published in their general form outlined in Ch. 4, although they underly several pa
pers mentioned below. The polynomial formulation of maximum margin Markov networks
presented in Ch. 5 was published for a less general case, using a dual decomposition tech
nique [Taskar et al., 2003a]. Work on associative Markov networks (Ch. 7) was published
with experiments on hypertext and newswire classiﬁcation [Taskar et al., 2004a]. A paper
14 CHAPTER 1. INTRODUCTION
on 3D object segmentation using AMNs, which presents a experiments on terrain classiﬁ
cation and other tasks, is currently under review (joint work with Drago Anguelov, Vassil
Chatalbashev, Dinkar Gupta, Geremy Heitz, Daphne Koller and Andrew Ng). Taskar et al.
[2002] and Taskar et al. [2003b] deﬁned and applied the Relational Markov networks
(Ch. 8), using maximum (conditional) likelihood estimation. Natural language parsing
in Ch. 9 was published in Taskar et al. [2004b]. Disulﬁde connectivity prediction using
perfect matchings in Ch. 10 (joint work with Vassil Chatalbashev and Daphne Koller) is
currently under review. Finally, work on correlation clustering in Ch. 11, done jointly with
Pieter Abbeel and Andrew Ng, has not been published.
Part I
Models and methods
15
Chapter 2
Supervised learning
In supervised learning, we seek a function h : A → ¸ that maps inputs x ∈ A to outputs
y ∈ ¸. The input space A is an arbitrary set (often A = IR
n
), while the output space ¸
we consider in this chapter discrete. A supervised learning problem with discrete outputs,
¸ = ¦y
1
, . . . , y
k
¦, where k is the number of classes, is called classiﬁcation. In handwritten
character recognition, for example, A is the set of images of letters and ¸ is the alphabet
(see Fig. 2.1).
The input to an algorithm is training data, a set of m i.i.d. (independent and identically
distributed) samples S = ¦(x
(i)
, y
(i)
)¦
m
i=1
drawn from a ﬁxed but unknown distribution D
over A ¸. The goal of a learning algorithm is to output a hypothesis h such that h(x)
will approximate y on new samples from the distribution (x, y) ∼ D.
Learning algorithms can be distinguished among several dimensions, chief among them
is the hypothesis class H of functions h the algorithm outputs. Numerous classes of func
tions have been well studied, including decision trees, neural networks, nearestneighbors,
generalized loglinear models and kernel methods (see Quinlan [2001]; Bishop [1995];
Hastie et al. [2001]; Duda et al. [2000], for indepth discussion of these and many other
models). We will concentrate on the last two classes, for several reasons we discuss be
low, including accuracy, efﬁciency, and extensibility to more complex structured prediction
tasks will consider in the next chapter.
The second crucial dimension of a learning algorithm is the criterion for selection of h
fromH. We arrive at such a criterion by quantifying what it means for h(x) to approximate
16
17
y. The risk functional 1
D
[(h)] measures the expected error of the approximation:
1
D
[h] = E
(x,y)∼D
[(x, y, h(x))], (2.1)
where the loss function : A ¸ ¸ → IR
+
measures the penalty for predicting h(x)
on the sample (x, y). In general, we assume that (x, y, ˆ y) = 0 if y = ˆ y.
A common loss function for classiﬁcation is 0/1 loss
0/1
(x, y, h(x)) ≡ 1I(y ,= h(x)),
where 1I() denotes the indicator function, that is, 1I(true) = 1 and 1I(false) = 0.
Since we do not generally know the distribution D, we estimate the risk of h using its
empirical risk 1
S
, computed on the training sample S:
1
S
[h] =
1
m
m
i=1
(x
(i)
, y
(i)
, h(x
(i)
)) =
1
m
m
i=1
i
(h(x
(i)
)), (2.2)
where we abbreviate (x
(i)
, y
(i)
, h(x
(i)
)) =
i
(h(x
(i)
)). For 0/1 loss, 1
S
[h] is simply the
proportion of training examples that h misclassiﬁes. 1
S
[h] is often called the training
error or training loss.
If our set of hypotheses, H, is large enough, we will be able to ﬁnd h that has zero or
very small empirical risk. However, simply selecting a hypothesis with lowest risk
h
∗
= arg min
h∈1
1
S
[h],
is generally not a good idea. For example, if A = IR, ¸ = IR and Hincludes all polynomi
als of degree m−1, we can always ﬁnd a polynomial h that passes through all the sample
points (x
(i)
, y
(i)
), i = (1, ..., m) assuming that all the x
(i)
are unique. This polynomial is
very likely to overﬁt the training data, that is, it will have zero empirical risk, but high ac
tual risk. The key to selecting a good hypothesis is to tradeoff complexity of class H (e.g.
the degree of the polynomial) with the error on the training data as measured by empirical
risk 1
S
. For a vast majority of supervised learning algorithms, this fundamental balance is
18 CHAPTER 2. SUPERVISED LEARNING
achieved by minimizing the weighted combination of the two criteria:
h
∗
= arg min
h∈1
_
T[h] + C1
S
[h]
_
, (2.3)
where T[h] measures the inherent dimension or complexity of h, and C ≥ 0 is a trade
off parameter. We will not go into derivation of various complexity measures T[h] here,
but simply adopt the standard measures as needed and refer the reader to Vapnik [1995];
Devroye et al. [1996]; Hastie et al. [2001] for details. The term T[h] is often called
regularization.
Depending on the complexity of the class H, the search for the optimal h
∗
in (2.3)
may be a daunting task
1
. For many classes, for example decision trees and multilayer
neural networks, it is intractable [Bishop, 1995; Quinlan, 2001], and we must resort to
approximate, greedy optimization methods. For these intractable classes, the search pro
cedure used by the learning algorithm is crucial. Below however, we will concentrate on
models where the optimal h
∗
can be found efﬁciently using convex optimization in poly
nomial time. Hence, the learning algorithms we consider are completely characterized by
the hypothesis class H, the loss function , and the regularization T[h].
In general, we consider hypothesis classes of the following parametric form:
h
w
(x) = arg max
y∈¸
f(w, x, y), (2.4)
where f(w, x, y) is a function f : ¼A ¸ → IR, where w ∈ ¼ is a set of parameters,
usually with ¼ ⊆ IR
n
. We assume that ties in the arg max are broken using some arbitrary
but ﬁxed rule. As we discuss below, this class of hypotheses is very rich and includes
many standard models. The formulation in (2.4) of the hypothesis class in terms of an
optimization procedure will become crucial to extending supervised learning techniques to
cases where the output space ¸ is more complex.
1
For classiﬁcation, minimizing the objective with the usual 0/1 training error is generally a very difﬁcult
problem with multiple maxima for most realistic H. See discussion in the next section about approaches to
dealing with 0/1 loss.
2.1. CLASSIFICATION WITH GENERALIZED LINEAR MODELS 19
a b c d e
Figure 2.1: Handwritten character recognition: sample letters from Kassel [1995] data set.
2.1 Classiﬁcation with generalized linear models
For classiﬁcation, we consider the generalized linear family of hypotheses H. Given n
realvalued basis functions f
j
: A ¸ → IR, a hypothesis h
w
∈ H is deﬁned by a set of n
coefﬁcients w
j
∈ IR such that:
h
w
(x) = arg max
y∈¸
n
i=1
w
j
f
j
(x, y) = arg max
y∈¸
w
¯
f (x, y). (2.5)
Consider the character recognition example in Fig. 2.1. Our input x is a vector of
pixel values of the image and y is the alphabet ¦a, . . . , z¦. We might have a basis function
f
j
(x, y) = 1I(x
row,col
= on ∧ y = char) for each possible (row, col) and char ∈ ¸,
where x
row,col
denotes the value of pixel (row, col). Since different letters tend to have
different pixels turned on, this very simple model captures enough information to perform
reasonably well.
The most common loss for classiﬁcation is 0/1 loss. Minimizing the 0/1 risk is generally
a very difﬁcult problem with multiple maxima for any large class H. The standard solution
is minimizing an upper bound on the 0/1 loss, (x, y, h(x)) ≥ (x, y, h(x)). (In addition
to computational advantages of this approach, there are statistical beneﬁts of minimizing a
convex upper bound [Bartlett et al., 2003]). Two of the primary classiﬁcation methods we
consider, logistic regression and support vector machines, differ primarily in their choice of
the upper bound on the training 0/1 loss. The regularization T[h
w
] for the linear family is
typically the norm of the parameters [[w[[
p
for p = 1, 2. Intuitively, a zero, or small weight
w
j
implies that the hypothesis h
w
does not depend on the value of f
j
(x, y) and hence is
simpler than a h
w
with a large weight w
j
.
20 CHAPTER 2. SUPERVISED LEARNING
−2 −1.5 −1 −0.5 0 0.5 1 1.5 2
0
0.5
1
1.5
2
2.5
3
3.5
log−loss
hinge−loss
0/1−loss
Figure 2.2: 0/1loss upper bounded by logloss and hingeloss. Horizontal axis shows
w
¯
f (x, y) −max
y
,=y
w
¯
f (x, y
t
), where y is the correct label for x, while the vertical axis
show the value of the associated loss. The logloss is shown up to an additive constant for
illustration purposes.
2.2 Logistic regression
In logistic regression, we assign a probabilistic interpretation to the hypothesis h
w
as deﬁn
ing a conditional distribution:
P
w
(y [ x) =
1
Z
w
(x)
exp¦w
¯
f (x, y)¦, (2.6)
where Z
w
(x) =
y∈¸
exp¦w
¯
f (x, y)¦. The optimal weights are selected by maximiz
ing the conditional likelihood of the data (minimizing the logloss) with some regulariza
tion. This approach is called the (regularized) maximum likelihood estimation. Common
choices for regularization are 1 or 2norm regularization on the weights; we use 2norm
below:
min
1
2
[[w[[
2
+ C
i
log Z
w
(x
(i)
) −w
¯
f (x
(i)
, y
(i)
), (2.7)
where C is a userspeciﬁed constant the determines the tradeoff between regularization
and likelihood of the data. The logloss log Z
w
(x) −w
¯
f (x, y) is an upper bound (up to a
constant) on the 0/1 loss
0/1
(see Fig. 2.2).
2.3. LOGISTIC DUAL AND MAXIMUM ENTROPY 21
2.3 Logistic dual and maximum entropy
The objective function is convex in the parameters w, so we have an unconstrained (differ
entiable) convex optimization problem. The gradient with respect to w is given by:
w+ C
i
E
i,w
[f
i
(x
(i)
, y)] −f
i
(x
(i)
, y
(i)
) = w−C
i
E
i,w
[∆f
i
(y)],
where E
i,w
[f(y)] =
y
f(y)P
w
(y [ x
(i)
) is the expectation under the conditional distribu
tion P
w
(y [ x
(i)
) and ∆f
i
(y) = f (x
(i)
, y
(i)
) − f (x
(i)
, y). Ignoring the regularization term,
the gradient is zero when the basis function expectations are equal to the basis functions
evaluated on the labels y
(i)
. It can be shown [Cover & Thomas, 1991] that the dual of the
maximum likelihood problem (without regularization) is the maximum entropy problem:
max −
i,y
P
w
(y [ x
(i)
) log P
w
(y [ x
(i)
) (2.8)
s.t. E
i,w
[∆f
i
(y)] = 0, ∀i.
We can interpret logistic regression as trying to match the empirical basis function expec
tations while maintaining a high entropy conditional distribution P
w
(y [ x).
2.4 Support vector machines
Support vector machines [Vapnik, 1995] select the weights based on the “margin” of con
ﬁdence of h
w
. In the multiclass SVM formulation [Weston & Watkins, 1998; Crammer &
Singer, 2001], the margin on example i quantiﬁes by how much the true label “wins” over
the wrong ones:
γ
i
=
1
[[w[[
min
y,=y
(i)
w
¯
f (x
(i)
, y
(i)
) −w
¯
f (x
(i)
, y) =
1
[[w[[
min
y,=y
(i)
w
¯
∆f
i
(y),
22 CHAPTER 2. SUPERVISED LEARNING
where ∆f
i
(y) = f (x
(i)
, y
(i)
) −f (x
(i)
, y). Maximizing the smallest such margin (and allow
ing for negative margins) is equivalent to solving the following quadratic program:
min
1
2
[[w[[
2
+ C
i
ξ
i
(2.9)
s.t. w
¯
∆f
i
(y) ≥
0/1
(y) −ξ
i
, ∀i, ∀y ∈ ¸.
Note that the slack variable ξ
i
is constrained to be positive in the above program since
w
¯
∆f
i
(y
(i)
) = 0 and
0/1
(y
(i)
) = 0. We can also express ξ
i
as max
y
0/1
i
(y) −w
¯
∆f
i
(y),
and the optimization problem Eq. (2.9) in a form similar to Eq. (2.7):
min
1
2
[[w[[
2
+ C
i
max
y
[
0/1
i
(y) −w
¯
∆f
i
(y)]. (2.10)
The hingeloss max
y
[
0/1
i
(y) − w
¯
∆f
i
(y)] is also an upper bound on the 0/1 loss
0/1
(see Fig. 2.2).
2.5 SVM dual and kernels
The form of the dual of Eq. (2.9) is crucial to efﬁcient solution of SVM and the ability to
use a high or even inﬁnite dimensional set of basis functions via kernels.
max
i,y
α
i
(y)
0/1
i
(y) −
1
2
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,y
α
i
(y)∆f
i
(y)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
(2.11)
s.t.
y
α
i
(y) = C, ∀i; α
i
(y) ≥ 0, ∀i, y.
In the dual, the α
i
(y) variables correspond to the w
¯
∆f
i
(y) ≥
0/1
(y)−ξ
i
constraints in the
primal Eq. (2.9). The solution to the dual α
∗
gives the solution to the primal as a weighted
combination of basis functions of examples:
w
∗
=
i,y
α
∗
i
(y)∆f
i
(y).
2.5. SVM DUAL AND KERNELS 23
The pairings of examples and incorrect labels, (i, y), that have nonzero α
∗
i
(y), are called
support vectors.
An important feature of the dual formulation is that the basis functions f appear only as
dot products. Expanding the quadratic term, we have:
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,y
α
i
(y)∆f
i
(y)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
=
i,y
j,¯ y
α
i
(y)α
j
(¯ y)∆f
i
(y)
¯
∆f
j
(¯ y).
Hence, as long as the dot product f (x, y)
¯
f (¯ x, ¯ y) can be computed efﬁciently, we can
solve Eq. (2.11) independently of the actual dimension of f . Note that at classiﬁcation
time, we also do not need to worry about the dimension of f since:
w
¯
f (x, ¯ y) =
i,y
α
i
(y)∆f
i
(y)
¯
f (x, ¯ y) =
i,y
α
i
(y)[f (x
(i)
, y
(i)
)
¯
f (x, ¯ y)−f (x
(i)
, y)
¯
f (x, ¯ y)].
For example, we might have basis functions that are polynomial of degree d in terms of
image pixels, f
j
(x, y) = 1I(x
row
1
,col
1
= on ∧ . . . ∧ x
row
d
,col
d
= on ∧ y = char) for each
possible (row
1
, col
1
) . . . (row
d
, col
d
) and char ∈ ¸. Computing this polynomial kernel
can be done independently of the dimension d, even though the number of basis functions
grows exponentially with d [Vapnik, 1995].
In fact, logistic regression can also be kernelized. However, the hinge loss formulation
usually produces sparse solutions in terms of the number of support vectors, while solutions
to the corresponding kernelized logloss problem are generally nonsparse (all examples
are support vectors) and require approximations for even relatively small datasets [Wahba
et al., 1993; Zhu & Hastie, 2001].
Chapter 3
Structured models
Consider once more the problem of character recognition. In fact, a more natural and useful
task is recognizing words and entire sentences. Fig. 3.1 shows an example handwritten
word “brace.” Distinguishing between the second letter and fourth letter (‘r’ and ‘c’) in
isolation is far from trivial, but in the context of the surrounding letters that together form
a word, this task is much less errorprone for humans and should be for computers as well.
In this chapter, we consider prediction problems in which the output is not a single
discrete value y, but a set of values y = (y
1
, . . . , y
L
), for example an entire sequence
of L characters. For concreteness, let the number of variables L be ﬁxed. The output
space ¸ ⊆ ¸
1
. . . ¸
L
we consider is a subset of product of output spaces of single
variables. In word recognition, each ¸
j
is the alphabet, while ¸ is the dictionary. This
joint output space is often a proper subset of the product of singleton output spaces, ¸ ⊂
¸
1
. . .¸
L
. In word recognition, we might restrict that the letter ‘q’ never follows by ‘z’ in
English. In addition to “hard” constraints, the output variables are often highly correlated,
e.g. consecutive letters in a word. We refer to joint spaces with constraints and correlations
as structured. We call problems with discrete output spaces structured classiﬁcation or
structured prediction. Structured models we consider in this chapter (and thesis) predict
the outputs jointly, respecting the constraints and exploiting the correlations in the output
space.
The range of prediction problems these broad deﬁnitions encompass is immense, aris
ing in ﬁelds as diverse as natural language analysis, machine vision, and computational
24
3.1. PROBABILISTIC MODELS: GENERATIVE AND CONDITIONAL 25
b r a c e
Figure 3.1: Handwritten word recognition: sample from Kassel [1995] data set.
biology, to name a few. The class of structured models H we consider is essentially of the
same form as in previous chapter, except that y has been replaced by y:
h
w
(x) = arg max
y : g(x,y)≤0
w
¯
f (x, y), (3.1)
where as before f (x, y) is a vector of functions f : A ¸ → IR
n
. The output space
¸ = ¦y : g(x, y) ≤ 0¦ is deﬁned using a vector of functions g(x, y) that deﬁne the
constraints, where g : A ¸ → IR
k
. This formulation is very general. Clearly, for
many f , g pairs, ﬁnding the optimal y is intractable. For the most part, we will restrict our
attention to models where this optimization problemcan be solved in polynomial time. This
includes, for example, probabilistic models like Markov networks (in certain cases) and
contextfree grammars, combinatorial optimization problems like mincut and matching,
convex optimization such as linear, quadratic and semideﬁnite programming. In other
cases, like intractable Markov networks (Ch. 8) and correlation clustering (Ch. 11), we use
an approximate polynomial time optimization procedure.
3.1 Probabilistic models: generative and conditional
The term model is often reserved for probabilistic models, which can be subdivided into
generative and conditional with respect to the prediction task. A generative model assigns
a normalized joint density p(x, y) to the input and output space A ¸ with
p(x, y) ≥ 0,
y∈¸
_
x∈.
p(x, y) = 1.
26 CHAPTER 3. STRUCTURED MODELS
A conditional model assigns a normalized density p(y [ x) only over the output space ¸
with
p(y [ x) ≥ 0,
y∈¸
p(y [ x) = 1 ∀x ∈ A.
Probabilistic interpretation of the model offers wellunderstood semantics and an im
mense toolbox of methods for inference and learning. It also provides an intuitive measure
of conﬁdence in the predictions of a model in terms of conditional probabilities. In addi
tion, generative models are typically structured to allow very efﬁcient maximum likelihood
learning. A very common class of generative models is the exponential family:
p(x, y) ∝ exp¦w
¯
f (x, y)¦.
For exponential families, the maximum likelihood parameters w with respect to the joint
distribution can be computed in closed form using the empirical basis function expectations
E
S
[f (x, y)] [DeGroot, 1970; Hastie et al., 2001].
Of course, this efﬁciency comes at a price. Any model is an approximation to the true
distribution underlying the data. A generative model must make simplifying assumptions
(more precisely, independence assumptions) about the entire p(x, y), while a conditional
model makes many fewer assumption by focusing on p(y [ y). Because of this, by opti
mizing the model to ﬁt the joint distribution p(x, y), we may be tuning the approximation
away from optimal conditional distribution p(y [ x), which we use to make the predictions.
Given sufﬁcient data, the conditional model will learn the best approximation to p(y [ x)
possible using w, while the generative model p(x, y) will not necessarily do so. Typically,
however, generative models actually need fewer samples to converge to a good estimate of
the joint distribution than conditional models need to accurately represent the conditional
distribution. In a regime with very few training samples (relative to the number of param
eters w), generative models may actually outperform conditional models [Ng & Jordan,
2001].
3.2. PREDICTION MODELS: NORMALIZED AND UNNORMALIZED 27
3.2 Prediction models: normalized and unnormalized
Probabilistic semantics are certainly not necessary for a good predictive model if we are
simply interested in the optimal prediction (the arg max in Eq. (3.1)). As we discussed
in the previous chapter, support vector machines, which do not represent a conditional
distribution, typically perform as well or better than logistic regression [Vapnik, 1995;
Cristianini & ShaweTaylor, 2000].
In general, we can often achieve higher accuracy models when we do not learn a nor
malized distribution over the outputs, but concentrate on the margin or decision boundary,
the difference between the optimal y and the rest. Even more importantly, in many cases
we discuss below, normalizing the model (summing over the entire ¸) is intractable, while
the optimal y can be found in polynomial time. This fact makes standard maximum like
lihood estimation infeasible. The learning methods we advocate in this thesis circumvent
this problem by requiring only the maximization problem to be tractable. We still heav
ily rely on the representation and inference tools familiar from probabilistic models for
the construction of and prediction in unnormalized models, but largely dispense with the
probabilistic interpretation when needed. Essentially, we use the term model very broadly,
to include any scheme that assigns scores to the output space ¸ and has a procedure for
ﬁnding the optimal scoring y.
In this chapter, we review basic concepts in probabilistic graphical models called Mar
kov networks or Markov randomﬁelds. We also brieﬂy touch upon examples of contextfree
grammars and combinatorial problems that will be explained in greater detail in Part III to
illustrate the range of prediction problems we address.
3.3 Markov networks
Markov networks provide a framework for a rich family of models for both discrete and
continuous prediction [Pearl, 1988; Cowell et al., 1999]. The models treat the inputs and
outputs as random variables X with domain A and Y with domain ¸ and compactly de
ﬁne a conditional density p(Y [ X) or distribution P(Y [ X) (we concentrate here on the
28 CHAPTER 3. STRUCTURED MODELS
conditional Markov networks or CRFs [Lafferty et al., 2001]). The advantage of a graphi
cal framework is that it can exploit sparseness in the correlations between outputs Y . The
graphical structure of the models encodes the qualitative aspects of the distribution: direct
dependencies as well as conditional independencies. The quantitative aspect of the model
is deﬁned by the potentials that are associated with nodes and cliques of the graph. Before
a formal deﬁnition, consider a ﬁrstorder Markov chain a model for the word recognition
task. In Fig. 3.2, the nodes are associated with output variables Y
i
and the edges correspond
to direct dependencies or correlations. We do not explicitly represent the inputs X in the
ﬁgure. For example, the model encodes that Y
j
is conditionally independent of the rest of
the variables given Y
j−1
, Y
j+1
. Intuitively, adjacent letters in a word are highly correlated,
but the ﬁrstorder model is making the assertion (which is certainly an approximation) that
once the value of a letter Y
j
is known, the correlation between a letter Y
b
before j and a
letter Y
a
after j is negligible. More precisely, we use a model where
P(Y
b
[ Y
j
, Y
a
, x) = P(Y
b
[ Y
j
, x), P(Y
a
[ Y
j
, Y
b
, x) = P(Y
a
[ Y
j
, x), b < j < a.
For the purposes of ﬁnding the most likely y, this conditional independence property means
that the optimization problem is decomposable: given that Y
j
= y
j
, it sufﬁces to separately
ﬁnd the optimal subsequence from 1 to j ending with y
j
, and the optimal subsequence
starting with y
j
from j to L.
3.3.1 Representation
The structure of a Markov network is deﬁned by an undirected graph ( = (1, c), where
the nodes are associated with variables 1 = ¦Y
1
, . . . , Y
L
¦. A clique is a set of nodes c ⊆ 1
that form a fully connected subgraph (every two nodes are connected by an edge). Note that
each subclique of a clique is also a clique, and we consider each node a singleton clique.
In the chain network in Fig. 3.2, the cliques are simply the nodes and the edges: ((() =
¦¦Y
1
¦, . . . , ¦Y
5
¦, ¦Y
1
, Y
2
¦, . . . , ¦Y
4
, Y
5
¦¦. We denote the set of variables in a clique c as
Y
c
, an assignment of variables in the clique as y
c
and the space of all assignments to
the clique as ¸
c
. We focus on discrete output spaces ¸ below, but many of the same
representation and inference concepts translate to continuous domains. No assumption is
3.3. MARKOV NETWORKS 29
Figure 3.2: Firstorder Markov chain: φ
i
(Y
i
) are node potentials, φ
i,i+1
(Y
i
, Y
i+1
) are edge
potentials (dependence on x is not shown).
made about A.
Deﬁnition 3.3.1 A Markov network is deﬁned by an undirected graph ( = (1, c) and a
set of potentials Φ = ¦φ
c
¦. The nodes are associated with variables 1 = ¦Y
1
, . . . , Y
L
¦.
Each clique c ∈ ((() is associated with a potential φ
c
(x, y
c
) with φ
c
: A ¸
c
→ IR
+
,
which speciﬁes a nonnegative value for each assignment y
c
to variables in Y
c
and any
input x. The Markov network ((, Φ) deﬁnes a conditional distribution:
P(y [ x) =
1
Z(x)
c∈((Ç)
φ
c
(x, y
c
),
where ((() is the set of all the cliques of the graph and Z(x) is the partition function
given by Z(x) =
y∈¸
c∈((Ç)
φ
c
(x, y
c
).
In our example Fig. 3.2, we have node and edge potentials. Intuitively, the node poten
tials quantify the correlation between the input x and the value of the node, while the edge
potentials quantify the correlation between the pair of adjacent output variables as well as
the input x. Potentials do not have a local probabilistic interpretation, but can be thought
of as deﬁning an unnormalized score for each assignment in the clique. Conditioned on
the image input, appropriate node potentials in our network should give high scores to the
correct letters (‘b’,‘r’,‘a’,‘c’,‘e’), though perhaps there would be some ambiguity with the
second and fourth letter. For simplicity, assume that the edge potentials would not depend
30 CHAPTER 3. STRUCTURED MODELS
on the images, but simply should give high scores to pairs of letters that tend to appear often
consecutively. Multiplied together, these scores should favor the correct output “brace”.
In fact, a Markov network is a generalized loglinear model, since the potentials φ
c
(x
c
, y
c
)
could be represented (in logspace) as a sum of basis functions over x, y
c
:
φ
c
(x
c
, y
c
) = exp
_
n
c
k=1
w
c,k
f
c,k
(x, y
c
)
_
= exp
_
w
¯
c
f
c
(x, y
c
)
¸
where n
c
is the number of basis functions for the clique c. Hence the log of the conditional
probability is given by:
log P(y [ x) =
c∈((Ç)
w
¯
c
f
c
(x, y
c
) −log Z
w
(x).
In case of node potentials for word recognition, we could use the same basis functions as
for individual character recognition: f
j,k
(x, y
j
) = 1I(x
j,row,col
= on ∧ y
j
= char) for each
possible (row, col) in x
j
, the window of the image that corresponds to letter j and each
char ∈ ¸
j
(we assume the input has been segmented into images x
j
that correspond to
letters). In general, we condition a clique only on a portion of the input x, which we denote
as x
c
. For the edge potentials, we can deﬁne basis functions for each combination of letters
(assume for simplicity no dependence on x) : f
j,j+1,k
(x, y
j
, y
j+1
) = 1I(y
j
= char
1
∧y
j+1
=
char
2
) for each char
1
∈ ¸
j
and char
2
∈ ¸
j+1
. In this problem (as well as many others),
we are likely to “tie” or “share” the parameters of the model w
c
across cliques. Usually, all
single node potentials would share the same weights and basis functions (albeit the relevant
portion of the input x
c
is different) and similarly for the pairwise cliques, no matter in what
position they appear in the sequence.
1
With slight abuse of notation, we stack all basis functions into one vector f . For the
sequence model, f has node functions and edge functions, so when c is a node, the edge
functions in f (x
c
, y
c
) are deﬁned to evaluate to zero. Similarly, when c is an edge, the node
1
Sometimes we might actually want some dependence on the position in the sequence, which can be
accomplished by adding more basis functions that condition on the position of the clique.
3.3. MARKOV NETWORKS 31
functions in f (x
c
, y
c
) are also deﬁned to evaluate to zero. Now we can write:
f (x, y) =
c∈((Ç)
f (x
c
, y
c
).
We stack the weights in the corresponding manner, so the most likely assignment according
to the model is given by:
arg max
y∈¸
log P
w
(y [ x) = arg max
y∈¸
w
¯
f (x, y),
in the same form as Eq. (3.1).
3.3.2 Inference
There are several important questions that can be answered by probabilistic models. The
task of ﬁnding the most likely assignment, known as maximum aposteriori (MAP) or most
likely explanation (MPE), is just one of such questions, but most relevant to our discussion.
The Viterbi dynamic programming algorithm solves this problem for chain networks in
O(L) time. Let the highest score of any subsequence from 1 to k > 1 ending with value y
k
be deﬁned as
φ
∗
k
(y
k
) = max
y
1..k−1
j
φ
j
(x, y
j
)φ
j
(x, y
j−1
, y
j
).
The algorithm computes the highest scores recursively:
φ
∗
1
(y
1
) = φ
1
(x, y
1
), ∀y
1
∈ ¸
1
;
φ
∗
k
(y
k
) = max
y
k−1
∈¸
k−1
φ
∗
k−1
(y
k−1
)φ
j
(x, y
k
)φ
j
(x, y
k−1
, y
k
), 1 < k ≤ L, ∀y
k
∈ ¸
k
.
The highest scoring sequence has score max
y
L
φ
∗
L
(y
L
). Using the arg max’s of the max’s in
the computation of φ
∗
, we can backtrace the highest scoring sequence itself. We assume
that score ties are broken in a predetermined way, say according to some lexicographic
order of the symbols.
32 CHAPTER 3. STRUCTURED MODELS
Figure 3.3: Diamond Markov network (added triangulation edge is dashed).
In general Markov networks, MAP inference is NPhard [Cowell et al., 1999]. How
ever, there are several important subclasses of networks that allow polynomial time infer
ence. The most important of these is the class of networks with low treewidth. We need the
concept of triangulation (or chordality) to formally deﬁne treewidth. Recall that a cycle
of length l in an undirected graph ( is a sequence of nodes (v
0
, v
1
, . . . , v
l
), distinct except
that v
0
= v
l
, which are connected by edges (v
i
, v
i+1
) ∈ (. A chord of this cycle is an edge
(v
i
, v
j
) ∈ ( between nonconsecutive nodes.
Deﬁnition 3.3.2 (Triangulated graph) An undirected graph ( is triangulated if every one
of its cycles of length ≥ 4 possesses a chord.
Singlyconnected graphs, like chains and trees, are triangulated since they contain no cy
cles. The simplest untriangulated network is the diamond in Fig. 3.3. To triangulate it,
we can add the edge (Y
1
, Y
3
) or (Y
2
, Y
4
). In general, there are many possible sets of edges
that can be added to triangulate a graph. The inference procedure creates a tree of cliques
using the graph augmented by triangulation. The critical property of a triangulation for the
inference procedure is the size of the largest clique.
Deﬁnition 3.3.3 (Treewidth of a graph) The treewidth of a triangulated graph ( is the
size of its largest clique minus 1. The treewidth of an untriangulated graph ( is the
minimum treewidth of all triangulations of (.
3.3. MARKOV NETWORKS 33
The treewidth of a chain or a tree is 1 and the treewidth of Fig. 3.3 is 2. Finding the mini
mum treewidth triangulation of a general graph is NPhard, but good heuristic algorithms
exist [Cowell et al., 1999].
The inference procedure is based on a data structure called junction tree that can be
constructed for a triangulated graph. The junction tree is an alternative representation of
the same distribution that allows simple dynamic programming inference similar to the
Viterbi algorithm for chains.
Deﬁnition 3.3.4 (Junction tree) A junction tree T = (1, c) for a triangulated graph ( is
a tree in which the nodes are a subset of the cliques of the graph, 1 ⊆ ((() and the edges
c satisfy the running intersection property: for any two cliques c and c
t
, the variables in
the intersection c ∩ c
t
are contained in the clique of every node of the tree on the (unique)
path between c and c
t
.
Fig. 3.4 shows a junction tree for the diamond network. Each of the original clique poten
tials must associated with exactly one node in the junction tree. For example, the potentials
for the ¦Y
1
, Y
3
, Y
4
¦ and ¦Y
1
, Y
3
, Y
4
¦ nodes are the product of the associated clique poten
tials:
φ
134
(Y
1
, Y
3
, Y
4
) = φ
1
(Y
1
)φ
4
(Y
4
)φ
14
(Y
1
, Y
4
)φ
34
(Y
3
, Y
4
),
φ
123
(Y
1
, Y
2
, Y
3
) = φ
2
(Y
2
)φ
3
(Y
3
)φ
12
(Y
1
, Y
2
)φ
23
(Y
2
, Y
3
).
Algorithms for constructing junction trees from triangulated graphs are described in detail
in Cowell et al. [1999].
The Viterbi algorithm for junction trees picks an arbitrary root r for the tree T and
proceeds recursively from the leaves to compute the highest scoring subtree at a node by
combining the subtrees with highest score from its children. We denote the leaves of the
tree as Lv(T ) and the children of node c (relative to the root r) as Ch
r
(c):
φ
∗
l
(y
l
) = φ
l
(x, y
l
), ∀l ∈ Lv(T ), ∀y
l
∈ ¸
l
;
φ
∗
c
(y
c
) = φ
c
(x, y
c
)
c
∈Ch
r
(c)
max
y
c
∼y
c
φ
∗
c
(y
c
), ∀c ∈ 1(T ) ¸ Lv(T ), ∀y
c
∈ ¸
c
,
34 CHAPTER 3. STRUCTURED MODELS
Figure 3.4: Diamond network junction tree. Each of the original potentials is associated
with a node in the tree.
where y
c
∼ y
c
denotes whether the partial assignment y
c
is consistent with the partial
assignment y
c
on the variables in the intersection of c and c
t
. The highest score is given by
max
y
r
φ
∗
r
(y
r
). Using the arg max’s of the max’s in the computation of φ
∗
, we can back
trace the highest scoring assignment itself. Note that this algorithm is exponential in the
treewidth, the size of the largest clique. Similar type of computations using the junction
tree can be used to compute the partition function Z
w
(x) (by simply replacing max by
)
as well as marginal probabilities P(y
c
[x) for the cliques of the graph [Cowell et al., 1999].
3.3.3 Linear programming MAP inference
In this section, we present an alternative inference method based on linear programming.
Although solving the MAP inference using a general LP solver is less efﬁcient than the
dynamic programming algorithms above, this formulation is crucial in viewing Markov
networks in a uniﬁed framework of the structured models we consider and to our develop
ment of common estimation methods in later chapters. Let us begin with a linear integer
program to compute the optimal assignment y. We represent an assignment as a set binary
variables µ
c
(y
c
), one for each clique c and each value of the clique y
c
, that denotes whether
the assignment has that value, such that:
log
c
φ
c
(x, y
c
) =
c,y
c
µ
c
(y
c
) log φ
c
(x, y
c
).
3.3. MARKOV NETWORKS 35
0 0 0 0
0 0 1 0
0 0 0 0
0 0 0 0
0 0 0 0
0 0 1 0
0 0 0 0
0 0 0 0
0
1
0
0
0
1
0
0
0 0 1 0 0 0 1 0
Figure 3.5: Example of marginal agreement: row sums of µ
12
(y
1
, y
2
) agree with µ
1
(y
1
),
column sums agree with µ
2
(y
2
).
We call these variables marginals, as they correspond to the marginals of a distribution that
has all of its mass centered on the MAP instantiation (assuming it is unique). There are
several elementary constraints that such marginals satisfy. First, they must sum to one for
each clique. Second, the marginals for cliques that share variables are consistent. For any
clique c ∈ ( and a subclique s ⊂ c, the assignment of the subclique, µ
s
(y
s
), must be
consistent with the assignment of the clique, µ
c
(y
c
). Together, these constraints deﬁne a
linear integer program:
max
c,y
c
µ
c
(y
c
) log φ
c
(x, y
c
) (3.2)
s.t.
y
c
µ
c
(y
c
) = 1, ∀c ∈ (; µ
c
(y
c
) ∈ ¦0, 1¦, ∀c ∈ (, ∀y
c
;
µ
s
(y
s
) =
y
c
∼y
s
µ
c
(y
t
c
), ∀s, c ∈ (, s ⊂ c, ∀y
s
.
For example, in case the network is a chain or a tree, we will have node and edge marginals
that sum to 1 and agree with each other as in Fig. 3.5.
Clearly, for any assignment y
t
, we can deﬁne µ
c
(y
c
) variables that satisfy the above
constraints by setting µ
c
(y
c
) = 1I(y
t
c
= y
c
). We can also show that converse is true: any
valid setting of µ
c
(y
c
) corresponds to a valid assignment y. In fact,
36 CHAPTER 3. STRUCTURED MODELS
Lemma 3.3.5 For a triangulated network with unique MAP assignment, the integrality
constraint in the integer program in Eq. (3.2) can be relaxed and the resulting LP is guar
anteed to have integer solutions.
A proof of this lemma appears in Wainwright et al. [2002]. Intuitively, the constraints force
the marginals µ
c
(y
c
) to correspond to some valid joint distribution over the assignments.
The optimal distribution with the respect to the objective puts all its mass on the MAP
assignment. If the MAP assignment is not unique, the value of the LP is the same as
the value of the integer program, and any linear combination of the MAP assignments
maximizes the LP.
In case the network is not triangulated, the set of marginals is not guaranteed to rep
resent a valid distribution. Consider, for example, the diamond network in Fig. 3.3 with
binary variables, with the following edge marginals that are consistent with the constraints:
µ
12
(0, 0) = µ
12
(1, 1) = 0.5, µ
12
(1, 0) = µ
12
(0, 1) = 0;
µ
23
(0, 0) = µ
23
(1, 1) = 0.5, µ
23
(1, 0) = µ
23
(0, 1) = 0;
µ
34
(0, 0) = µ
34
(1, 1) = 0.5, µ
34
(1, 0) = µ
34
(0, 1) = 0;
µ
14
(0, 0) = µ
34
(1, 1) = 0, µ
14
(1, 0) = µ
14
(0, 1) = 0.5.
The corresponding node marginals must all be set to 0.5. Note that the edge marginals for
(1, 2), (2, 3), (3, 4) disallow any assignment other than 0000 or 1111, but the edge marginal
for (1, 4) disallows any assignment that has Y
1
= Y
4
. Hence this set of marginals dis
allows all assignments. If we triangulate the graph and add the cliques ¦Y
1
, Y
2
, Y
3
¦ and
¦Y
1
, Y
3
, Y
4
¦ with their corresponding constraints, the above marginals will be disallowed.
In graphs where triangulation produces very large cliques, exact inference is intractable.
We can resort to the above LP without triangulation as an approximate inference procedure
(augmented with some procedure for rounding possibly fractional solutions). In Ch. 7, we
discuss another subclass of networks where MAP inference using LPs is tractable for any
network topology, but with a restricted type of potentials.
3.4. CONTEXT FREE GRAMMARS 37
Figure 3.6: Example parse tree from Penn Treebank [Marcus et al., 1993].
3.4 Context free grammars
Contextfree grammars are one of the primary formalisms for capturing the recursive struc
ture of syntactic constructions [Manning & Sch¨ utze, 1999]. For example, Fig. 3.6 shows
a parse tree for the sentence The screen was a sea of red. This tree is from the Penn Tree
bank [Marcus et al., 1993], a primary linguistic resource for expertannotated English text.
The nonterminal symbols (labels of internal nodes) correspond to syntactic categories such
as noun phrase (NP), verbal phrase (VP) or prepositional phrase (PP) and partofspeech
tags like nouns (NN), verbs (VBD), determiners (DT) and prepositions (IN). The terminal
symbols (leaves) are the words of the sentence.
For clarity of presentation, we restrict our grammars to be in Chomsky normal form
2
(CNF),
where all rules in the grammar are of the form: A →B C and A →D, where A, B and C
are nonterminal symbols, and D is a terminal symbol.
Deﬁnition 3.4.1 (CFG) A CFG ( consists of:
◦ A set of nonterminal symbols, ^
◦ A designated set of start symbols, ^
S
⊆ ^
2
Any CFG can be represented by another CFG in CNF that generates the same set of sentences.
38 CHAPTER 3. STRUCTURED MODELS
◦ A set of terminal symbols, T
◦ A set of productions, T = ¦T
B
, T
U
¦, divided into
Binary productions, T
B
= ¦A →B C : A, B, C ∈ ^¦ and
Unary productions, T
U
= ¦A →D : A ∈ ^, D ∈ T ¦.
Consider a very simple grammar:
◦ ^ = ¦S, NP, VP, PP, NN, VBD, DT, IN¦
◦ ^
S
= ¦S¦
◦ T = ¦The, the, cat, dog, tree, saw, from¦
◦ T
B
= ¦S → NP VP, NP → DT NN, NP → NP PP, VP → VBD NP,
VP →VP PP, PP →IN NP¦.
◦ T
U
= ¦DT → The, DT → the, NN → cat, NN → dog, NN → tree, VBD → saw,
IN → from¦
A grammar generates a sentence by starting with a symbol in ^
S
and applying the
productions in T to rewrite nonterminal symbols. For example, we can generate The cat
saw the dog by starting with S → NP VP, rewriting the NP as NP → DT NN with DT →
The and NN → cat, then rewriting the VP as VP → VBD NP with VBD → saw, again
using NP → DT NN, but now with DT → the and NN → dog. We can represent such
derivations using trees like in Fig. 3.6 or (more compactly) using bracketed expressions
like the one below:
[[The
DT
cat
NN
]
NP
[saw
VBD
[the
DT
dog
NN
]
NP
]
VP
]
S
.
The simple grammar above can generate sentences of arbitrary length, since it has sev
eral recursive productions. It can also generate the same sentence several ways. In general,
there are exponentially many parse trees that produce a sentence of length l. Consider the
sentence The cat saw the dog from the tree. The likely analysis of the sentence is that
the cat, sitting in the tree, saw the dog. An unlikely but possible alternative is that the cat
3.4. CONTEXT FREE GRAMMARS 39
actually saw the dog who lived near the tree or was tied to it in the past. Our grammar
allows both interpretations, with the difference being in the analysis of the toplevel VP:
[saw
VBD
[the
DT
dog
NN
]
NP
]
VP
[[from
IN
[the
DT
tree
NN
]
NP
]
PP
,
saw
VBD
[[the
DT
dog
NN
]
NP
[from
IN
[the
DT
tree
NN
]
NP
]
PP
]
NP
.
This kind of ambiguity, called prepositional attachment, is very common in many re
alistic grammars. A standard approach to resolving ambiguity is to use a PCFG to deﬁne
a joint probability distribution over the space of parse trees ¸ and sentences A. Standard
PCFG parsers use a Viterbistyle algorithm to compute arg max
y
P(x, y) as the most likely
parse tree for a sentence x. The distribution P(x, y) is deﬁned by assigning a probability
to each production and making sure that the sum of probabilities of all productions starting
with a each symbol is 1:
B,C:A→B C∈1
B
P(A →B C) = 1,
D:A→D∈1
U
P(A → D ) = 1, ∀A ∈ ^.
We also need to assign a probability to the different starting symbols P(A) ∈ ^
S
such that
A∈A
S
P(A) = 1. The probability of a tree is simply the product of probabilities of the
productions used in the tree (times the probability of the starting symbol). Hence the log
probability of a tree is a sum of the logprobabilities of its productions. By letting our basis
functions f (x, y) consist of the counts of the productions and w be their logprobabilities,
we can cast PCFG as a structured linear model (in log space). In Ch. 9, we will show how
to represent a parse tree as an assignment of variables Y with appropriate constraints to
express PCFGS (and more generally weighted CFGs) in the form of Eq. (3.1) as
h
w
(x) = arg max
y : g(x,y)≤0
w
¯
f (x, y),
and describe the associated algorithm to compute the highest scoring parse tree y given a
sentence x.
40 CHAPTER 3. STRUCTURED MODELS
3.5 Combinatorial problems
Many important computational tasks are formulated as combinatorial optimization prob
lems such as the maximum weight bipartite and perfect matching, spanning tree, graphcut,
edgecover, binpacking, and many others [Lawler, 1976; Papadimitriou & Steiglitz, 1982;
Cormen et al., 2001]. These problems arise in applications such as resource allocation,
job assignment, routing, scheduling, network design and many more. In some domains,
the weights of the objective function in the optimization problem are simple and natural
to deﬁne (for example, Euclidian distance or temporal latency), but in many others, con
structing the weights is an important and laborintensive design task. Treated abstractly, a
combinatorial space of structures, such as matchings or graphcuts or trees), together with
a scoring scheme that assigns weights to candidate outputs is a kind of a model.
As a particularly simple and relevant example, consider modeling the task of assigning
reviewers to papers as a maximum weight bipartite matching problem, where the weights
represent the “expertise” of each reviewer for each paper. More speciﬁcally, suppose we
would like to have R reviewers per paper, and that each reviewer be assigned at most P pa
pers. For each paper and reviewer, we have an a weight q
jk
indicating the qualiﬁcation level
of reviewer j for evaluating paper k. Our objective is to ﬁnd an assignment for reviewers
to papers that maximizes the total weight. We represent a matching with a set of binary
variables y
jk
that take the value 1 if reviewer j is assigned to paper k, and 0 otherwise. The
bipartite matching problem can be solved using a combinatorial algorithm or the following
linear program:
max
j,k
µ
jk
q
jk
(3.3)
s.t.
j
µ
jk
= R,
k
µ
jk
≤ P, 0 ≤ µ
jk
≤ 1.
This LP is guaranteed to produce integer solutions (as long as P and R are integers) for
any weights q(y) [Nemhauser & Wolsey, 1999].
The quality of the solution found depends critically on the choice of weights that de
ﬁne the objective. A simple scheme could measure the “expertise” as the percent of word
3.5. COMBINATORIAL PROBLEMS 41
overlap in the reviewer’s home page and the paper’s abstract. However, we would want to
weight certain words much more (words that are relevant to the subject and infrequent).
Constructing and tuning the weights for a problem is a difﬁcult and timeconsuming pro
cess, just as it is for Markov networks for handwriting recognition.
As usual, we will represent the objective q(y) as a weighted combination of a set of
basis functions w
¯
f (x, y). Let x
jk
denote the intersection of the set of words occurring in
webpage(j)∩abstract(k), the web page of a reviewer j and the abstract of the paper k. We
can deﬁne f
d
(x, y) =
jk
y
jk
1I(word
d
∈ x
jk
), the number of times word d was in both
the web page of a reviewer and the abstract of the paper that were matched in y. Then the
score q
jk
is simply q
jk
=
d
w
d
1I(word
d
∈ x
jk
), a weighted combination of overlapping
words. In the next chapter we will show how to learn the parameters w in much the same
way we learn the parameters w of a Markov network.
The space of bipartite matchings illustrates an important property of many structured
spaces: the maximization problem arg max
y∈¸
w
¯
f (x, y) is easier than the normalization
problem
y∈¸
exp¦w
¯
f (x, y)¦. The maximum weight bipartite matching can be found
in polynomial (cubic) time in the number of nodes in the graph using a combinatorial algo
rithm. However, even simply counting the number of matchings is #Pcomplete [Valiant,
1979; Garey & Johnson, 1979]. Note that counting is easier than normalization, which is
essentially weighted counting. This fact makes a probabilistic interpretation of the model as
a distribution over matchings intractable to compute. Similarly, exact maximum likelihood
estimation is intractable, since it requires computing the normalization.
Chapter 4
Structured maximum margin estimation
In the previous chapter, we described several important types of structured models of the
form:
h
w
(x) = arg max
y: g(x,y)≤0
w
¯
f (x, y), (4.1)
where we assume that the optimization problem max
y : g(x,y)≤0
w
¯
f (x, y) can be solved
or approximated by a compact convex optimization problem for some convex subset of
parameters w ∈ ¼. A compact problem formulation is polynomial in the description
length of the objective and the constraints.
Given a sample S = ¦(x
(i)
, y
(i)
)¦
m
i=1
, we develop methods for ﬁnding parameters w
such that:
arg max
y∈¸
(i)
w
¯
f (x
(i)
, y) ≈ y
(i)
, ∀i,
where ¸
(i)
= ¦y : g(x
(i)
, y) ≤ 0¦. In this chapter, we describe at an abstract level two
general approaches to structured estimation that we apply in the rest of the thesis. Both of
these approaches deﬁne a convex optimization problem for ﬁnding such parameters w.
There are several reasons to derive compact convex formulations. First and foremost,
we can ﬁnd globally optimal parameters (with ﬁxed precision) in polynomial time. Sec
ond, we can use standard optimization software to solve the problem. Although special
purpose algorithms that exploit the structure of a particular problem are often much faster
42
4.1. MAXMARGIN ESTIMATION 43
(see Ch. 6), the availability of offtheshelf software is very important for quick develop
ment and testing of such models. Third, we can analyze the generalization performance of
the framework without worrying about the actual algorithms used to carry out the optimiza
tion and the associated woes of intractable optimization problems: local minima, greedy
and heuristic methods, etc.
Our framework applies not only to the standard models typically estimated by prob
abilistic methods, such as Markov networks and contextfree grammars, but also to a
wide range of “unconventional” predictive models. Such models include graph cuts and
weighted matchings, where maximum likelihood estimation is intractable. We provide ex
act maximum margin solutions for several of these problems (Ch. 7 and Ch. 10).
In prediction problems where the maximization in Eq. (4.1) is intractable, we consider
convex programs that provide only an upper or lower bound on the true solution. We
discuss how to use these approximate solutions for approximate learning of parameters.
4.1 Maxmargin estimation
As in the univariate prediction, we measure the error of approximation using a loss func
tion . In structured problems, where we are jointly predicting multiple variables, the loss
is often not just the simple 01 loss or squared error. For structured classiﬁcation, a natural
loss function is a kind of Hamming distance between y
(i)
and h(x
(i)
): the number of vari
ables predicted incorrectly. We will explore these and more general loss functions in the
following chapters.
4.1.1 Minmax formulation
Throughout, we will adopt the hinge upper bound
i
(h(x
(i)
)) on the loss function for struc
tured classiﬁcation inspired by maxmargin criterion:
i
(h(x
(i)
)) = max
y∈¸
(i)
[w
¯
f
i
(y) +
i
(y)] −w
¯
f
i
(y
(i)
) ≥
i
(h(x
(i)
)),
44 CHAPTER 4. STRUCTURED MAXIMUM MARGIN ESTIMATION
where as before,
i
(h(x
(i)
)) = (x
(i)
, y
(i)
, h(x
(i)
)),
i
(h(x
(i)
)) = (x
(i)
, y
(i)
, h(x
(i)
)), and
f
i
(y) = f (x
(i)
, y). With this upper bound, the minmax formulation for structured classiﬁ
cation problem is analogous to multiclass SVM formulation in Eq. (2.9) and Eq. (2.10):
min
1
2
[[w[[
2
+ C
i
ξ
i
(4.2)
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥ max
y∈¸
(i)
[w
¯
f
i
(y) +
i
(y)], ∀i.
The above formulation is a convex quadratic program in w, since max
y∈¸
(i) [w
¯
f
i
(y) +
i
(y)] is convex in w (maximum of afﬁne functions is a convex function). For brevity, we
did not explicitly include the constraint that the parameters are in some legal convex set
(w ∈ ¼, most often IR
n
), but assume this throughout this chapter.
The problem with Eq. (4.2) is that the constraints have a very unwieldy form. An
other way to express this problem is using
i
[¸
(i)
[ linear constraints, which is generally
exponential in L
i
, the number of variables in y
i
.
min
1
2
[[w[[
2
+ C
i
ξ
i
(4.3)
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥ w
¯
f
i
(y) +
i
(y), ∀i, ∀y ∈ ¸
(i)
.
This form reveals the “maximum margin” nature of the formulation. We can interpret
1
[[w[[
w
¯
[f
i
(y
(i)
) − f
i
(y)] as the margin of y
(i)
over another y ∈ ¸
(i)
. Assuming ξ
i
are all
zero (say because C is very large), the constraints enforce
w
¯
f
i
(y
(i)
) −w
¯
f
i
(y) ≥
i
(y),
so minimizing [[w[[ maximizes the smallest such margin, scaled by the loss
i
(y). The
slack variables ξ
i
allow for violations of the constraints at a cost Cξ
i
. If the loss function is
not uniform over all the mistakes y ,= y
(i)
, then the constraints make costly mistakes (those
with high
i
(y)) less likely. In Ch. 5 we analyze the effect of nonuniform loss function
(Hamming distance type loss) on generalization, and show a strong connection between the
lossscaled margin and expected risk of the learned model.
The formulation in Eq. (4.3) is a standard QP with linear constraints, but its exponential
4.1. MAXMARGIN ESTIMATION 45
size is in general prohibitive. We now return to Eq. (4.2) and transform it to a a more man
ageable problem. The key to solving Eq. (4.2) efﬁciently is the lossaugmented inference
max
y∈¸
(i)
[w
¯
f
i
(y) +
i
(y)]. (4.4)
Even if max
y∈¸
(i) w
¯
f
i
(y) can be solved in polynomial time using convex optimization, the
form of the loss term
i
(y) is crucial for the lossaugmented inference to remain tractable.
The range of tractable losses will depend strongly on the problem itself (f and ¸). Even
within the range of tractable losses, some are more efﬁciently computable than others. A
large part of the development of structured estimation methods in the following chapters
is identifying appropriate loss functions for the application and designing convex formula
tions for the lossaugmented inference.
Assume that we ﬁnd such a formulation in terms of a set of variables µ
i
, with a concave
(in µ
i
) objective
¯
f
i
(w, µ
i
) and subject to convex constraints ¯ g
i
(µ
i
):
max
y∈¸
(i)
[w
¯
f
i
(y) +
i
(y)] = max
µ
i
: g
i
(µ
i
)≤0
¯
f
i
(w, µ
i
). (4.5)
We call such formulation compact if the number of variables µ
i
and constraints ¯ g
i
(µ
i
) is
polynomial in L
i
, the number of variables in y
(i)
.
Note that max
µ
i
: g
i
(µ
i
)≤0
¯
f
i
(w, µ
i
) must be convex in w, since Eq. (4.4) is. Likewise,
we can assume that it is feasible and bounded if Eq. (4.4) is. In the next section, we de
velop a maxmargin formulation that uses Lagrangian duality (see [Boyd & Vandenberghe,
2004] for an excellent review) to deﬁne a joint, compact convex problem for estimating the
parameters w.
To make the symbols concrete, consider the example of the reviewerassignment prob
lem we discussed in the previous chapter: we would like a bipartite matching with R re
viewers per paper and at most P papers per reviewer. Each training sample i consists of a
matching of N
(i)
p
papers and N
(i)
r
reviewers from some previous year. Let x
jk
denote the
intersection of the set of words occurring in the web page of a reviewer j and the abstract of
the paper k. Let y
jk
indicate whether reviewer j is matched to the paper k. We can deﬁne
a basis function f
d
(x
jk
, y
jk
) = y
jk
1I(word
d
∈ x
jk
), which indicates whether the word d is
46 CHAPTER 4. STRUCTURED MAXIMUM MARGIN ESTIMATION
in both the web page of a reviewer and the abstract of the paper that are matched in y. We
abbreviate the vector of all the basis functions for each edge jk as y
jk
f
(i)
jk
= f (x
(i)
jk
, y
jk
).
We assume that the loss function decomposes over the variables y
ij
. For example, the
Hamming loss simply counts the number of different edges in the matchings y and y
(i)
:
H
i
(y) =
jk
0/1
i,jk
(y
jk
) =
jk
1I(y
jk
,= y
(i)
jk
) = RN
(i)
p
−
jk
y
jk
y
(i)
jk
.
The last equality follows from the fact that any valid matching for example i has R review
ers for N
(i)
p
papers, hence RN
(i)
p
−
jk
y
jk
y
(i)
jk
represents exactly the number of edges that
are different between y and y
(i)
. Combining the two pieces, we have
w
¯
f (x
(i)
, y) =
jk
[w
¯
f (x
jk
, y
jk
) +
0/1
i,jk
(y
jk
)] = RN
(i)
p
+
jk
y
jk
[w
¯
f
jk
−y
(i)
jk
].
The lossaugmented inference problem can be then written as an LP in µ
i
similar
to Eq. (3.3) (without the constant term RN
(i)
p
):
max
jk
µ
i,jk
[w
¯
f
jk
−y
(i)
jk
]
s.t.
j
µ
i,jk
= R,
k
µ
i,jk
≤ P, 0 ≤ µ
i,jk
≤ 1.
In terms of Eq. (4.5),
¯
f
i
and ¯ g
i
are afﬁne in µ
i
:
¯
f
i
(w, µ
i
) = RN
(i)
p
+
i,j
µ
i,jk
[w
¯
f
jk
−y
(i)
jk
]
and ¯ g
i
(µ
i
) ≤ 0 ⇔
j
µ
i,jk
= R,
k
µ
i,jk
≤ P, 0 ≤ µ
i,jk
≤ 1.
In general, when we can express max
y∈¸
(i) w
¯
f (x
(i)
, y) as an LP and we use a loss
function this is linear in the number of mistakes, we have a linear program of this form for
the lossaugmented inference:
d
i
+ max (F
i
w+c
i
)
¯
µ
i
s.t. A
i
µ
i
≤ b
i
, µ
i
≥ 0, (4.6)
for appropriately deﬁned d
i
, F
i
, c
i
, A
i
, b
i
, which depend only on x
(i)
, y
(i)
, f (x, y) and
g(x, y). Note that the dependence on w is linear and only in the objective of the LP. If
this LP is compact (the number of variables and constraints is polynomial in the number of
4.1. MAXMARGIN ESTIMATION 47
label variables), then we can use it to solve the maxmargin estimation problem efﬁciently
by using convex duality.
The Lagrangian associated with Eq. (4.4) is given by
L
i,w
(µ
i
, λ
i
) =
¯
f
i
(w, µ
i
) −λ
¯
i
¯ g
i
(µ
i
), (4.7)
where λ
i
≥ 0 is a vector of Lagrange multipliers, one for each constraint function in
¯ g
i
(µ
i
). Since we assume that
¯
f
i
(w, µ
i
) is concave in µ
i
and bounded on the nonempty set
µ
i
: ¯ g
i
(µ
i
) ≤ 0, we have strong duality:
max
µ
i
: g
i
(µ
i
)≤0
¯
f
i
(w, µ
i
) = min
λ
i
≥0
max
µ
i
L
i,w
(µ
i
, λ
i
).
For many forms of
¯
f and ¯ g, we can write the Lagrangian dual min
λ
i
≥0
max
µ
i
L
i,w
(µ
i
, λ
i
)
explicitly as:
min h
i
(w, λ
i
) (4.8)
s.t. q
i
(w, λ
i
) ≤ 0,
where h
i
(w, λ
i
) and q
i
(w, λ
i
) are convex in both w and λ
i
. (We folded λ
i
≥ 0 into
q
i
(w, λ
i
) for brevity.) Since the original problem had polynomial size, the dual is polyno
mial size as well. For example, the dual of the LP in Eq. (4.6) is
d
i
+ min b
¯
i
λ
i
s.t. A
¯
i
λ
i
≥ F
i
w+c
i
, λ
i
≥ 0, (4.9)
where h
i
(w, λ
i
) = d
i
+b
¯
i
λ
i
and q
i
(w, λ
i
) ≤ 0 is ¦F
i
w+c
i
−A
¯
i
λ
i
≤ 0, −λ
i
≤ 0¦.
Plugging Eq. (4.8) into Eq. (4.2), we get
min
1
2
[[w[[
2
+ C
i
ξ
i
(4.10)
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥ min
q
i
(w,λ
i
)≤0
h
i
(w, λ
i
), ∀i.
Moreover, we can combine the minimization over λ with minimization over ¦w, ξ¦. The
48 CHAPTER 4. STRUCTURED MAXIMUM MARGIN ESTIMATION
reason for this is that if the right hand side is not at the minimum, the constraint is tighter
than necessary, leading to a suboptimal solution w. Optimizing jointly over λ as well will
produce a solution to ¦w, ξ¦ that is optimal.
min
1
2
[[w[[
2
+ C
i
ξ
i
(4.11)
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥ h
i
(w, λ
i
), ∀i;
q
i
(w, λ
i
) ≤ 0, ∀i.
Hence we have a joint and compact convex optimization program for estimating w.
The exact form of this program depends strongly on
¯
f and ¯ g. For our LPbased example,
we have a QP with linear constraints:
min
1
2
[[w[[
2
+ C
i
ξ
i
(4.12)
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥ d
i
+b
¯
i
λ
i
, ∀i;
A
¯
i
λ
i
≥ F
i
w+c
i
, ∀i;
λ
i
≥ 0, ∀i.
4.1.2 Certiﬁcate formulation
In the previous section, we assumed a compact convex formulation of the lossaugmented
max in Eq. (4.4). There are several important combinatorial problems which allow poly
nomial time solution yet do not have a compact convex optimization formulation. For
example, maximum weight perfect (nonbipartite) matching and spanning tree problems
can be expressed as linear programs with exponentially many constraints, but no polyno
mial formulation is known [Bertsimas & Tsitsiklis, 1997; Schrijver, 2003]. Both of these
problems, however, can be solved in polynomial time using combinatorial algorithms. In
some cases, though, we can ﬁnd a compact certiﬁcate of optimality that guarantees that
y
(i)
= arg max
y
[w
¯
f
i
(y) +
i
(y)] without expressing lossaugmented inference as a com
pact convex program. Intuitively, just verifying that a given assignment is optimal is some
times easier than actually ﬁnding it.
4.1. MAXMARGIN ESTIMATION 49
Consider the maximum weight spanning tree problem. A basic property of a span
ning tree is that cutting any edge (j, k) in the tree creates two disconnected sets of nodes
(1
j
[jk], 1
k
[jk]), where j ∈ 1
j
[jk] and k ∈ 1
k
[jk]. A spanning tree is optimal with respect
to a set of edge weights if and only if for every edge (j, k) in the tree connecting 1
j
[jk] and
1
k
[jk], the weight of (j, k) is larger than (or equal to) the weight of any other edge (j
t
, k
t
)
in the graph with j
t
∈ 1
j
[jk], k
t
∈ 1
k
[jk] [Cormen et al., 2001]. We discuss the conditions
for optimality of perfect matchings in Ch. 10. Suppose that we can ﬁnd a compact convex
formulation of these conditions via a polynomial (in L
i
) set of functions q
i
(w, ν
i
), jointly
convex in w and auxiliary variables ν
i
:
∃ν
i
s.t. q
i
(w, ν
i
) ≤ 0 ⇔ w
¯
f
i
(y
(i)
) ≥ w
¯
f
i
(y) +
i
(y), ∀y ∈ ¸
(i)
.
Then the following joint convex program in wand ν computes the maxmargin parameters:
min
1
2
[[w[[
2
(4.13)
s.t. q
i
(w, ν
i
) ≤ 0, ∀i.
Expressing the spanning tree optimality does not require additional variables ν
i
, but in
other problems, such as in perfect matching optimality in Ch. 10, such auxiliary variables
are needed. In the spanning tree problem, suppose y
jk
encodes whether edge (j, k) is in
the tree and the score of the edge is given by w
¯
f
i,jk
for some basis functions f (x
(i)
jk
, y
jk
).
We also assume that the loss function decomposes into a sum of losses over the edges, with
loss for each wrong edge given by
i,jk
. Then the optimality conditions are:
w
¯
f
i,jk
≥ w
¯
f
i,j
k
+
i,j
k
, ∀jk, j
t
k
t
s.t. y
(i)
jk
= 1, j
t
∈ 1
j
[jk], k
t
∈ 1
k
[jk].
For a full graph, we have
_
[1
(i)
[
3
) constraints for each example i, where [1
(i)
[ is the number
of nodes in the graph for example i.
Note that this formulation does not allow for violations of the margin constraints (it has
no slack variables ξ
i
). If the basis functions are not sufﬁciently rich to ensure that each y
(i)
is optimal, then Eq. (4.1.2) may be infeasible. Essentially, this formulation requires that
the upper bound on the empirical risk be zero, 1
S
[h
w
] = 0, and minimizes the complexity
50 CHAPTER 4. STRUCTURED MAXIMUM MARGIN ESTIMATION
of the hypothesis h
w
as measured by the norm of the weights.
If the problem is infeasible, the designer could add more basis functions f (x, y) that
take into account additional information about x. One could also add slack variables for
each example and each constraint that would allow violations of optimality conditions with
some penalty. However, these slack variables would not represent upper bounds on the loss
as they are in the minmax formulation, and therefore are less justiﬁed.
4.2 Approximations: upper and lower bounds
There are structured prediction tasks for which we might not be able to solve the estimation
problem exactly. Often, we cannot compute max
y∈¸
(i) [w
¯
f
i
(y) +
i
(y)] exactly or explic
itly, but can only upper or lower bound it. Fig. 4.1 shows schematically how approximating
of the max subproblem reduces or extends the feasible space of w and ξ and leads to ap
proximate solutions. The nature of these lower and upper bounds depends on the problem,
but we consider two general cases below.
4.2.1 Constraint generation
When neither compact maximization or optimality formulation is possible, but the max
imization problem can be solved or approximated by a combinatorial algorithm, we can
resort to constraint generation or cutting plane methods. Consider Eq. (4.3), where we
have an exponential number of linear constraints, one for each i and y ∈ ¸
(i)
. Only a sub
set of those constraints will be active at the optimal solution w. In fact, not more than the
number of parameters n plus the number of examples m can be active in general, since that
is the number of variables. If we can identify a small number of constraints that are critical
to the solution, we do not have to include all of them. Of course, identifying these con
straints is in general as difﬁcult as solving the problem, but a greedy approach of adding the
most violated constraints often achieves good approximate solutions after adding a small
(polynomial) number of constraints. If we continue adding constraints until there are no
more violated ones, the resulting solution is optimal.
We assume that we have an algorithm that produces y = arg max
y∈¸
(i) [w
¯
f
i
(y) +
4.2. APPROXIMATIONS: UPPER AND LOWER BOUNDS 51
Upperbound
Exact
Lowerbound
×
+
Figure 4.1: Exact and approximate constraints on the maxmargin quadratic program. The
solid red line represents the constraints imposed by the assignments y ∈ Y
(i)
, whereas the
dashed and dotted lines represent approximate constraints. The approximate constraints
may coincide with the exact constraints in some cases, and be more stringent or relaxed in
others. The parabolic contours represent the value of the objective function and ‘+’, ‘x’ and
‘o’ mark the different optima.
i
(y)]. The algorithm is described in Fig. 4.2. We maintain, for each example i, a small
but growing set of assignments
¯
¸
(i)
⊂ ¸
(i)
. At each iteration, we solve the problem with a
subset of constraints:
min
1
2
[[w[[
2
+ C
i
ξ
i
(4.14)
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥ w
¯
f
i
(y) +
i
(y), ∀i, ∀y ∈
¯
¸
(i)
.
The only difference between Eq. (4.3) and Eq. (4.14) is that ¸
(i)
has been replaced by
¯
¸
(i)
.
We then compute y = arg max
y∈¸
(i) [w
¯
f
i
(y) +
i
(y)] for each i and check whether the
constraint w
¯
f
i
(y
(i)
) + ξ
i
+ ≥ w
¯
f
i
(y) +
i
(y), is violated, where is a user deﬁned
precision parameter. If it is violated, we set
¯
¸
(i)
=
¯
¸
(i)
∪ y. The algorithm terminates
when no constraints are violated. In Fig. 4.1, the lowerbound on the constraints provided
by
¯
¸
(i)
∪y keeps tightening with each iteration, terminating when the desired precision is
reached. We note that if the algorithm that produces y = arg max
y∈¸
(i) [w
¯
f
i
(y)+
i
(y)] is
52 CHAPTER 4. STRUCTURED MAXIMUM MARGIN ESTIMATION
Input: precision parameter .
1. Initialize:
¯
¸
(i)
= ¦¦, ∀ i.
2. Set violation = 0 and solve for w and ξ by optimizing
min
1
2
[[w[[
2
+ C
i
ξ
i
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥ w
¯
f
i
(y) +
i
(y), ∀i, ∀y ∈
¯
¸
(i)
.
3. For each i,
Compute y = arg max
y∈¸
(i) [w
¯
f
i
(y) +
i
(y)],
if w
¯
f
i
(y
(i)
) + ξ
i
+ ≤ w
¯
f
i
(y) +
i
(y),
then set
¯
¸
(i)
=
¯
¸
(i)
∪ y and violation = 1
4. if violation = 1 goto 2.
Return w.
Figure 4.2: A constraint generation algorithm.
suboptimal, the approximation error of the solution we achieve might be much greater than
. The number of constraints that must be added before the algorithm terminates depends
on the precision and problem speciﬁc characteristics. See [Bertsimas & Tsitsiklis, 1997;
Boyd & Vandenberghe, 2004] for a more indepth discussion of cutting planes methods.
This approach may also be computationally faster in providing a very good approximation
in practice if the explicit convex programming formulation is polynomial in size, but very
large, while the maximization algorithm is comparatively fast.
4.2.2 Constraint strengthening
In many problems, the maximization problem we are interested in may be very expensive
or intractable. For example, we consider MAP inference in large treewidth Markov net
works in Ch. 8, multiway cut in Ch. 7, graphpartitioning in Ch. 11. Many such problems
can be written as integer programs. Relaxations of such integer programs into LPs, QPs
or SDPs often provide excellent approximation algorithms [Hochbaum, 1997; Nemhauser
& Wolsey, 1999]. The relaxation usually deﬁnes a larger feasible space
¯
¸
(i)
⊃ ¸
(i)
over
4.3. RELATED WORK 53
which the maximization is done, where y ∈
¯
¸
(i)
may correspond to a “fractional” assign
ment. For example, a solution to the MAP LP in Eq. (3.2) for an untriangulated network
may not correspond to any valid assignment. In such a case, the approximation is an over
estimate of the constraints:
max
y∈
¸
(i)
[w
¯
f
i
(y) +
i
(y)] ≥ max
y∈¸
(i)
[w
¯
f
i
(y) +
i
(y)].
Hence the constraint set is tightened with such invalid assignments. Fig. 4.1 shows how the
overestimate reduces the feasible space of w and ξ.
Note that for every setting of the weights w that produces fractional solutions for the
relaxation, the approximate constraints are tightened because of the additional invalid as
signments. In this case, the approximate MAP solution has higher value than any integer
solution, including the true assignment y
(i)
, thereby driving up the corresponding slack ξ
i
.
By contrast, for weights wfor which the MAP approximation is integervalued, the margin
has the standard interpretation as the difference between the score of y
(i)
and the MAP y
(according to w). As the objective includes a penalty for the slack variable, intuitively,
minimizing the objective tends to drive the weights w away from the regions where the so
lutions to the approximation are fractional. In essence, the estimation algorithm is ﬁnding
weights that are not necessarily optimal for an exact maximization algorithm, but (close to)
optimal for the particular approximate maximization algorithm used. In practice, we will
show experimentally that such approximations often work very well.
4.3 Related work
Our maxmargin formulation is related to a body of work called inverse combinatorial and
convex optimization [Burton & Toint, 1992; Zhang & Ma, 1996; Ahuja & Orlin, 2001;
Heuberger, 2004]. An inverse optimization problem is deﬁned by an instance of an opti
mization problem max
y∈¸
w
¯
f (y), a set of nominal weights w
0
, and a target solution y
t
.
The goal is to ﬁnd the weights w closest to the nominal w
0
in some norm, which make the
54 CHAPTER 4. STRUCTURED MAXIMUM MARGIN ESTIMATION
target solution optimal:
min [[w−w
0
[[
p
s.t. w
¯
f (y
t
) ≥ w
¯
f (y), ∀y ∈ ¸.
Most of the attention has been on L
1
and L
∞
norms, but L
2
norm is also used.
The study of inverse problems began with geophysical scientists (see [Tarantola, 1987]
for indepth discussion of a wide range of applications). Modeling a complex physical
system often involves a large number of parameters which scientists ﬁnd hard or impossible
to set correctly. Provided educated guesses for the parameters w
0
and the behavior of the
system as a target, the inverse optimization problem attempts to match the behavior while
not perturbing the “guesstimate” too much.
Although there is a strong connection between inverse optimization problems and our
formulations, the goals are very different than ours. In our framework, we are learning
a parameterized objective function that depends on the input x and will generalize well
in prediction on new instances. Moreover, we do not assume as given a nominal set of
weights. Note that if we set w
0
= 0, then w = 0 is trivially the optimal solution. The
solution w depends critically on the choice of nominal weights, which is not appropriate in
the learning setting.
The inverse reinforcement learning problem [Ng & Russell, 2000; Abbeel & Ng, 2004]
is much closer to our setting. The goal is to learn a reward function that will cause a rational
agent to act similar to the observed behavior of an expert. A full description of the problem
is beyond our scope, but we brieﬂy describe the Markov decision process (MDP) model
commonly used for sequential decision making problems where an agent interacts with its
environment. The environment is modeled as a system that can be in one of a set of discrete
states. At every time step, the agent chooses an action from a discrete set of actions and the
system transitions to a next state with a probability that depends on the current state and
the action taken. The agent collects a reward at each step, which generally depends on the
on the current and the next state and the action taken. A rational agent executes a policy
(essentially, a state to action mapping) that maximizes its expected reward. To map this
problem (approximately) to our setting, note that a policy roughly corresponds to the labels
4.4. CONCLUSION 55
y, the state sequence correspond to the input x and the reward for a state/action sequence is
assumed to be w
¯
f (x, y) for some basis functions w
¯
f (x, y). The goal is to learn wfroma
set of state/action sequences (x
(i)
, y
(i)
) of the expert such that the maximizing the expected
reward according to the system model makes the agent imitate the expert. This and related
problems are formulated as a convex program in Ng and Russell [2000] and Abbeel and
Ng [2004].
4.4 Conclusion
In this chapter, we presented two formulations of structured maxmargin estimation that
deﬁne a compact convex optimization problem. The ﬁrst formulation, minmax, relies on
the ability to express inference in the model as a compact convex optimization problem.
The second one, certiﬁcate, only requires expressing optimality of a given assignment ac
cording to the model. Our framework applies to a wide range of prediction problems that
we explore in the rest of the thesis, including Markov networks, context free grammars, and
many combinatorial structures such as matchings and graphcuts. The estimation problem
is tractable and exact whenever the prediction problem can be formulated as a compact
convex optimization problem or a polynomial time combinatorial algorithm with compact
convex optimality conditions. When the prediction problem is intractable or very expen
sive to solve exactly, we resort to approximations that only provide upper/lower bounds
on the predictions. The estimated parameters are then approximate, but produce accurate
approximate prediction models in practice.
Because our approach only relies using the maximum in the model for prediction, and
does not require a normalized distribution P(y [ x) over all outputs, maximum margin
estimation can be tractable when maximum likelihood is not. For example, to learn a prob
abilistic model P(y [ x) over bipartite matchings using maximum likelihood requires com
puting the normalizing partition function, which is #Pcomplete [Valiant, 1979; Garey &
Johnson, 1979]. By contrast, maximum margin estimation can be formulated as a compact
QP with linear constraints. Similar results hold for nonbipartite matchings and mincuts.
In models that are tractable for both maximum likelihood and maximum margin, (such
as lowtreewidth Markov networks, context free grammars, many other problems in which
56 CHAPTER 4. STRUCTURED MAXIMUM MARGIN ESTIMATION
inference is solvable by dynamic programming), our approach has an additional advantage.
Because of the hingeloss, the solutions to the estimation are relatively sparse in the dual
space (as in SVMs), which makes the use of kernels much more efﬁcient. Maximum like
lihood estimation with kernels results in models that are generally nonsparse and require
pruning or greedy support vector selection methods [Lafferty et al., 2004; Altun et al.,
2004].
The forthcoming formulations in the thesis follow the principles laid out in this chapter.
The range of applications of these principles is very broad and leads to estimation prob
lems with very interesting structure in each particular problem, from Markov networks and
contextfree grammars to graph cuts and perfect matchings.
Part II
Markov networks
57
Chapter 5
Markov networks
Markov networks are extensively used to model complex sequential, spatial, and relational
interactions in prediction problems arising in many ﬁelds. These problems involve labeling
a set of related objects that exhibit local consistency. In sequential labeling problems (such
as handwriting recognition), the labels (letters) of adjacent inputs (images) are highly corre
lated. Sequential prediction problems arise in natural language processing (partofspeech
tagging, speech recognition, information extraction [Manning & Sch¨ utze, 1999]), compu
tational biology (gene ﬁnding, protein structure prediction, sequence alignment [Durbin
et al., 1998]), and many other ﬁelds. In image processing, neighboring pixels exhibit spa
tial label coherence in denoising, segmentation and stereo correspondence [Besag, 1986;
Boykov et al., 1999a]. In hypertext or bibliographic classiﬁcation, labels of linked and
cocited documents tend to be similar [Chakrabarti et al., 1998; Taskar et al., 2002]. In
proteomic analysis, location and function of proteins that interact are often highly corre
lated [Vazquez et al., 2003]. Markov networks compactly represent complex joint distribu
tions of the label variables by modeling their local interactions. Such models are encoded
by a graph, whose nodes represent the different object labels, and whose edges represent
and quantify direct dependencies between them. For example, a Markov network for the
hypertext domain would include a node for each webpage, encoding its label, and an edge
between any pair of webpages whose labels are directly correlated (e.g., because one links
to the other).
We address the problem of maxmargin estimation the parameters of Markov networks
58
5.1. MAXIMUM LIKELIHOOD ESTIMATION 59
for such structured classiﬁcation problems. We show a compact convex formulation that
seamlessly integrates kernels with graphical models. We analyze the theoretical general
ization properties of maxmargin estimation and derive a novel marginbased bound for
structured classiﬁcation.
We are given a labeled training sample S = ¦(x
(i)
, y
(i)
)¦
m
i=1
, drawn from a ﬁxed dis
tribution D over A ¸. We assume the structure of the network is given: we have a
mapping from an input x to the corresponding Markov network graph ((x) = ¦1, c¦
where the nodes 1 map to the variables in y. We abbreviate ((x
(i)
) as (
(i)
below. In hand
writing recognition, this mapping depends on the segmentation algorithm that determines
how many letters the sample image contains and splits the image into individual images
for each letter. It also depends on the basis functions we use to model the dependencies of
the problem, for example, ﬁrstorder Markov chain or a higherorder models. Note that the
topology and size of the graph (
(i)
, might be different for each example i. For instance, the
training sequences might have different lengths.
We focus on conditional Markov networks (or CRFs [Lafferty et al., 2001]), which
represent P(y [ x) instead of generative models P(x, y). The loglinear representation we
have described in Sec. 3.3.1 is deﬁned via a vector of n basis functions f (x, y):
log P
w
(y [ x) = w
¯
f (x, y) −log Z
w
(x),
where Z
w
(x) =
y
exp¦w
¯
f (x, y)¦ and w ∈ IR
n
. Before we present the maximum
margin estimation, we review the standard maximum likelihood method.
5.1 Maximum likelihood estimation
The regularized maximum likelihood approach of learning the weights w of a Markov net
work is similar to logistic regression we described in Sec. 2.2. The objective is to minimize
the training logloss with an additional regularization term, usually the squarednorm of the
weights w [Lafferty et al., 2001]:
1
2
[[w[[
2
−C
i
log P
w
(y
(i)
[ x
(i)
) =
1
2
[[w[[
2
+ C
i
log Z
w
(x
(i)
) −w
¯
f
i
(y
(i)
),
60 CHAPTER 5. MARKOV NETWORKS
where f
i
(y) = f (x
(i)
, y).
This objective function is convex in the parameters w, so we have an unconstrained
convex optimization problem. The gradient with respect to w is given by:
w+ C
i
_
E
i,w
[f
i
(y)] −f
i
(y
(i)
)
¸
= w−C
i
E
i,w
[∆f
i
(y)],
where E
i,w
[f
i
(y)] =
y∈¸
f
i
(y)P
w
(y [ x
(i)
) is the expectation under the conditional dis
tribution P
w
(y [ x
(i)
) and ∆f
i
(y) = f (x
(i)
, y
(i)
) −f (x
(i)
, y), as before. To compute the ex
pectations, we can use inference in the Markov network to calculate marginals P
w
(y
c
[ x
(i)
)
for each clique c in the network Sec. 3.3.2. Since the basis functions decompose over the
cliques of the network, the expectation decomposes as well:
E
i,w
[f
i
(y)] =
c∈(
(i)
y
c
∈¸
(i)
c
f
i,c
(y
c
)P
w
(y
c
[ x
(i)
).
Second order methods for solving unconstrained convex optimization problems, such
as Newton’s method, require the second derivatives as well as the gradient. Let δf
i
(y) =
f
i
(y) − E
i,w
[f
i
(y)]. The Hessian of the objective depends on the covariances of the basis
functions:
I + C
i
E
i,w
_
δf
i
(y)δf
i
(y)
¯
¸
,
where I is a n n identity matrix. Computing the Hessian is more expensive than the
gradient, since we need to calculate joint marginals of every pair of cliques c and c
t
,
P
w
(y
c∪c
[ x
i
) as well as covariances of all basis functions, which is quadratic in the num
ber of cliques and the number of functions. A standard approach is to use an approximate
second order method that does not need to compute the Hessian, but uses only the gradient
information [Nocedal & Wright, 1999; Boyd & Vandenberghe, 2004]. Conjugate Gradients
or LBFGS methods have been shown to work very well on large estimation problems [Sha
& Pereira, 2003; Pinto et al., 2003], even with millions of parameters w.
5.2. MAXIMUM MARGIN ESTIMATION 61
5.2 Maximum margin estimation
For maximummargin estimation, we begin with the minmax formulation from Sec. 4.1:
min
1
2
[[w[[
2
+ C
i
ξ
i
(5.1)
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥ max
y
[w
¯
f
i
(y) +
i
(y)], ∀i.
We know from Sec. 3.3.3 how to express max
y
w
¯
f
i
(y) as an LP, but the important differ
ence is the loss function
i
. The simplest loss is the 0/1 loss
i
(y) ≡ 1I(y
(i)
,= y). In fact
this loss for sequence models was used by Collins [2001] and Altun et al. [2003]. However,
in structured problems, where we are predicting multiple labels, the loss is often not just
the simple 0/1 loss, but may depend on the number of labels and type of labels predicted
incorrectly or perhaps the number of cliques of labels predicted incorrectly. In general, we
assume that the loss, like the basis functions, decomposes over the cliques of labels.
Assumption 5.2.1 The loss function
i
(y) is decomposable:
i
(y) =
c∈((Ç
(i)
)
(x
(i)
c
, y
(i)
c
, y
c
) =
c∈((Ç
(i)
)
i,c
(y
c
).
We will focus on decomposable loss functions below. A natural choice that we use in our
experiments is the Hamming distance:
H
(x
(i)
, y
(i)
, y) =
v∈1
(i)
1I(y
(i)
v
,= y
v
).
With this assumption, we can express this inference problem for a triangulated graph
as a linear program for each example i as in Sec. 3.3.3:
max
c,y
c
µ
i,c
(y
c
)[w
¯
f
i,c
(y
c
) +
i,c
(y
c
)] (5.2)
s.t.
y
c
µ
i,c
(y
c
) = 1, ∀i, ∀c ∈ (
(i)
; µ
i,c
(y
c
) ≥ 0, ∀c ∈ (
(i)
, ∀y
c
;
µ
i,s
(y
s
) =
y
c
∼y
s
µ
i,c
(y
t
c
), ∀s, c ∈ (
(i)
, s ⊂ c, ∀y
s
,
62 CHAPTER 5. MARKOV NETWORKS
where (
(i)
= (((
(i)
) are the cliques of the Markov network for example i.
As we showed before, the constraints ensure that the µ
i
’s form a proper distribution. If
the most likely assignment is unique, then the distribution that maximizes the objective puts
all its weight on that assignment. (If the arg max is not unique, any convex combination of
the assignments is a valid solution). The dual of Eq. (5.2) is given by:
min
c
λ
i,c
(5.3)
s.t. λ
i,c
+
s⊃c
m
i,s,c
(y
c
) −
s⊂c, y
s
∼y
c
m
i,c,s
(y
t
s
) ≥ w
¯
f
i,c
(y
c
) +
i,c
(y
c
), ∀c ∈ (
(i)
, ∀y
c
.
In this dual, the λ
i,c
variables correspond to the normalization constraints, while m
i,c,s
(y
c
)
variables correspond to the agreement constraints in the primal in Eq. (5.2).
Plugging the dual into Eq. (5.1) for each example i and maximizing jointly over all the
variables (w, ξ, λ and m), we have:
min
1
2
[[w[[
2
+ C
i
ξ
i
(5.4)
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥
i,c
λ
i,c
, ∀i;
λ
i,c
+
s⊃c
m
i,s,c
(y
c
) −
s⊂c, y
s
∼y
c
m
i,c,s
(y
t
s
) ≥ w
¯
f
i,c
(y
c
) +
i,c
(y
c
), ∀c ∈ (
(i)
, ∀y
c
.
In order to gain some intuition about this formulation, we make a change of variables from
λ
i,c
to ξ
i,c
:
λ
i,c
= w
¯
f
i,c
(y
(i)
c
) + ξ
i,c
, ∀i, ∀c ∈ (
(i)
.
The reason for naming the newvariables using the letter ξ will be clear in the following. For
readability, we also introduce variables that capture the effect of all the agreement variables
m:
M
i,c
(y
c
) =
s⊂c, y
s
∼y
c
m
i,c,s
(y
t
s
) −
s⊃c
m
i,s,c
(y
c
), ∀i, ∀c ∈ (
(i)
, ∀y
c
.
5.2. MAXIMUM MARGIN ESTIMATION 63
With these new variables, we have:
min
1
2
[[w[[
2
+ C
i
ξ
i
(5.5)
s.t. ξ
i
≥
c
ξ
i,c
, ∀i;
w
¯
f
i,c
(y
(i)
c
) + ξ
i,c
≥ w
¯
f
i,c
(y
c
) +
i,c
(y
c
) + M
i,c
(y
c
), ∀i, ∀c ∈ (
(i)
, ∀y
c
;
M
i,c
(y
c
) =
s⊂c, y
s
∼y
c
m
i,c,s
(y
t
s
) −
s⊃c
m
i,s,c
(y
c
), ∀i, ∀c ∈ (
(i)
, ∀y
c
.
Note that ξ
i
=
c
ξ
i,c
at the optimum, since the slack variable ξ
i
only appears only in the
constraint ξ
i
≥
c
ξ
i,c
and the objective minimizes Cξ
i
. Hence we can simply eliminate
this set of variables:
min
1
2
[[w[[
2
+ C
i,c
ξ
i,c
(5.6)
s.t. w
¯
f
i,c
(y
(i)
c
) + ξ
i,c
≥ w
¯
f
i,c
(y
c
) +
i,c
(y
c
) + M
i,c
(y
c
), ∀i, ∀c ∈ (
(i)
, ∀y
c
;
M
i,c
(y
c
) =
s⊂c, y
s
∼y
c
m
i,c,s
(y
t
s
) −
s⊃c
m
i,s,c
(y
c
), ∀i, ∀c ∈ (
(i)
, ∀y
c
.
Finally, we can write this in a form that resembles our original formulation Eq. (5.1), but
deﬁned at a local level, for each clique:
min
1
2
[[w[[
2
+ C
i,c
ξ
i,c
(5.7)
s.t. w
¯
f
i,c
(y
(i)
c
) + ξ
i,c
≥ max
y
c
[w
¯
f
i,c
(y
c
) +
i,c
(y
c
) + M
i,c
(y
c
)], ∀i, ∀c ∈ (
(i)
;
M
i,c
(y
c
) =
s⊂c, y
s
∼y
c
m
i,c,s
(y
t
s
) −
s⊃c
m
i,s,c
(y
c
), ∀i, ∀c ∈ (
(i)
, ∀y
c
.
Note that without M
i,c
and m
i,c,s
variables, we essentially treat each clique as an indepen
dent classiﬁcation problem: for each clique we have a hinge upperbound on the local loss,
or a margin requirement. The m
i,c,s
(y
s
) variables correspond to a certain kind of messages
between cliques that distribute “credit” to cliques to fulﬁll this margin requirement from
other cliques which have sufﬁcient margin.
64 CHAPTER 5. MARKOV NETWORKS
Figure 5.1: Firstorder chain shown as a set of cliques (nodes and edges). Also shown are
the corresponding local slack variables ξ for each clique and messages m between cliques.
As an example, consider the ﬁrstorder Markov chain in Fig. 5.1. The set of cliques
consists of the ﬁve nodes and the four edges. Suppose for the sake of this example that
our training data consists of only one training sample. The ﬁgure shows the local slack
variables ξ and messages m between cliques for this sample. For brevity of notion in this
example, we drop the dependence on the sample index i in the indexing of the variables
(we also used y
(∗)
j
instead of y
(i)
j
below). For concreteness, below we use the Hamming
loss
H
, which decomposes into local terms
j
(y
j
) = 1I(y
j
,= y
(∗)
j
) for each node and is
zero for the edges.
The constraints associated with the node cliques in this sequence are:
w
¯
f
1
(y
(∗)
1
) + ξ
1
≥ w
¯
f
1
(y
1
) + 1I(y
1
,= y
(∗)
1
) −m
1,12
(y
1
), ∀y
1
;
w
¯
f
2
(y
(∗)
2
) + ξ
2
≥ w
¯
f
2
(y
2
) + 1I(y
2
,= y
(∗)
2
) −m
2,12
(y
2
) −m
2,23
(y
2
), ∀y
2
;
w
¯
f
3
(y
(∗)
3
) + ξ
3
≥ w
¯
f
3
(y
3
) + 1I(y
3
,= y
(∗)
3
) −m
3,23
(y
3
) −m
3,34
(y
3
), ∀y
3
;
w
¯
f
4
(y
(∗)
4
) + ξ
4
≥ w
¯
f
4
(y
4
) + 1I(y
4
,= y
(∗)
4
) −m
4,34
(y
4
) −m
4,45
(y
4
), ∀y
4
;
w
¯
f
5
(y
(∗)
5
) + ξ
5
≥ w
¯
f
5
(y
5
) + 1I(y
5
,= y
(∗)
5
) −m
5,45
(y
5
), ∀y
5
.
5.3. M
3
N DUAL AND KERNELS 65
The edge constraints are:
w
¯
f
12
(y
(∗)
1
, y
(∗)
2
) + ξ
12
≥ w
¯
f
12
(y
1
, y
2
) + m
1,12
(y
1
) + m
2,12
(y
2
), ∀y
1
, y
2
;
w
¯
f
23
(y
(∗)
2
, y
(∗)
3
) + ξ
23
≥ w
¯
f
23
(y
2
, y
3
) + m
2,23
(y
2
) + m
3,23
(y
3
), ∀y
2
, y
3
;
w
¯
f
34
(y
(∗)
3
, y
(∗)
4
) + ξ
34
≥ w
¯
f
34
(y
3
, y
4
) + m
3,34
(y
3
) + m
4,34
(y
4
), ∀y
3
, y
4
;
w
¯
f
45
(y
(∗)
4
, y
(∗)
5
) + ξ
45
≥ w
¯
f
45
(y
4
, y
5
) + m
4,45
(y
4
) + m
5,45
(y
5
), ∀y
4
, y
5
.
5.3 M
3
N dual and kernels
In the previous section, we showed a derivation of a compact formulation based on LP
inference. In this section, we develop an alternative dual derivation that provides a very
interesting interpretation of the problem and is a departure for specialpurpose algorithms
we develop. We begin with the formulation as in Eq. (4.3):
min
1
2
[[w[[
2
+ C
i
ξ
i
(5.8)
s.t. w
¯
∆f
i
(y) ≥
i
(y) −ξ
i
, ∀i, y,
where ∆f
i
(y) ≡ f (x
(i)
, y
(i)
) −f (x
(i)
, y). The dual is given by:
max
i,y
α
i
(y)
i
(y) −
1
2
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,y
α
i
(y)∆f
i
(y)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
(5.9)
s.t.
y
α
i
(y) = C, ∀i; α
i
(y) ≥ 0, ∀i, y.
In the dual, the exponential number of α
i
(y) variables correspond to the exponential num
ber of constraints in the primal. We make two small transformations to the dual that do not
change the problem: we normalize α’s by C (by letting α
i
(y) = Cα
t
i
(y)), so that they sum
66 CHAPTER 5. MARKOV NETWORKS
to 1 and divide the objective by C. The resulting dual is given by:
max
i,y
α
i
(y)
i
(y) −
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,y
α
i
(y)∆f
i
(y)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
(5.10)
s.t.
y
α
i
(y) = 1, ∀i; α
i
(y) ≥ 0, ∀i, y.
As in multiclass SVMs, the solution to the dual α gives the solution to the primal as a
weighted combination: w
∗
= C
i,y
α
∗
i
(y)∆f
i
(y).
Our main insight is that the variables α
i
(y) in the dual formulation Eq. (5.10) can be
interpreted as a kind of distribution over y, since they lie in the simplex
y
α
i
(y) = 1; α
i
(y) ≥ 0, ∀y.
This dual distribution does not represent the probability that the model assigns to an instan
tiation, but the importance of the constraint associated with the instantiation to the solution.
The dual objective is a function of expectations of
i
(y) and ∆f
i
(y) with respect to α
i
(y).
Since
i
(y) =
c
i,c
(y
c
) and ∆f
i
(y) =
c
∆f
i,c
(y
c
) decompose over the cliques of the
Markov network, we only need clique marginals of the distribution α
i
(y) to compute their
expectations. We deﬁne the marginal dual variables as follows:
µ
i,c
(y
c
) =
y
∼y
c
α
i
(y
t
), ∀i, ∀c ∈ (
(i)
, ∀y
c
, (5.11)
where y
t
∼ y
c
denotes whether the partial assignment y
c
is consistent with the full assign
ment y
t
. Note that the number of µ
i,c
(y
c
) variables is small (polynomial) compared to the
number of α
i
(y) variables (exponential) if the size of the largest clique is constant with
respect to the size of the network.
Now we can reformulate our entire QP (5.10) in terms of these marginal dual variables.
Consider, for example, the ﬁrst term in the objective function (ﬁxing a particular i):
y
α
i
(y)
i
(y) =
y
α
i
(y)
c
i,c
(y
c
) =
c,y
c
i,c
(y
c
)
y
∼y
c
α
i
(y
t
) =
c,y
c
µ
i,c
(y
c
)
i,c
(y
c
).
5.3. M
3
N DUAL AND KERNELS 67
The decomposition of the second term in the objective is analogous.
y
α
i
(y)∆f
i
(y) =
c,y
c
∆f
i,c
(y
c
)
y
∼y
c
α
i
(y
t
) =
c,y
c
µ
i,c
(y
c
)∆f
i,c
(y
c
).
Let us denote the the objective of Eq. (5.10) as Q(α). Note that it only depends on
α
i
(y) through its marginals µ
i,c
(y
c
), that is, Q(α) = Q
t
(/(α)), where / denotes the
marginalization operator deﬁned by Eq. (5.11) . The domain of this operator, T[/], is
the product of simplices for all the m examples. What is its range, 1[/], the set of legal
marginals? Characterizing this set (also known as marginal polytope) compactly will allow
us to work in the space of µ’s:
max
α∈T[/]
Q(α) ⇔ max
µ∈1[/]
Q
t
(µ).
Hence we must ensure that µ
i
corresponds to some distribution α
i
, which is exactly
what the constraints in the LP for MAP inference enforce (see discussion of Lemma 3.3.5).
Therefore, when all (
(i)
are triangulated, the following structured dual QP has the same
primal solution (w
∗
) as the original exponential dual QP in Eq. (5.10):
max
i,c,y
c
µ
i,c
(y
c
)
i,c
(y
c
) −
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,c,y
c
µ
i,c
(y
c
)∆f
i,c
(y
c
)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
(5.12)
s.t.
y
c
µ
i,c
(y
c
) = 1, ∀i, ∀c ∈ (
(i)
; µ
i,c
(y
c
) ≥ 0, ∀i, ∀c ∈ (
(i)
, ∀y
c
;
µ
i,s
(y
s
) =
y
c
∼y
s
µ
i,c
(y
t
c
), ∀i, ∀s, c ∈ (
(i)
, s ⊂ c, ∀y
s
.
The solution to the structured dual µ
∗
gives us the primal solution:
w
∗
= C
i,c,y
c
µ
∗
i,c
(y
c
)∆f
i,c
(y
c
).
In this structured dual, we only enforce that there exists an α
i
consistent with µ
i
, but do
not make a commitment about what it is. In general, the α distribution is not unique, but
there is a continuum of distributions consistent with a set of marginals. The objective of
68 CHAPTER 5. MARKOV NETWORKS
the QP Eq. (5.10) does not distinguish between these distributions, since it only depends on
their marginals. The maximumentropy distribution α
i
consistent with a set of marginals
µ
i
, however, is unique for a triangulated model and can be computed using the junction tree
T
(i)
for the network [Cowell et al., 1999].
Speciﬁcally, associated with each edge (c, c
t
) in the tree T
(i)
is a set of variables called
the separator s = c ∩ c
t
. Note that each separator s and complement of a separator c ¸ s is
also a clique of the original graph, since it is a subclique of a larger clique. We denote the
set of separators as o
(i)
. Now we can deﬁne the maximumentropy distribution α
i
(y) as
follows:
α
i
(y) =
c∈T
(i)
µ
i,c
(y
c
)
s∈S
(i)
µ
i,s
(y
s
)
. (5.13)
Again, by convention 0/0 ≡ 0.
Kernels
Note that the solution is a weighted combination of local basis functions and the objective
of Eq. (5.12) can be expressed in terms of dot products between local basis functions
∆f
i,c
(y
c
)
¯
∆f
j,¯ c
(y
¯ c
) = [f (x
(i)
c
, y
(i)
c
) −f (x
(i)
c
, y
c
)]
¯
[f (x
(j)
¯ c
, y
(j)
¯ c
) −f (x
(j)
¯ c
, y
¯ c
)].
Hence, we can locally kernelize our models and solve Eq. (5.12) efﬁciently. Kernels are
typically deﬁned on the input, e.g. k(x
(i)
c
, x
(j)
¯ c
). In our handwriting example, we use a
polynomial kernel on the pixel values for the node cliques. We usually extend the kernel
over the input space to the joint input and output space by simply deﬁning
f (x
c
, y
c
)
¯
f (x
¯ c
, y
¯ c
) ≡ 1I(y
c
= y
¯ c
)k(x
c
, x
¯ c
).
Of course, other deﬁnitions are possible and may be useful when the assignments in each
clique y
c
have interesting structure. In Sec. 6.2 we experiment with several kernels for
the handwriting example. As in SVMs, the solutions to the maxmargin QP are typically
sparse in the µ variables. Hence, each logpotential in the network “remembers” only a
small proportion of the relevant training data inputs.
5.4. UNTRIANGULATED MODELS 69
Figure 5.2: Diamond Markov network (added triangulation edge is dashed and threenode
marginals are in dashed rectangles).
5.4 Untriangulated models
If the underlying Markov net is not chordal, we must address the problem by triangulating
the graph, that is, adding ﬁllin edges to ensure triangulation. For example, if our graph is
a 4cycle Y
1
—Y
2
—Y
3
—Y
4
—Y
1
as in Fig. 5.2, we can triangulate the graph by adding an
arc Y
1
—Y
3
. This will introduce new cliques Y
1
, Y
2
, Y
3
and Y
1
, Y
3
, Y
4
and the corresponding
marginals, µ
123
(y
1
, y
2
, y
3
) and µ
134
(y
1
, y
3
, y
4
). We can then use this new graph to produce
the constraints on the marginals:
y
1
µ
123
(y
1
, y
2
, y
3
) = µ
23
(y
2
, y
3
), ∀y
2
, y
3
;
y
3
µ
123
(y
1
, y
2
, y
3
) = µ
12
(y
1
, y
2
), ∀y
1
, y
2
;
y
1
µ
134
(y
1
, y
3
, y
4
) = µ
34
(y
3
, y
4
), ∀y
3
, y
4
;
y
3
µ
134
(y
1
, y
3
, y
4
) = µ
13
(y
1
, y
3
), ∀y
1
, y
3
.
The new marginal variables appear only in the constraints; they do not add any new basis
functions nor change the objective function.
70 CHAPTER 5. MARKOV NETWORKS
In general, the number of constraints introduced is exponential in the number of vari
ables in the new cliques — the treewidth of the graph. Unfortunately, even sparsely con
nected networks, for example 2D grids often used in image analysis, have large treewidth.
However, we can still solve the QP in the structured primal Eq. (5.6) or the structured
dual Eq. (5.12) deﬁned by an untriangulated graph. Such a formulation, which enforces
only local consistency of marginals, optimizes our objective only over a relaxation of the
marginal polytope. However, the learned parameters produce very accurate approximate
models in practice, as experiments in Ch. 8 demonstrate.
Note that we could also strengthen the untriangulated relaxation without introducing
an exponential number of constraints. For example, we can add positive semideﬁnite con
straints on the marginals µ used by Wainwright and Jordan [2003], which tend to improve
the approximation of the marginal polytope. Although this and other more complex relax
ations are a very interesting area of future development, they are often much more expen
sive.
The approximate QP does not guarantee that the learned model using exact inference
minimizes the true objective: (upperbound on) empirical risk plus regularization. But do
we really need these optimal parameters if we cannot perform exact inference? A more
useful goal is to make sure that training error is minimized using the approximate infer
ence procedure via the untriangulated LP. We conjecture that the parameters learned by
the approximate QP in fact do that to some degree. For instance, consider the separable
case, where 100% accuracy is achievable on the training data by some parameter setting w
such that approximate inference (using the untriangulated LP) produces integral solutions.
Solving the problem as C → ∞ will ﬁnd this solution even though it may not be optimal
(in terms of the norm of the w) using exact inference. For C in intermediate range, the
formulation trades off fractionality of the untriangulated LP solutions with complexity of
the weights [[w[[
2
.
5.5 Generalization bound
In this section, we show a generalization bound for the task of structured classiﬁcation that
allows us to relate the error rate on the training set to the generalization error. To the best
5.5. GENERALIZATION BOUND 71
of our knowledge, this bound is the ﬁrst to deal with structured error, such as the Hamming
distance. Our analysis of Hamming loss allows to prove a signiﬁcantly stronger result than
previous bounds for the 0/1 loss, as we detail below.
Our goal in structured classiﬁcation is often to minimize the number of misclassiﬁed
labels, or the Hamming distance between y and h(x). An appropriate error function is the
average perlabel loss
L(w, x, y) =
1
L
H
(y, arg max
y
w
¯
f (x, y
t
)),
where Lis the number of label variables in y. As in other generalization bounds for margin
based classiﬁers, we relate the generalization error to the margin of the classiﬁer. Consider
an upper bound on the above loss:
L(w, x, y) ≤ L(w, x, y) = max
y
: w
f (y)≤w
f (y
)
1
L
H
(y, y
t
).
This upper bound is tight if y = arg max
y
w
¯
f (x, y
t
), Otherwise, it is adversarial: it
picks from all y
t
which are better (w
¯
f (y) ≤ w
¯
f (y
t
)), one that maximizes the Hamming
distance from y. We can now deﬁne a γmargin perlabel loss:
L(w, x, y) ≤ L(w, x, y) ≤ L
γ
(w, x, y) = max
y
: w
f (y)≤w
f (y
)+γ
H
(y,y
)
1
L
H
(y, y
t
).
This upper bound is even more adversarial: it is tight if y = arg max
y
[w
¯
f (x, y
t
) +
H
(y, y
t
)], otherwise, it picks from all y
t
which are better when helped by γ
H
(y, y
t
), one
that maximizes the Hamming distance from y. Note that the loss we minimize in the max
margin formulation is very closely related (although not identical to) this upper bound.
We can now prove that the generalization accuracy of any hypothesis w is bounded by
its empirical γmargin perlabel loss, plus a term that grows inversely with the margin.To
state the bound, we need to deﬁne several other factors it depends upon. Let N
c
be the
maximum number of cliques in ((x), V
c
be the maximum number of values in a clique
[Y
c
[, q be the maximum number of cliques that have a variable in common, and R
c
be
an upperbound on the 2norm of clique basis functions. Consider a ﬁrstorder sequence
72 CHAPTER 5. MARKOV NETWORKS
model as an example, with L as the maximumlength, and V the number of values a variable
takes. Then N
c
= 2L − 1 since we have L node cliques and L − 1 edge cliques; V
c
= V
2
because of the edge cliques; and q = 3 since nodes in the middle of the sequence participate
in 3 cliques: previouscurrent edge clique, node clique, and currentnext edge clique.
Theorem 5.5.1 For the family of hypotheses parameterized by w, and any δ > 0, there
exists a constant K such that for any γ > 0 perlabel margin, and m > 1 samples, the
expected perlabel loss is bounded by:
E
D
[L(w, x, y)] ≤ E
S
[L
γ
(w, x, y)] +
¸
K
m
_
R
2
c
[[w[[
2
q
2
γ
2
[ln m + ln N
c
+ ln V
c
] + ln
1
δ
_
,
with probability at least 1 −δ.
Proof: See Appendix A.1 for the proof details and the exact value of the constant K.
The ﬁrst term upper bounds the training error of w. Low loss E
S
[L
γ
(w, x, y)] at high
margin γ quantiﬁes the conﬁdence of the prediction model. The second term depends on
[[w[[/γ, which corresponds to the complexity of the classiﬁer (normalized by the margin
level). Thus, the result provides a bound to the generalization error that trades off the
effective complexity of the hypothesis space with the training error.
The proof uses a covering number argument analogous to previous results in SVMs [Zhang,
2002]. However we propose a novel method for covering the space of structured prediction
models by using a cover of the individual clique basis function differences ∆f
i,c
(y
c
). This
new type of cover is polynomial in the number of cliques, yielding signiﬁcant improve
ments in the bound. Speciﬁcally, our bound has a logarithmic dependence on the number
of cliques (ln N
c
) and depends only on the 2norm of the basis functions perclique (R
c
).
This is a signiﬁcant gain over the previous result of Collins [2001] for 0/1 loss, which has
linear dependence (inside the square root) on the number of nodes (L), and depends on
the joint 2norm of all of the basis functions for an example (which is ∼ N
c
R
c
). Such a
result was, until now, an open problem for marginbased sequence classiﬁcation [Collins,
2001]. Finally, for sequences, note that if
L
m
= O(1) (for example, in OCR, if the number
of instances is at least a constant times the length of a word), then our bound is independent
of the number of labels L.
5.6. RELATED WORK 73
5.6 Related work
The application of marginbased estimation methods to parsing and sequence modeling was
pioneered by Collins [2001] using the VotedPerceptron algorithm [Freund & Schapire,
1998]. He provides generalization guarantees (for 0/1 loss) that hold for separable case and
depend on the number of mistakes the perceptron makes before convergence. Remarkably,
the bound does not explicitly depend on the length of the sequence, although undoubtedly
the number of mistakes does.
Collins [2004] also suggested an SVMlike formulation (with exponentially many con
straints) and a constraint generation method for solving it. His generalization bound (for
0/1 loss) based on the SVMlike margin, however, has linear dependence (inside the square
root) on the number of nodes (L). It also depends on the joint 2norm of all of the basis
functions for an example (which is ∼ N
c
R
c
). By considering the more natural Hamming
loss, we achieve a much tighter analysis.
Altun et al. [2003] have applied the exponentialsize formulation with constraint gen
eration we described in Sec. 4.2.1 to problems natural language processing. In a followup
paper, Tsochantaridis et al. [2004] show that only a polynomial number of constraints are
needed to be generated to guarantee a ﬁxed level of precision of the solution. However,
the number of constraints in many important cases is several orders higher (in L) than in
the the approach we present. In addition, the corresponding problem needs to be resolved
(or at least approximately resolved) after each additional constraint is added, which is pro
hibitively expensive for large number of examples and label variables.
The work of Guestrin et al. [2003] presents LP decompositions based on graphical
model structure for the value function approximation problem in factored MDPs (Markov
decision processes with structure). Describing the exact setting is beyond our scope, but it
sufﬁces to say that our original decomposition of the maxmargin QP was inspired by the
proposed technique to transform an exponential set of constraints into a polynomial one
using a triangulated graph.
There has been a recent explosion of work in maximum conditional likelihood estima
tion of Markov networks. The work of Lafferty et al. [2001] has inspired many applications
in natural language, computational biology, computer vision and relational modeling [Sha
74 CHAPTER 5. MARKOV NETWORKS
& Pereira, 2003; Pinto et al., 2003; Kumar & Hebert, 2003; Sutton et al., 2004; Taskar
et al., 2002; Taskar et al., 2003b]. As in the case of logistic regression, maximum condi
tional likelihood estimation for Markov networks can also be kernelized [Altun et al., 2004;
Lafferty et al., 2004]. However, the solutions are nonsparse and the proposed algorithms
are forced to use greedy selection of support vectors or heuristic pruning methods.
5.7 Conclusion
We use graph decomposition to derive an exact, compact, convex maxmargin formulation
for Markov networks with sequence and other lowtreewidth structure. Our formulation
avoids the exponential blowup in the number of constraints in the maxmargin QP that
plagued previous approaches. The seamless integration of kernels with graphical models
allows us to create very rich models that leverage the immense amount of research in kernel
design and graphical model decompositions. We also use approximate graph decomposi
tion to derive a compact approximate formulation for Markov networks in which inference
is intractable.
We provide theoretical guarantees on the average perlabel generalization error of our
models in terms of the training set margin. Our generalization bound signiﬁcantly tightens
previous results of Collins [Collins, 2001] and suggests possibilities for analyzing perlabel
generalization properties of graphical models.
In the next chapter, we present an efﬁcient algorithm that exploits graphical model
inference and show experiments on a large handwriting recognition task that utilize the
powerful representational capability of kernels.
Chapter 6
M
3
N algorithms and experiments
Although the number of variables and constraints in the structured dual in Eq. (5.12) is
polynomial in the size of the data, unfortunately, for standard QP solvers, the problem is
often too large even for small training sets. Instead, we use a coordinate dual ascent method
analogous to the sequential minimal optimization (SMO) used for SVMs [Platt, 1999].
We apply our M
3
N framework and structured SMO algorithm to a handwriting recogni
tion task. We show that our models signiﬁcantly outperform other approaches by incorpo
rating highdimensional decision boundaries of polynomial kernels over character images
while capturing correlations between consecutive characters.
6.1 Solving the M
3
N QP
Let us begin by considering the primal and dual QPs for multiclass SVMs:
min
1
2
[[w[[
2
+ C
i
ξ
i
max
i,y
α
i
(y)
i
(y) −
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,y
α
i
(y)∆f
i
(y)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
s.t. w
∆f
i
(y) ≥ (y) −ξ
i
, ∀i, y. s.t.
y
α
i
(y) = 1, ∀i; α
i
(y) ≥ 0, ∀i, y.
The KKT conditions [Bertsekas, 1999; Boyd & Vandenberghe, 2004] provide sufﬁcient
and necessary criteria for optimality of a dual solution α. As we describe below, these
conditions have certain locality with respect to each example i, which allows us to perform
75
76 CHAPTER 6. M
3
N ALGORITHMS AND EXPERIMENTS
the search for optimal α by repeatedly considering one example at a time.
A feasible dual solution α and a primal solution deﬁned by:
w = C
i,y
α
i
(y)∆f
i
(y) (6.1)
ξ
i
= max
y
[
i
(y) −w∆f
i
(y)] = max
y
[
i
(y) +w
¯
f
i
(y)] −w
¯
f
i
(y
(i)
),
are optimal if they satisfy the following two types of constraints:
α
i
(y) = 0 ⇒ w
¯
∆f
i
(y) >
i
(y) −ξ
i
; (KKT1)
α
i
(y) > 0 ⇒ w
¯
∆f
i
(y) =
i
(y) −ξ
i
. (KKT2),
We can express these conditions as
α
i
(y) = 0 ⇒ w
¯
f
i
(y) +
i
(y) < max
y
[w
¯
f
i
(y
t
) +
i
(y
t
)]; (KKT1)
α
i
(y) > 0 ⇒ w
¯
f
i
(y) +
i
(y) = max
y
[w
¯
f
i
(y
t
) +
i
(y
t
)]. (KKT2)
To simplify the notation, we deﬁne
v
i
(y) = w
¯
f
i
(y) +
i
(y); v
i
(y) = max
y
,=y
[w
¯
f
i
(y
t
) +
i
(y
t
)].
With these deﬁnitions, we have
α
i
(y) = 0 ⇒v
i
(y) < v
i
(y); (KKT1) α
i
(y) > 0 ⇒v
i
(y) ≥ v
i
(y); (KKT2).
In practice, however, we will enforce KKT conditions up to a given tolerance 0 < ¸1.
α
i
(y) = 0 ⇒v
i
(y) ≤ v
i
(y) + ; α
i
(y) > 0 ⇒v
i
(y) ≥ v
i
(y) −. (6.2)
Essentially, α
i
(y) can be zero only if v
i
(y) is at most larger than the all others. Con
versely, α
i
(y) can be nonzero only if v
i
(y) is at most smaller than the all others.
Note that the normalization constraints on the dual variables α are local to each exam
ple i. This allows us to perform dual blockcoordinate ascent where a block corresponds to
6.1. SOLVING THE M
3
N QP 77
1. Initialize: α
i
(y) = 1I(y = y
(i)
), ∀ i, y.
2. Set violation = 0,
3. For each i,
4. If α
i
violates (KKT1) or (KKT2),
5. Set violation = 1,
6. Find feasible α
t
i
such that Q(α
t
i
, α
−i
) > Q(α
i
, α
−i
) and set α
i
= α
t
i
.
7. If violation = 1 goto 2.
Figure 6.1: Blockcoordinate dual ascent.
the vector of dual variables α
i
for a single example i. The general form of blockcoordinate
ascent algorithm as shown in Fig. 6.1 is essentially coordinate ascent on blocks α
i
, main
taining the feasibility of the dual. When optimizing with respect to a single block i, the
objective function can be split into two terms:
Q(α) = Q(α
−i
) +Q(α
i
, α
−i
),
where α
−i
denotes all dual α
k
variables for k other than i. Only the second part of the
objective Q(α
i
, α
−i
) matters for optimizing with respect to α
i
. The algorithm starts with
a feasible dual solution α and improves the objective blockwise until all KKT condi
tions are satisﬁed. Checking the constraints requires computing w and ξ from α according
to Eq. (6.1).
As long as the local ascent step over α
i
is guaranteed to improve the objective when
KKT conditions are violated, the algorithm will converge to the global maximum in a ﬁnite
number of steps (within the precision). This allows us to focus on efﬁcient updates to a
single block of α
i
at a time.
Let α
t
i
(y) = α
i
(y) + λ(y). Note that
y
λ(y) = 0 and α
i
(y) + λ(y) ≥ 0 so that α
t
i
is
feasible. We can write the objective Q(α
−i
) +Q(α
t
i
, α
−i
) in terms of λ and α:
j,y
α
j
(y)
j
(y) +
y
λ(y)
i
(y) −
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
y
λ(y)∆f
i
(y) +
j,y
α
j
(y)∆f
j
(y)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
.
78 CHAPTER 6. M
3
N ALGORITHMS AND EXPERIMENTS
By dropping all terms that do not involve λ, and making the substitution
w = C
j,y
α
j
(y)∆f
j
(y), we get:
y
λ(y)
i
(y) −w
¯
_
y
λ(y)∆f
i
(y)
_
−
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
y
λ(y)∆f
i
(y)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
.
Since
y
λ(y) = 0,
y
λ(y)∆f
i
(y) =
y
λ(y)f
i
(y
(i)
) −
y
λ(y)f
i
(y) = −
y
λ(y)f
i
(y).
Below we also make the substitution v
i
(y) = w
¯
f
i
(y) +
i
(y) to get the optimization
problem for λ:
max
y
λ(y)v
i
(y) −
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
y
λ(y)f
i
(y)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
s.t.
y
λ(y) = 0; α
i
(y) + λ(y) ≥ 0, ∀y.
6.1.1 SMO
We do not need to solve the optimization subproblem above at each pass through the data.
All that is required is an ascent step, not a full optimization. Sequential Minimal Opti
mization (SMO) approach takes an ascent step that modiﬁes the least number of variables.
In our case, we have the simplex constraint, so we must change at least two variables in
order to respect the normalization constraint (by moving weight from one dual variable to
another). We address a strategy for selecting the two variables in the next section, but for
now assume we have picked λ(y
t
) and λ(y
tt
). Then we have δ = λ(y
t
) = −λ(y
tt
) in order
to sum to 1. The optimization problem becomes a single variable quadratic program in δ:
max [v
i
(y
t
) −v
i
(y
tt
)]δ −
1
2
C[[f
i
(y
t
) −f
i
(y
tt
)[[
2
δ
2
(6.3)
s.t. α
i
(y
t
) + δ ≥ 0; α
i
(y
tt
) −δ ≥ 0.
6.1. SOLVING THE M
3
N QP 79
−0.5 −0.4 −0.3 −0.2 −0.1 0 0.1 0.2 0.3 0.4 0.5
−2
−1.5
−1
−0.5
0
0.5
Figure 6.2: Representative examples of the SMO subproblem. Horizonal axis represents δ
with two vertical lines depicting the upper and lower bounds c and d. Vertical axis repre
sents the objective. Optimum either occurs at the maximum of the parabola if it is feasible
or the upper or lower bound otherwise.
With a = v
i
(y
t
) −v
i
(y
tt
), b = C[[f
i
(y
t
) −f
i
(y
tt
)[[
2
, c = −α
i
(y
t
), d = α
i
(y
tt
), we have:
max [aδ −
b
2
δ
2
] s.t. c ≤ δ ≤ d, (6.4)
where the optimum is achieved at the maximum of the parabola a/b if c ≤ a/b ≤ d or at
the boundary c or d (see Fig. 6.1.1). Hence the solution is given by simply clipping a/b:
δ
∗
= max(c, min(d, a/b)).
The key advantage of SMO is the simplicity of this update. Computing the coefﬁcients
involves dot products (or kernel evaluations) to compute w
¯
f
i
(y
t
) and w
¯
f
i
(y
tt
) as well as
(f
i
(y
t
) −f
i
(y
tt
))
¯
(f
i
(y
t
) −f
i
(y
tt
)).
6.1.2 Selecting SMO pairs
How do we actually select such a pair to guarantee that we make progress in optimizing
the objective? Note that at least one of the assignments y must violate (KKT1) or (KKT2),
80 CHAPTER 6. M
3
N ALGORITHMS AND EXPERIMENTS
1. Set violation = 0.
2. For each y,
3. KKT1: If α
i
(y) = 0 and v
i
(y) > v
i
(y) + ,
4. Set y
t
= y and violation = 1 and goto 7.
5. KKT2: If α
i
(y) > 0 and v
i
(y) < v
i
(y) −,
6. Set y
t
= y and violation = 2 and goto 7.
7. If violation > 0,
8. For each y ,= y
t
,
9. If violation = 1 and α
i
(y) > 0,
10. Set y
tt
= y and goto 13.
11. If violation = 2 and v
i
(y) > v
i
(y
t
),
12. Set y
tt
= y and goto 13.
13. Return y
t
and y
tt
.
Figure 6.3: SMO pair selection.
because otherwise α
i
is optimal with respect to the current α
−i
. The selection algorithm is
outlined in Fig. 6.3.
The ﬁrst variable in the pair, y
t
, corresponds to a violated condition, while the second
variable, y
tt
, is chosen to guarantee that solving Eq. (6.3) will result in improving the ob
jective. There are two cases, corresponding to violation of KKT1 and violation of KKT2.
Case KKT1. α
i
(y
t
) = 0 but v
i
(y
t
) > v
i
(y
t
) + . This is the case where i, y
t
is a not
support vector but should be. We would like to increase α
i
(y
t
), so we need α
i
(y
tt
) > 0
to borrow from. There will always be a such a y
tt
since
y
α
i
(y) = 1 and α
i
(y
t
) = 0.
Since v
i
(y
t
) > v
i
(y
t
) + , v
i
(y
t
) > v
i
(y
tt
) + , so the linear coefﬁcient in Eq. (6.4) is
a = v
i
(y
t
) −v
i
(y
tt
) > . Hence the unconstrained maximum is positive a/b > 0. Since the
upperbound d = α
i
(y
tt
) > 0, we have enough freedom to improve the objective.
Case KKT2. α
i
(y
t
) > 0 but v
i
(y
t
) < v
i
(y
t
) −. This is the case where i, y
t
is a support
vector but should not be. We would like to decrease α
i
(y
t
), so we need v
i
(y
tt
) > v
i
(y
t
)
so that a/b < 0. There will always be a such a y
tt
since v
i
(y
t
) < v
i
(y
t
) − . Since the
6.1. SOLVING THE M
3
N QP 81
lowerbound c = −α
i
(y
t
) < 0, again we have enough freedom to improve the objective.
Since at each iteration we are guaranteed to improve the objective if the KKT conditions
are violated and the objective is bounded, we can use the SMO in the blockcoordinate
ascent algorithm to converge in a ﬁnite number of steps. To the best of our knowledge,
there are no upper bounds on the speed of convergence of SMO, but experimental evidence
has shown it a very effective algorithm for SVMs [Platt, 1999]. Of course, we can improve
the speed of convergence by adding heuristics in the selection of the pair, as long as we
guarantee that improvement is possible when KKT conditions are violated.
6.1.3 Structured SMO
Clearly, we cannot perform the above SMO updates in the space of α directly for the
structured problems, since the number of α variables is exponential. The constraints on µ
variables are much more complicated, since each µ participates not only in nonnegativity
and normalization constraints, but also cliqueagreement constraints. We cannot limit our
ascent steps to changing only two µ variables at a time, because in order to make a change
in one clique and stay feasible, we need to modify variables in overlapping cliques. For
tunately, we can perform SMO updates on α variables implicitly in terms of the marginal
dual variables µ.
The diagram in Fig. 6.1.3 shows the abstract outline of the algorithm. The key steps in
the SMO algorithm are checking for violations of the KKT conditions, selecting the pair y
t
and y
tt
, computing the corresponding coefﬁcients a, b, c, d and updating the dual. We will
show how to do these operations by doing all the hard work in terms of the polynomially
many marginal µ
i
variables and auxiliary “maxmarginals” variables.
Structured KKT conditions
As before, we deﬁne v
i
(y) = w
¯
f
i
(y) +
i
(y). The KKT conditions are, for all y:
α
i
(y) = 0 ⇒ v
i
(y) ≤ v
i
(y); α
i
(y) > 0 ⇒ v
i
(y) ≥ v
i
(y). (6.5)
82 CHAPTER 6. M
3
N ALGORITHMS AND EXPERIMENTS
select
& lift
SMO
update
project
Figure 6.4: Structured SMO diagram. We use marginals µ to select an appropriate pair of
instantiations y
t
and y
tt
and reconstruct their α values. We then perform the simple SMO
update and project the result back onto the marginals.
Of course, we cannot check these explicitly. Instead, we deﬁne maxmarginals for each
clique in the junction tree c ∈ T
(i)
and its values y
c
, as:
´ v
i,c
(y
c
) = max
y∼y
c
[w
¯
f
i
(y) +
i
(y)], ´ α
i,c
(y
c
) = max
y∼y
c
α
i
(y).
We also deﬁne ´ v
i,c
(y
c
) = max
y
c
,=y
c
´ v
i,c
(y
t
c
) = max
y,∼y
c
[w
¯
f
i
(y) +
i
(y)]. Note that we
do not explicitly represent α
i
(y), but we can reconstruct the maximumentropy one from
the marginals µ
i
by using Eq. (5.13). Both ´ v
i,c
(y
c
) and ´ α
i,c
(y
c
) can be computed by using
the Viterbi algorithm (one pass propagation towards the root and one outwards from the
root [Cowell et al., 1999]). We can now express the KKT conditions in terms of the max
marginals for each clique c ∈ T
(i)
and its values y
c
:
´ α
i,c
(y
c
) = 0 ⇒ ´ v
i,c
(y
c
) ≤ ´ v
i,c
(y
c
); ´ α
i,c
(y
c
) > 0 ⇒ ´ v
i,c
(y
c
) ≥ ´ v
i,c
(y
c
). (6.6)
Theorem 6.1.1 The KKT conditions in Eq. (6.5) and Eq. (6.6) are equivalent.
Proof:
Eq. (6.5) ⇒Eq. (6.6). Assume Eq. (6.5). Suppose, we have a violation of KKT1: for
some c, y
c
, ´ α
i,c
(y
c
) = 0, but ´ v
i,c
(y
c
) > ´ v
i,c
(y
c
). Since ´ α
i,c
(y
c
) = max
y∼y
c
α
i
(y) = 0,
6.1. SOLVING THE M
3
N QP 83
then α
i
(y) = 0, ∀y ∼ y
c
. Hence, by Eq. (6.5), v
i
(y) ≤ v
i
(y), ∀y ∼ y
c
. But ´ v
i,c
(y
c
) >
´ v
i,c
(y
c
) implies the opposite: there exists y ∼ y
c
such that v
i
(y) > ´ v
i,c
(y
c
), which also
implies v
i
(y) > v
i
(y), a contradiction.
Now suppose we have a violation of KKT2: for some i, y
c
, ´ α
i,c
(y
c
) > 0, but ´ v
i,c
(y
c
) <
´ v
i,c
(y
c
). Then v
i
(y) < v
i
(y), ∀y ∼ y
c
. But ´ α
i,c
(y
c
) > 0 implies there exists y ∼ y
c
such
that α
i
(y) > 0. For that y, by Eq. (6.5), v
i
(y) ≥ v
i
(y), a contradiction.
Eq. (6.6) ⇒ Eq. (6.5). Assume Eq. (6.6). Suppose we have a violation of KKT1:
for some y, α
i
(y) = 0, but v
i
(y) > v
i
(y). This means that y is the optimum of v
i
(),
hence ´ v
i,c
(y
c
) = v
i
(y) > v
i
(y) > ´ v
i,c
(y
c
), ∀c ∈ T
(i)
, y
c
∼ y. But by Eq. (6.6), if
´ v
i,c
(y
c
) > ´ v
i,c
(y
c
), then we cannot have ´ α
i,c
(y
c
) = 0. Hence all the yconsistent α
i
max
marginals are positive ´ α
i,c
(y
c
) > 0, ∀c ∈ T
(i)
, and it follows that all the yconsistent
marginals µ
i
are positive as well µ
i,c
(y
c
) > 0, ∀c ∈ T
(i)
(since sum upperbounds max).
But α
i
(y) =
c∈T
(i)
µ
i,c
(y
c
)
c∈S
(i)
µ
i,s
(y
s
)
, so if all the yconsistent marginals are positive, then α
i
(y) > 0,
a contradiction.
Now suppose we have a violation of KKT2: for some y, α
i
(y) > 0, but v
i
(y) <
v
i
(y). Since α
i
(y) > 0, we know that all the yconsistent α
i
maxmarginals are positive
´ α
i,c
(y
c
) > 0, ∀c ∈ T
(i)
. By Eq. (6.6), ´ v
i,c
(y
c
) ≥ ´ v
i,c
(y
c
), ∀c ∈ T
(i)
. Note that trivially
max
y
v
i
(y
t
) = max(´ v
i,c
(y
t
c
), ´ v
i,c
(y
t
c
)) for any clique c and clique assignment y
t
c
. Since
´ v
i,c
(y
c
) ≥ ´ v
i,c
(y
c
), ∀c ∈ T
(i)
, then max
y
v
i
(y
t
) = ´ v
i,c
(y
c
), , ∀c ∈ T
(i)
. That is, ´ v
i,c
(y
c
)
is the optimal value. We will show that v
i
(y) = ´ v
i,c
(y
c
), a contradiction. To show that this,
we consider any two adjacent nodes in the tree T
(i)
, cliques a and b, with a separator s, and
show that ´ v
i,a∪b
(y
a∪b
) = ´ v
i,a
(y
a
) = ´ v
i,b
(y
b
). By chaining this equality from the root of the
tree to all the leaves, we get v
i
(y) = ´ v
i,c
(y
c
) for any c.
We need to introduce some more notation to deal with the two parts of the tree induced
by cutting the edge between a and b. Let ¦A, B¦ be a partition of the nodes T
(i)
(cliques
of (
(i)
) resulting from removing the edge between a and b such that a ∈ A and b ∈ B.
We denote the two subsets of an assignment y as y
A
and y
B
(with overlap at y
s
). The
value of an assignment v
i
(y) can be decomposed into two parts: v
i
(y) = v
i,A
(y
A
) +
v
i,B
(y
B
), where v
i,A
(y
A
) and v
i,B
(y
B
) only count the contributions of their constituent
cliques. Take any maximizer, y
(a)
∼ y
a
with v
i
(y
(a)
) = ´ v
i,a
(y
a
) ≥ ´ v
i,a
(y
a
) and any
maximizer y
(b)
∼ y
b
with v
i
(y
(b)
) = ´ v
i,b
(y
b
) ≥ ´ v
i,b
(y
b
), which by deﬁnition agree with y
84 CHAPTER 6. M
3
N ALGORITHMS AND EXPERIMENTS
on the intersection s. We decompose the two associated values into the corresponding parts:
v
i
(y
(a)
) = v
i
(y
(a)
A
)+v
i
(y
(a)
B
) and v
i
(y
(b)
) = v
i
(y
(b)
A
)+v
i
(y
(b)
B
). We create a newassignment
that combines the best of the two: y
(s)
= y
(b)
A
∪ y
(a)
B
. Note that v
i
(y
(s)
) = v
i
(y
(b)
A
) +
v
i
(y
(a)
B
) = ´ v
i,s
(y
s
), since we essentially ﬁxed the intersection s and maximized over the
rest of the variables in A and B separately. Now ´ v
i,a
(y
a
) = ´ v
i,b
(y
b
) ≥ ´ v
i,s
(y
s
) since they
are optimal as we said above. Hence we have v
i
(y
(a)
A
) + v
i
(y
(a)
B
) = v
i
(y
(b)
A
) + v
i
(y
(b)
B
) ≥
v
i
(y
(b)
A
) + v
i
(y
(a)
B
) which implies that v
i
(y
(a)
A
) ≥ v
i
(y
(b)
A
) and v
i
(y
(b)
B
) ≥ v
i
(y
(a)
B
). Now we
create another assignment that clamps the value of both a and b: y
(a∪b)
= y
(a)
A
∪ y
(b)
B
. The
value of this assignment is optimal v
i
(y
(a∪b)
) = v
i
(y
(a)
A
) + v
i
(y
(b)
B
) = v
i
(y
(a)
) = v
i
(y
(b)
).
Structured SMO pair selection and update
As in multiclass problems, we will select the ﬁrst variable in the pair, y
t
, corresponding to
a violated condition, while the second variable, y
tt
, to guarantee that solving Eq. (6.3) will
result in improving the objective. Having selected y
t
and y
tt
, the coefﬁcients for the one
variable QP in Eq. (6.4) are a = v
i
(y
t
)−v
i
(y
tt
), b = C[[f
i
(y
t
)−f
i
(y
tt
)[[
2
, c = −α
i
(y
t
), d =
α
i
(y
tt
). As before, we enforce approximate KKT conditions in the algorithm in Fig. 6.5.
We have two cases, corresponding to violation of KKT1 and violation of KKT2.
Case KKT1. ´ α
i,c
(y
t
c
) = 0 but ´ v
i,c
(y
t
c
) > ´ v
i,c
(y
t
c
)+. We have set y
t
= arg max
y∼y
c
v
i
(y),
so v
i
(y
t
) = ´ v
i,c
(y
t
c
) > ´ v
i,c
(y
t
c
) + > v
i
(y
t
) + and α
i
(y
t
) = 0. This is the case where
i, y
t
is a not support vector but should be. We would like to increase α
i
(y
t
), so we need
α
i
(y
tt
) > 0 to borrow from. There will always be a such a y
tt
(with y
tt
c
,= y
t
c
) since
y
α
i
(y) = 1 and α
i
(y
t
) = 0. We can ﬁnd one by choosing y
c
for which ´ α
i,c
(y
c
) > 0,
which guarantees that for y
tt
c
= arg max
y∼y
c
α
i
(y), α
i
(y
tt
) > 0. Since v
i
(y
t
) ≥ v
i
(y
t
) +,
v
i
(y
t
) ≥ v
i
(y
tt
) +, so the linear coefﬁcient in Eq. (6.4) is a = v
i
(y
t
) −v
i
(y
tt
) > . Hence
the unconstrained maximum is positive a/b > 0. Since the upperbound d = α
i
(y
tt
) > 0,
we have enough freedom to improve the objective.
Case KKT2. ´ α
i,c
(y
t
c
) > 0 but ´ v
i,c
(y
t
c
) < ´ v
i,c
(y
t
c
)−. We have set y
t
= arg max
y∼y
c
α
i
(y),
so α
i
(y
t
) = ´ α
i,c
(y
t
c
) > 0 and v
i
(y
t
) < ´ v
i,c
(y
t
c
) < ´ v
i,c
(y
t
c
) − < v
i
(y
t
) − . This is the
case where i, y
t
is a support vector but should not be. We would like to decrease α
i
(y
t
),
so we need v
i
(y
tt
) > v
i
(y
t
) so that a/b < 0. There will always be a such a y
tt
since
6.2. EXPERIMENTS 85
1. Set violation = 0.
2. For each c ∈ T
(i)
, y
c
3. KKT1: If ´ α
i,c
(y
c
) = 0, and ´ v
i,c
(y
c
) > ´ v
i,c
(y
c
) + ,
4. Set y
t
c
= y
c
, y
t
= arg max
y∼y
c
v
i
(y) and violation = 1 and goto 7.
5. KKT2: If ´ α
i,c
(y
c
) > 0, and ´ v
i,c
(y
c
) < ´ v
i,c
(y
c
) −,
6. Set y
t
c
= y
c
, y
t
= arg max
y∼y
c
α
i
(y) and violation = 2 and goto 7.
7. If violation > 0,
8. For each y
c
,= y
t
c
,
9. If violation = 1 and ´ α
i,c
(y
c
) > 0,
10. Set y
tt
c
= arg max
y∼y
c
α
i
(y) and goto 13.
11. If violation = 2 and ´ v
i,c
(y
c
) > ´ v
i,c
(y
t
c
),
12. Set y
tt
= arg max
y∼y
c
v
i
(y) and goto 13.
13. Return y
t
and y
tt
.
Figure 6.5: Structured SMO pair selection.
v
i
(y
t
) < v
i
(y
t
) − . We can ﬁnd one by choosing y
c
for which ´ v
i,c
(y
c
) > ´ v
i,c
(y
c
) − ,
which guarantees that for y
tt
c
= arg max
y∼y
c
v
i
(y), v
i
(y
tt
) > v
i
(y
t
) − , Since the lower
bound c = −α
i
(y
t
) < 0, again we have enough freedom to improve the objective.
Having computed new values α
t
i
(y
t
) = α
i
(y
t
) + δ and α
t
i
(y
tt
) = α
i
(y
t
) − δ, we need
to project this change onto the marginal dual variables µ
i
. The only marginal affected are
the ones consistent with y
t
and/or y
tt
, and the change is very simple:
µ
t
i,c
(y
c
) = µ
i,c
(y
c
) + δ1I(y
c
∼ y
t
) −δ1I(y
c
∼ y
tt
).
6.2 Experiments
We selected a subset of ∼ 6100 handwritten words, with average length of ∼ 8 characters,
from 150 human subjects, from the data set collected by Kassel [1995]. Each word was
divided into characters, each character was rasterized into an image of 16 by 8 binary
86 CHAPTER 6. M
3
N ALGORITHMS AND EXPERIMENTS
0
0.05
0.1
0.15
0.2
0.25
0.3
0.35
LogReg CRF mSVM M^3N
T
e
s
t
e
r
r
o
r
(
a
v
e
r
a
g
e
p
e
r

c
h
a
r
a
c
t
e
r
)
linear quadratic cubic
(a) (b)
Figure 6.6: (a) 3 example words from the OCR data set; (b) OCR: Average per
character test error for logistic regression, CRFs, multiclass SVMs, and M
3
Ns, using linear,
quadratic, and cubic kernels.
pixels. (See Fig. 6.6(a).) In our framework, the image for each word corresponds to x, a
label of an individual character to ¸
j
, and a labeling for a complete word to ¸. Each label
¸
j
takes values from one of 26 classes ¦a, . . . , z¦.
The data set is divided into 10 folds of ∼ 600 training and ∼ 5500 testing examples.
The accuracy results, summarized in Fig. 6.6(b), are averages over the 10 folds. We im
plemented a selection of stateoftheart classiﬁcation algorithms: independent label ap
proaches, which do not consider the correlation between neighboring characters — lo
gistic regression, multiclass SVMs as described in Eq. (2.9), and oneagainstall SVMs
(whose performance was slightly lower than multiclass SVMs); and sequence approaches
— CRFs, and our proposed M
3
networks. Logistic regression and CRFs are both trained by
maximizing the conditional likelihood of the labels given the features, using a zeromean
diagonal Gaussian prior over the parameters, with a standard deviation between 0.1 and
1. The other methods are trained by margin maximization. Our features for each label
¸
j
are the corresponding image of ith character. For the sequence approaches (CRFs and
M
3
), we used an indicator basis function to represent the correlation between ¸
j
and ¸
i+1
.
6.3. RELATED WORK 87
For marginbased methods (SVMs and M
3
), we were able to use kernels (both quadratic
and cubic were evaluated) to increase the dimensionality of the feature space. We used
the structured SMO algorithm with about 3040 iterations through the data. Using these
highdimensional feature spaces in CRFs is not feasible because of the enormous number
of parameters.
Fig. 6.6(b) shows two types of gains in accuracy: First, by using kernels, marginbased
methods achieve a very signiﬁcant gain over the respective likelihood maximizing methods.
Second, by using sequences, we obtain another signiﬁcant gain in accuracy. Interestingly,
the error rate of our method using linear features is 16% lower than that of CRFs, and
about the same as multiclass SVMs with cubic kernels. Once we use cubic kernels our
error rate is 45% lower than CRFs and about 33% lower than the best previous approach.
For comparison, the previously published results, although using a different setup (e.g., a
larger training set), are about comparable to those of multiclass SVMs.
6.3 Related work
The kerneladatron [Friess et al., 1998] and votedperceptron algorithms [Freund &Schapire,
1998] for largemargin classiﬁers have a similar online optimization scheme. Collins
[2001] have applied votedperceptron to structured problems in natural language. Although
headtohead comparisons have not been performed, it seems that, empirically, less passes
(about 3040) are needed for our algorithm than in the perceptron literature.
Recently, the Exponentiated Gradient [Kivinen & Warmuth, 1997] algorithm has been
adopted to solve our structured QP for maxmargin estimation [Bartlett et al., 2004]. Al
though the EG algorithm has attractive convergence properties, it has yet to be shown to
learn faster than Structured SMO, particularly in the early iterations through the dataset.
6.4 Conclusion
In this chapter, we address the large (though polynomial) size of our quadratic program
using an effective optimization procedure inspired by SMO. In our experiments with the
OCRtask, our sequence model signiﬁcantly outperforms other approaches by incorporating
88 CHAPTER 6. M
3
N ALGORITHMS AND EXPERIMENTS
highdimensional decision boundaries of polynomial kernels over character images while
capturing correlations between consecutive characters. Overall, we believe that M
3
net
works will signiﬁcantly further the applicability of high accuracy marginbased methods to
realworld structured data. In the next two chapters, we apply this framework to important
classes of Markov networks for spatial and relational data.
Chapter 7
Associative Markov networks
In the previous chapter, we considered applications of sequencestructured Markov net
works, which allow very efﬁcient inference and learning. The chief computational bottle
neck in applying Markov networks for other largescale prediction problems is inference,
which is NPhard in general networks suitable in a broad range of practical Markov network
structures, including gridtopology networks [Besag, 1986].
One can address the tractability issue by limiting the structure of the underlying net
work. In some cases, such as the quadtree model used for image segmentation [Bouman &
Shapiro, 1994], a tractable structure is determined in advance. In other cases (e.g., [Bach &
Jordan, 2001]), the network structure is learned, subject to the constraint that inference on
these networks is tractable. In many cases, however, the topology of the Markov network
does not allow tractable inference. For example, in hypertext, the network structure can
mirror the hyperlink graph, which is usually highly interconnected, leading to computa
tionally intractable networks.
In this chapter, we show that optimal learning is feasible for an important subclass of
Markov networks — networks with attractive potentials. This subclass, called associa
tive Markov networks (AMNs), contains networks of discrete variables with K labels and
arbitrarysize clique potentials with K parameters that favor the same labels for all vari
ables in the clique. Such positive interactions capture the “guilt by association” pattern of
reasoning present in many domains, in which connected (“associated”) variables tend to
have the same label. AMNs are a natural ﬁt object recognition and segmentation, webpage
89
90 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS
classiﬁcation, and many other applications.
In the maxmargin estimation framework, the inference subtask is one of ﬁnding the
best joint (MAP) assignment to all of the variables in a Markov network. By contrast, other
learning tasks (e.g., maximizing the conditional likelihood of the target labels given the
features) require that we compute the posterior probabilities of different label assignments,
rather than just the MAP.
The MAP problem can naturally be expressed as an integer programming problem. We
use a linear program relaxation of this integer program in the minmax formulation. We
show that, for associative Markov networks of over binary variables (K = 2), this linear
program provides exact answers. To our knowledge, our method is the ﬁrst to allowtraining
Markov networks of arbitrary connectivity and topology. For the nonbinary case (K > 2),
the approximate linear programis not guaranteed to be optimal but we can bound its relative
error. Our empirical results suggest that the solutions of the resulting approximate max
margin formulation work well in practice.
We present an AMNbased method for object segmentation of complex from 3D range
data. By constraining the class of Markov networks to AMNs, our models can be learned
efﬁciently and at runtime, scale up to tens of millions of nodes and edges. The proposed
learning formulation effectively and directly learns to exploit a large set of complex surface
and volumetric features, while balancing the spatial coherence modeled by the AMN.
7.1 Associative networks
Associative interactions arise naturally in the context of image processing, where nearby
pixels are likely to have the same label [Besag, 1986; Boykov et al., 1999b]. In this setting,
a common approach is to use a generalized Potts model [Potts, 1952], which penalizes
assignments that do not have the same label across the edge: φ
ij
(k, l) = λ
ij
, ∀k ,= l and
φ
ij
(k, k) = 1, where λ
ij
≤ 1.
For binaryvalued Potts models, Greig et al. [1989] show that the MAP problem can be
formulated as a mincut in an appropriately constructed graph. Thus, the MAP problem can
be solved exactly for this class of models in polynomial time. For L > 2, the MAP problem
7.2. LP INFERENCE 91
is NPhard, but a procedure based on a relaxed linear program guarantees a factor 2 approx
imation of the optimal solution [Boykov et al., 1999b; Kleinberg & Tardos, 1999]. Our
associative potentials extend the Potts model in several ways. Importantly, AMNs allow
different labels to have different attraction strength: φ
ij
(k, k) = λ
ij
(k), where λ
ij
(k) ≥ 1,
and φ
ij
(k, l) = 1, ∀k ,= l. This additional ﬂexibility is important in many domains, as
different labels can have very diverse afﬁnities. For example, foreground pixels tend to
have locally coherent values while background is much more varied.
In a second important extension, AMNs admit nonpairwise interactions between vari
ables, with potentials over cliques involving m variables φ(µ
i1
, . . . , µ
im
). In this case, the
clique potentials are constrained to have the same type of structure as the edge potentials:
There are K parameters φ
c
(k, . . . , k) = λ
c
(k) ≥ 1 and the rest of the entries are set to 1.
In particular, using this additional expressive power, AMNs allow us to encode the pattern
of (soft) transitivity present in many domains. For example, consider the problem of pre
dicting whether two proteins interact [Vazquez et al., 2003]; this probability may increase
if they both interact with another protein. This type of transitivity could be modeled by a
ternary clique that has high λ for the assignment with all interactions present.
More formally, we deﬁne associative functions and potentials as follows.
Deﬁnition 7.1.1 A function g : ¸ →IR is associative for a graph ( over Kary variables if
it can be written as:
g(y) =
v∈1
K
k=1
g
v
(k)1I(y
v
= k) +
c∈(\1
K
k=1
g
c
(k)1I(y
c
= k, . . . , k); g
c
(k) ≥ 0, ∀c ∈ (¸1,
where 1 are the nodes and ( are the cliques of the graph (. A set of potentials φ(y) is
associative if φ(y) = e
g(y)
and g(y) is associative.
7.2 LP Inference
We can write an integer linear program for the problem of ﬁnding the maximum of an
associative function g(y), where we have a “marginal” variable µ
v
(k) for each node v ∈ 1
and each label k, which indicates whether node v has value k, and µ
c
(k) for each clique c
92 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS
(containing more than one variable) and label k, which represents the event that all nodes
in the clique c have label k:
max
v∈1
K
k=1
µ
v
(k)g
v
(k) +
c∈(\1
K
k=1
µ
c
(k)g
c
(k) (7.1)
s.t. µ
c
(k) ∈ ¦0, 1¦, ∀c ∈ (, k;
K
k=1
µ
v
(k) = 1, ∀v ∈ 1;
µ
c
(k) ≤ µ
v
(k), ∀c ∈ ( ¸ 1, v ∈ c, k.
Note that we substitute the constraint µ
c
(k) =
_
v∈c
µ
v
(k) by linear inequality con
straints µ
c
(k) ≤ µ
v
(k). This works because the coefﬁcient g
c
(k) is nonnegative and we
are maximizing the objective function. Hence at the optimum, µ
c
(k) = min
v
µ
v
(k) , which
is equivalent to µ
c
(k) =
_
v∈c
µ
v
(k), when µ
v
(k) are binary.
It can be shown that in the binary case, the linear relaxation of Eq. (7.1), (where the
constraints µ
c
(k) ∈ ¦0, 1¦ are replaced by µ
c
(k) ≥ 0), is guaranteed to produce an integer
solution when a unique solution exists.
Theorem 7.2.1 If K = 2, for any associative function g, the linear relaxation of Eq. (7.1)
has an integral optimal solution.
See Appendix A.2.1 for the proof. This result states that the MAP problem in binary AMNs
is tractable, regardless of network topology or clique size. In the nonbinary case (L > 2),
these LPs can produce fractional solutions and we use a rounding procedure to get an
integral solution.
Theorem 7.2.2 If K > 2, for any associative function g, the linear relaxation of Eq. (7.1)
has a solution that is larger than the solution of the integer program by at most the number
of variables in the largest clique.
In the appendix, we also show that the approximation ratio of the rounding procedure is the
inverse of the size of the largest clique (e.g.,
1
2
for pairwise networks). Although artiﬁcial
examples with fractional solutions can be easily constructed by using symmetry, it seems
that in real data such symmetries are often broken. In fact, in all our experiments with
L > 2 on real data, we never encountered fractional solutions.
7.3. MINCUT INFERENCE 93
7.3 Mincut inference
We can also use efﬁcient mincut algorithms to perform exact inference on the learned
models for K = 2 and approximate inference for K > 2. For simplicity, we focus on the
pairwise AMN case. We ﬁrst consider the case of binary AMNs, and later show how to use
the local search algorithm developed by Boykov et al. [1999a] to perform (approximate)
inference in the general multiclass case. For pairwise, binary AMNs, the objective of the
integer program in Eq. (7.1) is:
max
v∈1
[µ
v
(1)g
v
(1) + µ
v
(2)g
v
(2)] +
uv∈c
[µ
uv
(1)g
uv
(1) + µ
uv
(2)g
uv
(2)]. (7.2)
7.3.1 Graph construction
We construct a graph in which the mincut will correspond to the optimal MAP labeling
for the above objective. First, we recast the objective as minimization by simply reversing
the signs on the value of each θ.
min −
v∈1
[µ
v
(1)g
v
(1) + µ
v
(2)g
v
(2)] −
uv∈c
[µ
uv
(1)g
uv
(1) + µ
uv
(2)g
uv
(2)]. (7.3)
The graph will consist of a vertex for each node in the AMN, along with the 1 and 2
terminals. In the ﬁnal (1
1
, 1
2
) cut, the 1
1
set will correspond to label 1, and the 1
2
set will
correspond to label 2. We will show how to deal with the node terms (those depending only
on a single variable) and the edge terms (those depending on a pair of variables), and then
how to combine the two.
Node terms
Consider a node term −µ
v
(1)g
v
(1) −µ
v
(2)g
v
(2). Such a term corresponds to the node po
tential contribution to our objective function for node v. For each node term corresponding
to node v we add a vertex v to the mincut graph. We then look at ∆
v
= g
v
(1) − g
v
(2),
and create an edge of weight [∆
v
[ from v to either 1 or 2, depending on the sign of ∆
v
.
The reason for that is that the ﬁnal mincut graph must consist of only positive weights. An
94 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS
1 2 v
1 2 v
1
2
u v
Figure 7.1: Mincut graph construction of node (left) and edge (right) terms.
example is presented in Fig. 7.3.1.
From Fig. 7.3.1, we see that if the AMN consisted of only node potentials, the graph
construction above would add an edge from each node to its more likely label. Thus if we
run mincut, we would simply get a cut with cost 0, since for each introduced vertex we
have only one edge of positive weight to either 1 or 2, and we would always choose not to
cut any edges.
Edge Terms
Now consider an edge term of the form −µ
uv
(1)g
uv
(1) − µ
uv
(2)g
uv
(2). To construct a
mincut graph for the edge term we will introduce two vertices u and v. We will connect
vertex u to 1 with an edge of weight g
uv
(1), connect v to 2 with an edge of weight g
uv
(2)
and connect u to v with an edge of weight g
uv
(1) + g
uv
(2). Fig. 7.3.1 shows an example.
Observe what happens when both nodes are on the 1
2
side of the cut: the value of the
mincut is g
uv
(1), which must be less than g
uv
(2) or the mincut would have placed them
both on the 1 side. When looking at edge terms in isolation, a cut that places each node
in different sets will not occur, but when we combine the graphs for node terms and edge
terms, such cuts will be possible.
We can take the individual graphs we created for node and edge terms and merge them
7.3. MINCUT INFERENCE 95
by adding edge weights together (and treating missing edges as edges with weight 0). It
can be shown that the resulting graph will represent the same objective (in the sense that
running mincut on it will optimize the same objective) as the sum of the objectives of each
graph. Since our MAPinference objective is simply a sumof node and edge terms, merging
the node and edge term graphs will result in a graph in which mincut will correspond to
the MAP labeling.
7.3.2 Multiclass case
The graph construction above ﬁnds the best MAP labeling for the binary case, but in prac
tice we would often like to handle multiple classes in AMNs. One of the most effective
algorithms for minimizing energy functions like ours is the αexpansion algorithm pro
posed by Boykov et al. [1999a]. The algorithm performs a series of “expansion” moves
each of which involves optimization over two labels, and it can be shown that it converges
to within a factor of 2 of the global minimum.
Expansion Algorithm
Consider a current labeling µ and a particular label k ∈ 1, . . . , K. Another labeling µ
t
is
called an “αexpansion” move (following Boykov et al. [1999a]) from µ if µ
t
v
,= k implies
µ
t
v
= µ
v
(where µ
v
is the label of the node v in the AMN.) In other words, a kexpansion
from a current labeling allows each label to either stay the same, or change to k.
The αexpansion algorithm cycles through all labels k in either a ﬁxed or random order,
and ﬁnds the new labeling whose objective has the lowest value. It terminates when there
is no αexpansion move for any label k that has a lower objective than the current labeling
(Fig. 7.2).
The key part of the algorithm is computing the best αexpansion labeling for a ﬁxed
k and a ﬁxed current labeling µ. The mincut construction from earlier allows us to do
exactly that since an αexpansion move essentially minimizes a MAPobjective over two
labels: it either allows a node to retain its current label, or switch to the label α. In this
new binary problem we will let label 1 represent a node keeping its current label and label
2 will denote a node taking on the new label k. In order to construct the right coefﬁcients
96 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS
1. Begin with arbitrary labeling µ
2. Set success := 0
3. For each label k ∈ ¦1, . . . K¦
3.1 Compute ˆ µ = arg min −g(µ
t
) among µ
t
within one αexpansion of µ.
3.2 If E(ˆ µ) < E(µ), set µ := ˆ µ and success := 1
4. If success = 1 goto 2.
5. Return µ
Figure 7.2: αexpansion algorithm
for the new binary objective we need to consider several factors. Below, let θ
tk
i
and θ
tk,k
ij
denote the node and edge coefﬁcients associated with the new binary objective:
◦ Node Potentials For each node i in the current labeling whose current label is not α,
we let θ
t0
i
= θ
y
i
i
, and θ
t1
i
= θ
α
i
, where y
i
denotes the current label of node i, and θ
y
i
denotes the coefﬁcient in the multiclass AMN MAP objective. Note that we ignore
nodes with label α altogether since an αexpansion move cannot change their label.
◦ Edge Potentials For each edge (i, j) ∈ E whose nodes have labels different from α,
we add a new edge potential, with weights θ
t1
ij
= θ
α,α
ij
. If the two nodes of the edge
currently have the same label, we set θ
t0
ij
= θ
y
i
,y
j
ij
, and if the two nodes currently have
different labels we let θ
t0
ij
= 0. For each edge (i, j) ∈ E in which exactly one of the
nodes has label α in the current labeling, we add θ
α,α
ij
, to the node potential θ
t1
i
of the
node whose label is different from α.
After we have constructed the new binary MAP objective as above, we can apply the
mincut construction from before to get the optimal labeling within one αexpansion from
the current one. Veksler [1999] shows that the αexpansion algorithm converges in O(N)
iterations where N is the number of nodes. As noted in Boykov et al. [1999a] and as we
have observed in our experiments, the algorithm terminates only after a few iterations with
most of the improvement occurring in the ﬁrst 23 expansion moves.
7.4. MAXMARGIN ESTIMATION 97
7.4 Maxmargin estimation
The potentials of the AMN are once again loglinear combinations of basis functions. We
will need the following assumption to ensure that w
¯
f (x, y) is associative:
Assumption 7.4.1 Basis functions f are componentwise associative for ((x) for any (x, y).
Recall that this implies that for cliques larger than one, all basis functions evaluate to 0
for assignments where the values of the nodes are not equal and are nonnegative for the
assignments where the values of the nodes are equal. To ensure that w
¯
f (x, y) is associa
tive, it is useful to separate the basis functions with support only on nodes from those with
support on larger cliques.
Deﬁnition 7.4.2 Let
˙
f be the subset of basis functions f with support only on singleton
cliques:
˙
f = ¦f ∈ f : ∀ x ∈ A, y ∈ ¸, c ∈ ((((x)), [c[ > 1, f
c
(x
c
, y
c
) = 0¦.
Let
¨
f = f ¸
˙
f be the rest of the basis functions. Let ¦ ˙ w, ¨ w¦ = w be the corresponding
subsets of parameters.
It is easy to verify that any nonnegative combination of associative functions is asso
ciative, and any combination of basis functions with support only on singleton cliques is
also associative, so we have:
Lemma 7.4.3 w
¯
f (x, y) is associative for ((x) for any (x, y) whenever Assumption 7.4.1
holds and ¨ w ≥ 0.
We must make similar associative assumption on the loss function in order to guarantee
that the LP inference can handle it.
Assumption 7.4.4 The loss function (x
(i)
, y
(i)
, y) is associative for (
(i)
for all i.
In practice, this restriction is fairly mild, and the Hamming loss, which we use in general
ization bounds and experiments, is associative.
98 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS
Using the above Assumptions 7.4.1 and 7.4.4 and some algebra (see Appendix A.2.3
for derivation), we have the following maxmargin QP for AMNs:
min
1
2
[[w[[
2
+ C
i,v∈1
(i)
ξ
i,v
(7.4)
s.t. w
¯
∆f
i,v
(k) −
c⊃v
m
i,c,v
(k) ≥
i,v
(k) −ξ
i,v
, ∀i, v ∈ 1
(i)
, k;
¨ w
¯
∆
¨
f
i,c
(k) +
v∈c
m
i,c,v
(k) ≥
i,c
(k), ∀i, c ∈ (
(i)
¸ 1
(i)
, k;
m
i,c,v
(k) ≥ −¨ w
¯
¨
f
i,c
(y
(i)
c
)/[c[, ∀i, c ∈ (
(i)
¸ 1
(i)
, v ∈ c, k;
¨ w ≥ 0;
where f
i,c
(k) = f
i,c
(k, . . . , k) and
i,c
(k) =
i,c
(k, . . . , k).
While this primal is more complex than the regular M
3
N factored primal in Eq. (5.4),
the basic structure of the ﬁrst two sets of constraints remains the same: we have local
margin requirements and “credit” passed around through messages m
i,c,v
(k). The extra
constraints are due to the associativity constraints on the resulting model.
The dual of Eq. (7.4) (see derivation in Sec. A.2.3) is given by:
max
i,c∈(
(i)
, k
µ
i,c
(k)
i,c
(k) −
C
2
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,v∈1
(i)
, k
µ
i,v
(k)∆
˙
f
i,v
(k)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
−
C
2
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¨ ν +
i,c∈(
(i)
, k
µ
i,c
(k)∆
¨
f
i,c
(k)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
s.t. µ
i,c
(k) ≥ 0, ∀i, ∀c ∈ (
(i)
, k;
K
k=1
µ
i,v
(k) = 1, ∀i, ∀v ∈ 1
(i)
;
µ
i,c
(k) ≤ µ
i,v
(k), ∀i, ∀c ∈ (
(i)
¸ 1
(i)
, v ∈ c, k;
¨ ν ≥ 0.
In the dual, there are marginals µ for each node and clique, for each value k, similar
to Eq. (5.12). However, the constraints are different, and not surprisingly, are essentially
the constraints from the inference LP relaxation in Eq. (7.1).
7.5. EXPERIMENTS 99
The dual and primal solutions are related by
˙ w =
i,v∈1
(i)
, k
µ
i,v
(k)∆
˙
f
i,v
(k); ¨ w = ¨ ν +
i,c∈(
(i)
, k
µ
i,c
(k)∆
¨
f
i,c
(k).
The ¨ ν variables simply ensure that ¨ ware positive (if any component
i,c∈(
(i)
, k
µ
i,c
(k)∆
¨
f
i,c
(k)
is negative, maximizing the objective will force the corresponding component of ¨ ν to cancel
it out). Note that the objective can be written in terms of dot products of node basis func
tions ∆
˙
f
i,v
(k)
¯
∆
˙
f
j,¯ v
(
¯
k), so they can be kernelized. Unfortunately, the edge basis functions
cannot be kernelized because of the nonnegativity constraint.
For K = 2, the LP inference is exact, so that Eq. (7.4) learns exact maxmargin weights
for Markov networks of arbitrary topology. For K > 2, the linear relaxation leads to a
strengthening of the constraints on w by potentially adding constraints corresponding to
fractional assignments as in the case of untriangualated networks. Thus, the optimal choice
w, ξ for the original QP may no longer be feasible, leading to a different choice of weights.
However, as our experiments show, these weights tend to do well in practice.
7.5 Experiments
We applied associative Markov networks to the task of terrain classiﬁcation. Terrain clas
siﬁcation is very useful for autonomous mobile robots in realworld environments for path
planning, target detection, and as a preprocessing step for other perceptual tasks. The
Stanford Segbot Project
1
has provided us with a laser range maps of the Stanford campus
collected by a moving robot equipped with SICK2 laser sensors Fig. 7.5. The data consists
of around 35 million points, represented as 3D coordinates in an absolute frame of refer
ence Fig. 7.5. Thus, the only available information is the location of points. Each reading
was a point in 3D space, represented by its (x, y, z) coordinates in an absolute frame of
reference. Thus, the only available information is the location of points, which was fairly
noisy because of localization errors.
Our task is to classify the laser range points into four classes: ground, building, tree,
1
Many thanks to Michael Montemerlo and Sebastian Thrun for sharing the data.
100 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS
Figure 7.3: Segbot: roving robot equipped with SICK2 laser sensors.
and shrubbery. Since classifying ground points is trivial given their absolute zcoordinate
(height), we classify them deterministically by thresholding the z coordinate at a value
close to 0. After we do that, we are left with approximately 20 million nonground points.
Each point is represented simply as a location in an absolute 3D coordinate system. The
features we use require preprocessing to infer properties of the local neighborhood of a
point, such as how planar the neighborhood is, or how much of the neighbors are close to
the ground. The features we use are invariant to rotation in the xy plane, as well as the
density of the range scan, since scans tend to be sparser in regions farther from the robot.
Our ﬁrst type of feature is based on the principal plane around it. For each point we
sample 100 points in a cube of radius 0.5 meters. We run PCA on these points to get the
plane of maximum variance (spanned by the ﬁrst two principal components). We then par
tition the cube into 3 3 3 bins around the point, oriented with respect to the principal
plane, and compute the percentage of points lying in the various subcubes. We use a num
ber of features derived from the cube such as the percentage of points in the central column,
the outside corners, the central plane, etc. These features capture the local distribution well
and are especially useful in ﬁnding planes. Our second type of feature is based on a column
7.5. EXPERIMENTS 101
Figure 7.4: 3D laser scan range map of the Stanford Quad.
around each point. We take a cylinder of radius 0.25 meters, which extends vertically to
include all the points in a “column”. We then compute what percentage of the points lie in
various segments of this vertical column (e.g., between 2m and 2.5m). Finally, we also use
an indicator feature of whether or not a point lies within 2m of the ground. This feature is
especially useful in classifying shrubbery.
For training we select roughly 30 thousand points that represent the classes well: a
segment of a wall, a tree, some bushes. We considered three different models: SVM,
VotedSVM and AMNs. All methods use the same set of features, augmented with a
quadratic kernel.
The ﬁrst model is a multiclass SVM with a quadratic kernel over the above features.
This model (Fig. 7.5, right panel and Fig. 7.7, top panel) achieves reasonable performance
102 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS
Figure 7.5: Terrain classiﬁcation results showing Stanford Memorial Church obtained
with SVM, VotedSVM and AMN models. (Color legend: buildings/red, trees/green,
shrubs/blue, ground/gray).
in many places, but fails to enforce local consistency of the classiﬁcation predictions. For
example arches on buildings and other less planar regions are consistently confused for
trees, even though they are surrounded entirely by buildings.
We improved upon the SVM by smoothing its predictions using voting. For each point
we took its local neighborhood (we varied the radius to get the best possible results) and
assigned the point the label of the majority of its 100 neighbors. The VotedSVM model
(Fig. 7.5, middle panel and Fig. 7.7, middle panel) performs slightly better than SVM: for
example, it smooths out trees and some parts of the buildings. Yet it still fails in areas like
arches of buildings where the SVM classiﬁer has a locally consistent wrong prediction.
The ﬁnal model is a pairwise AMN over laser scan points, with associative potentials
to ensure smoothness. Each point is connected to 6 of its neighbors: 3 of them are sampled
randomly from the local neighborhood in a sphere of radius 0.5m, and the other 3 are
sampled at random from the vertical cylinder column of radius 0.25m. It is important to
ensure vertical consistency since the SVMclassiﬁer is wrong in areas that are higher off the
7.5. EXPERIMENTS 103
0 0.5 1 1.5 2 2.5
x 10
7
0
50
100
150
200
250
Problem size (nodes and edges)
R
u
n
n
i
n
g
t
i
m
e
(
s
e
c
o
n
d
s
)
Mincut inference performance
Figure 7.6: The running time (in seconds) of the mincutbased inference algorithm for
different problem sizes. The problem size is the sum of the number of nodes and the
number of edges. Note the near linear performance of the algorithm and its efﬁciency even
for large models.
ground (due to the decrease in point density) or because objects tend to look different as we
vary their zcoordinate (for example, tree trunks and tree crowns look different). While we
experimented with a variety of edge features including various distances between points,
we found that even using only a constant feature performs well.
We trained the AMN model using CPLEX to solve the quadratic program; the train
ing took about an hour on a Pentium 3 desktop. The inference over each segment was
performed using mincut with αexpansion moves as described above. We used a pub
licly available implementation of the mincut algorithm, which uses bidirectional search
trees for augmenting paths (see Boykov and Kolmogorov [2004]). The implementation is
largely dominated by I/O time, with the actual mincut taking less than two minutes even
for the largest segment. The performance is summarized in Fig. 7.6, and as we can see, it
is roughly linear in the size of the problem (number of nodes and number of edges).
We can see that the predictions of the AMN (Fig. 7.5, left panel and Fig. 7.7, bot
tom panel) are much smoother: for example building arches and tree trunks are predicted
104 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS
correctly. We also handlabeled around 180 thousand points of the test set (Fig. 7.8) and
computed accuracies of the predictions shown in Fig. 7.9 (excluding ground, which was
classiﬁed by preprocessing). The differences are dramatic: SVM: 68%, VotedSVM: 73%
and AMN: 93%. See more results, including a ﬂythrough movie of the data, at
http://ai.stanford.edu/˜btaskar/3Dmap/.
7.6 Related work
Several authors have considered extensions to the Potts model. Kleinberg and Tardos
[1999] extend the multiclass Potts model to have more general edge potentials, under the
constraints that negative log of the edge potentials form a metric on the set of labels. They
also provide a solution based on a relaxed LP that has certain approximation guarantees.
More recently, Kolmogorov and Zabih [2002] showed how to optimize energy func
tions containing binary and ternary interactions using graph cuts, as long as the parameters
satisfy a certain regularity condition. Our deﬁnition of associative potentials below also
satisﬁes the Kolmogorov and Zabih regularity condition for K = 2. However, the structure
of our potentials is simpler to describe and extend for the multiclass case. In fact, we can
extend our maxmargin framework to estimate their more general potentials by expressing
inference as a linear program.
Our terrain classiﬁcation approach is most closely related to work in vision applying
conditional random ﬁelds (CRFs) to 2D images. Kumar and Hebert [2003] train CRFs
using a pseudolikelihood approximation to the distribution P(Y [ X) since estimating
the true conditional distribution is intractable. Unlike their work, our learning formulation
provides an exact and tractable optimization algorithm, as well as formal guarantees for
binary classiﬁcation problems. Moreover, unlike their work, our approach can also handle
multiclass problems in a straightforward manner.
7.7 Conclusion
In this chapter, we provide an algorithm for maxmargin training of associative Markov
networks, a subclass of Markov networks that allows only positive interactions between
7.7. CONCLUSION 105
related variables. Our approach relies on a linear programming relaxation of the MAP
problem, which is the key component in the quadratic program associated with the max
margin formulation. We thus provide a polynomial time algorithm which approximately
solves the maximum margin estimation problem for any associative Markov network. Im
portantly, our method is guaranteed to ﬁnd the optimal (marginmaximizing) solution for all
binaryvalued AMNs, regardless of the clique size or the connectivity. To our knowledge,
this algorithm is the ﬁrst to provide an effective learning procedure for Markov networks
of such general structure.
Our results in the binary case rely on the fact that the LP relaxation of the MAP problem
provides exact solutions. In the nonbinary case, we are not guaranteed exact solutions, but
we can prove constantfactor approximation bounds on the MAP solution returned by the
relaxed LP. It would be interesting to see whether these bounds provide us with guarantees
on the quality (e.g., the margin) of our learned model.
We present largescale experiments with terrain segmentation and classiﬁcation from
3D range data involving AMNs with tens of millions of nodes and edges. The class of
associative Markov networks appears to cover a large number of interesting applications.
We have explored only a computer vision application in this chapter, and consider another
one (hypertext classiﬁcation) in the next. It would be very interesting to consider other
applications, such as extracting protein complexes from proteinprotein interaction data, or
predicting links in relational data. The mincut based inference is able to handle very large
networks, and it is an interesting challenge to apply the algorithm to even larger models
and develop efﬁcient distributed implementations.
However, despite the prevalence of fully associative Markov networks, it is clear that
many applications call for repulsive potentials. While clearly we cannot introduce fully
general potentials into AMNs without running against the NPhardness of the general prob
lem, it would be interesting to see whether we can extend the class of networks we can learn
effectively.
106 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS
Figure 7.7: Results from the SVM, VotedSVM and AMN models.
7.7. CONCLUSION 107
Figure 7.8: Labeled part of the test set: ground truth (top) and SVM predictions (bottom).
108 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS
Figure 7.9: Predictions of the VotedSVM (top) and AMN (bottom) models.
Chapter 8
Relational Markov networks
In the previous chapters, we have seen how sequential and spatial correlation between
labels can be exploited for tremendous accuracy gains. In many other supervised learning
tasks, the entities to be labeled are related with each other in very complex ways, not just
sequentially or spatially. For example, in hypertext classiﬁcation, the labels of linked pages
are highly correlated. Astandard approach is to classify each entity independently, ignoring
the correlations between them. In this chapter, we present a framework that builds on
Markov networks and provides a ﬂexible language for modeling rich interaction patterns in
structured data. We provide experimental results on a webpage classiﬁcation task, showing
that accuracy can be signiﬁcantly improved by modeling relational dependencies.
Many realworld data sets are innately relational: hyperlinked webpages, crosscitations
in patents and scientiﬁc papers, social networks, medical records, and more. Such data con
sist of entities of different types, where each entity type is characterized by a different set
of attributes. Entities are related to each other via different types of links, and the link
structure is an important source of information.
Consider a collection of hypertext documents that we want to classify using some set
of labels. Most naively, we can use a bag of words model, classifying each webpage solely
using the words that appear on the page. However, hypertext has a very rich structure that
this approach loses entirely. One document has hyperlinks to others, typically indicating
that their topics are related. Each document also has internal structure, such as a partition
into sections; hyperlinks that emanate from the same section of the document are even
109
110 CHAPTER 8. RELATIONAL MARKOV NETWORKS
more likely to point to similar documents. When classifying a collection of documents,
these are important cues, that can potentially help us achieve better classiﬁcation accuracy.
Therefore, rather than classifying each document separately, we want to provide a form of
collective classiﬁcation, where we simultaneously decide on the class labels of all of the
entities together, and thereby can explicitly take advantage of the correlations between the
labels of related entities.
We propose the use of a joint probabilistic model for an entire collection of related enti
ties. We introduce the framework of relational Markov networks (RMNs), which compactly
deﬁnes a Markov network over a relational data set. The graphical structure of an RMN is
based on the relational structure of the domain, and can easily model complex patterns over
related entities. For example, we can represent a pattern where two linked documents are
likely to have the same topic. We can also capture patterns that involve groups of links: for
example, consecutive links in a document tend to refer to documents with the same label.
As we show, the use of an undirected graphical model avoids the difﬁculties of deﬁning
a coherent generative model for graph structures in directed models. It thereby allows us
tremendous ﬂexibility in representing complex patterns.
8.1 Relational classiﬁcation
Consider hypertext as a simple example of a relational domain. A relational domain is
deﬁned by a schema, which describes entities, their attributes and relations between them.
In our domain, there are two entity types: Doc and Link. If a webpage is represented as a
bag of words, Doc would have a set of boolean attributes Doc.HasWord
k
indicating whether
the word k occurs on the page. It would also have the label attribute Doc.Label, indicating
the topic of the page, which takes on a set of categorical values. The Link entity type has
two attributes: Link.From and Link.To, both of which refer to Doc entities.
In general, a schema speciﬁes of a set of entity types c = ¦E
1
, . . . , E
n
¦. Each type E is
associated with three sets of attributes: content attributes E.X(for example, Doc.HasWord
k
),
label attributes E.Y (for example, Doc.Label), and reference attributes E.R (for example,
Link.To). For simplicity, we restrict label and content attributes to take on categorical val
ues. Reference attributes include a special unique key attribute E.K that identiﬁes each
8.1. RELATIONAL CLASSIFICATION 111
entity. Other reference attributes E.R refer to entities of a single type E
t
= Range(E.R)
and take values in Domain(E
t
.K).
An instantiation 1 of a schema c speciﬁes the set of entities 1(E) of each entity type
E ∈ c and the values of all attributes for all of the entities. For example, an instantiation
of the hypertext schema is a collection of webpages, specifying their labels, words they
contain and links between them. We will use 1.X, 1.Y and 1.R to denote the content,
label and reference attributes in the instantiation 1; 1.x, 1.y and 1.r to denote the values
of those attributes. The component 1.r, which we call an instantiation skeleton or instan
tiation graph, speciﬁes the set of entities (nodes) and their reference attributes (edges). A
hypertext instantiation graph speciﬁes a set of webpages and links between them, but not
their words or labels. Taskar et al. [2001] suggest the use of probabilistic relational mod
els (PRMs) for the collective classiﬁcation task. PRMs [Koller & Pfeffer, 1998; Friedman
et al., 1999; Getoor et al., 2002] are a relational extension of Bayesian networks [Pearl,
1988]. A PRM speciﬁes a probability distribution over instantiations consistent with a
given instantiation graph by specifying a Bayesiannetworklike templatelevel probabilis
tic model for each entity type. Given a particular instantiation graph, the PRM induces
a large Bayesian network over that instantiation that speciﬁes a joint probability distribu
tion over all attributes of all of the entities. This network reﬂects the interactions between
related instances by allowing us to represent correlations between their attributes.
In our hypertext example, a PRM might use a naive Bayes model for words, with a di
rected edge between Doc.Label and each attribute Doc.HadWord
k
; each of these attributes
would have a conditional probability distribution P(Doc.HasWord
k
[ Doc.Label) associ
ated with it, indicating the probability that word k appears in the document given each of
the possible topic labels. More importantly, a PRM can represent the interdependencies
between topics of linked documents by introducing an edge from Doc.Label to Doc.Label
of two documents if there is a link between them. Given a particular instantiation graph
containing some set of documents and links, the PRM speciﬁes a Bayesian network over all
of the documents in the collection. We would have a probabilistic dependency from each
document’s label to the words on the document, and a dependency from each document’s
label to the labels of all of the documents to which it points. Taskar et al. show that this
approach works well for classifying scientiﬁc documents, using both the words in the title
112 CHAPTER 8. RELATIONAL MARKOV NETWORKS
and abstract and the citationlink structure.
However the application of this idea to other domains, such as webpages, is problematic
since there are many cycles in the link graph, leading to cycles in the induced “Bayesian
network”, which is therefore not a coherent probabilistic model. Getoor et al. [2001] sug
gest an approach where we do not include direct dependencies between the labels of linked
webpages, but rather treat links themselves as random variables. Each two pages have a
“potential link”, which may or may not exist in the data. The model deﬁnes the probability
of the link existence as a function of the labels of the two endpoints. In this link exis
tence model, labels have no incoming edges from other labels, and the cyclicity problem
disappears. This model, however, has other fundamental limitations. In particular, the re
sulting Bayesian network has a random variable for each potential link — N
2
variables for
collections containing N pages. This quadratic blowup occurs even when the actual link
graph is very sparse. When N is large (e.g., the set of all webpages), a quadratic growth is
intractable. Even more problematic are the inherent limitations on the expressive power im
posed by the constraint that the directed graph must represent a coherent generative model
over graph structures. The link existence model assumes that the presence of different
edges is a conditionally independent event. Representing more complex patterns involving
correlations between multiple edges is very difﬁcult. For example, if two pages point to the
same page, it is more likely that they point to each other as well. Such interactions between
many overlapping triples of links do not ﬁt well into the generative framework.
Furthermore, directed models such as Bayesian networks and PRMs are usually trained
to optimize the joint probability of the labels and other attributes, while the goal of clas
siﬁcation is a discriminative model of labels given the other attributes. The advantage
of training a model only to discriminate between labels is that it does not have to trade
off between classiﬁcation accuracy and modeling the joint distribution over nonlabel at
tributes. In many cases, discriminatively trained models are more robust to violations of
independence assumptions and achieve higher classiﬁcation accuracy than their generative
counterparts.
8.2. RELATIONAL MARKOV NETWORKS 113
Label 1
Label 2
Label 3
Figure 8.1: An unrolled Markov net over linked documents. The links follow a common
pattern: documents with the same label tend to link to each other more often.
8.2 Relational Markov networks
We now extend the framework of Markov networks to the relational setting. A relational
Markov network (RMN) speciﬁes a conditional distribution over all of the labels of all
of the entities in an instantiation given the relational structure and the content attributes.
(We provide the deﬁnitions directly for the conditional case, as the unconditional case is a
special case where the set of content attributes is empty.) Roughly speaking, it speciﬁes the
cliques and potentials between attributes of related entities at a template level, so a single
model provides a coherent distribution for any collection of instances from the schema.
For example, suppose that pages with the same label tend to link to each other, as
in Fig. 8.1. We can capture this correlation between labels by introducing, for each link, a
clique between the labels of the source and the target page. The potential on the clique will
have higher values for assignments that give a common label to the linked pages.
To specify what cliques should be constructed in an instantiation, we will deﬁne a no
tion of a relational clique template. Arelational clique template speciﬁes tuples of variables
in the instantiation by using a relational query language. For our link example, we can write
the template as a kind of SQL query:
SELECT doc1.Category, doc2.Category
114 CHAPTER 8. RELATIONAL MARKOV NETWORKS
FROM Doc doc1, Doc doc2, Link link
WHERE link.From = doc1.Key and link.To = doc2.Key
Note the three clauses that deﬁne a query: the FROM clause speciﬁes the cross prod
uct of entities to be ﬁltered by the WHERE clause and the SELECT clause picks out the
attributes of interest. Our deﬁnition of clique templates contains the corresponding three
parts.
A relational clique template C = (F, W, S) consists of three components:
◦ F = ¦F
i
¦ — a set of entity variables, where an entity variable F
i
is of type E(F
i
).
◦ W(F.R) — a boolean formula using conditions of the form F
i
.R
j
= F
k
.R
l
.
◦ F.S ⊆ F.X∪ F.Y — a selected subset of content and label attributes in F.
For the clique template corresponding to the SQL query above, Fconsists of doc1, doc2
and link of types Doc, Doc and Link, respectively. W(F.R) is link.From = doc1.Key ∧
link.To = doc2.Key and F.S is doc1.Category and doc2.Category.
A clique template speciﬁes a set of cliques in an instantiation 1:
C(1) ≡ ¦c = f .S : f ∈ 1(F) ∧ W(f .r)¦,
where f is a tuple of entities ¦f
i
¦ in which each f
i
is of type E(F
i
); 1(F) = 1(E(F
1
))
. . . 1(E(F
n
)) denotes the crossproduct of entities in the instantiation; the clause W(f .r)
ensures that the entities are related to each other in speciﬁed ways; and ﬁnally, f .S selects
the appropriate attributes of the entities. Note that the clique template does not specify the
nature of the interaction between the attributes; that is determined by the clique potentials,
which will be associated with the template.
This deﬁnition of a clique template is very ﬂexible, as the WHERE clause of a tem
plate can be an arbitrary predicate. It allows modeling complex relational patterns on the
instantiation graphs. To continue our webpage example, consider another common pattern
in hypertext: links in a webpage tend to point to pages of the same category. This pattern
can be expressed by the following template:
SELECT doc1.Category, doc2.Category
8.2. RELATIONAL MARKOV NETWORKS 115
FROM Doc doc1, Doc doc2, Link link1, Link link2
WHERE link1.From = link2.From and link1.To = doc1.Key
and link2.To = doc2.Key and not doc1.Key = doc2.Key
Depending on the expressive power of our template deﬁnition language, we may be able
to construct very complex templates that select entire subgraph structures of an instantia
tion. We can easily represent patterns involving three (or more) interconnected documents
without worrying about the acyclicity constraint imposed by directed models. Since the
clique templates do not explicitly depend on the identities of entities, the same template can
select subgraphs whose structure is fairly different. The RMN allows us to associate the
same clique potential parameters with all of the subgraphs satisfying the template, thereby
allowing generalization over a wide range of different structures.
A Relational Markov network (RMN) / = (C, Φ) speciﬁes a set of clique templates
C and corresponding potentials Φ = ¦φ
C
¦
C∈C
to deﬁne a conditional distribution:
P(1.y [ 1.x, 1.r)
=
1
Z(1.x, 1.r)
C∈C
c∈C(7)
φ
C
(1.x
c
, 1.y
c
)
where Z(1.x, 1.r) is the normalizing partition function:
Z(1.x, 1.r) =
7.y
C∈C
c∈C(7)
φ
C
(1.x
c
, 1.y
t
c
)
.
Using the loglinear representation of potentials, φ
C
(V
C
) = exp¦w
¯
C
f
C
(V
C
)¦, we can
write
log P(1.y [ 1.x, 1.r) = w
¯
f (1.x, 1.y, 1.r) −log Z(1.x, 1.r)
where
f
C
(1.x, 1.y, 1.r) =
c∈C(7)
f
C
(1.x
c
, 1.y
c
)
is the sum over all appearances of the template C(1) in the instantiation, and f is the vector
116 CHAPTER 8. RELATIONAL MARKOV NETWORKS
of all f
C
.
Given a particular instantiation 1 of the schema, the RMN / produces an unrolled
Markov network over the attributes of entities in 1. The cliques in the unrolled network
are determined by the clique templates C. We have one clique for each c ∈ C(1), and
all of these cliques are associated with the same clique potential φ
C
. In our webpage
example, an RMN with the link basis function described above would deﬁne a Markov net
in which, for every link between two pages, there is an edge between the labels of these
pages. Fig. 8.1 illustrates a simple instance of this unrolled Markov network.
8.3 Approximate inference and learning
Applying both maximum likelihood and maximum margin learning in the relational setting
is requires inference in very large and complicated networks, where exact inference is
typically intractable. We therefore resort to approximate methods.
Maximum likelihood estimation
For maximum likelihood learning, we need to compute basis function expectations, not
just the most likely assignment. There is a wide variety of approximation schemes for this
problem, including MCMC and variational methods. We chose to use belief propagation
for its simplicity and relative efﬁciency and accuracy. Belief Propagation (BP) is a local
message passing algorithm introduced by Pearl [1988]. It is guaranteed to converge to the
correct marginal probabilities for each node only for singly connected Markov networks.
However, recent analysis [Yedidia et al., 2000] provides some theoretical justiﬁcation. Em
pirical results [Murphy et al., 1999] show that it often converges in general networks, and
when it does, the marginals are a good approximation to the correct posteriors. As our
results in Sec. 8.4 show, this approach works well in our domain. We refer the reader to
Yedidia et al. for a detailed description of the BP algorithm.
We provide a brief outline of one variant of BP, referring to [Murphy et al., 1999]
for more details. For simplicity, we assume a pairwise network where all potentials are
associated only with nodes and edges given by:
8.3. APPROXIMATE INFERENCE AND LEARNING 117
P(Y
1
, . . . , Y
n
) =
1
Z
ij
ψ
ij
(Y
i
, Y
j
)
i
ψ
i
(Y
i
)
where ij ranges over the edges of the network and ψ
ij
(Y
i
, Y
j
) = φ(x
ij
, Y
i
, Y
j
), ψ
i
(Y
i
) =
φ(x
i
, Y
i
).
The belief propagation algorithm is very simple. At each iteration, each node Y
i
sends
the following messages to all its neighbors N(i):
m
ij
(Y
j
) ←α
y
i
ψ
ij
(y
i
, Y
j
)ψ
i
(y
i
)
k∈N(i)−j
m
ki
(Y
i
)
where α is a (different) normalizing constant. This process is repeated until the messages
converge. At any point in the algorithm, the marginal distribution of any node Y
i
is approx
imated by
b
i
(Y
i
) = αψ
i
(Y
i
)
k∈N(i)
m
ki
(Y
i
)
and the marginal distribution of a pair of nodes connected by an edge is approximated by
b
ij
(Y
i
, Y
j
) = αψ
ij
(Y
i
, Y
j
)ψ
i
(Y
i
)ψ
j
(Y
j
)
k∈N(i)−j
m
ki
(Y
i
)
l∈N(j)−i
m
lj
(Y
j
)
These approximate marginals are precisely what we need for the computation of the
basis function expectations and performing classiﬁcation. Computing the expected basis
function expectations involves summing their expected values for each clique using the
approximate marginals b
i
(Y
i
) and b
ij
(Y
i
, Y
j
). Similarly, we use max
y
i
b
i
(Y
i
) at prediction
time. Note that we can also max −product variant of loopy BP, with
m
ij
(Y
j
) ←αmax
y
i
ψ
ij
(y
i
, Y
j
)ψ
i
(y
i
)
k∈N(i)−j
m
ki
(Y
i
)
to compute approximate posterior “max”marginals and use those for prediction. In our
experiments, this results in less accurate classiﬁcation, so we use posterior marginal pre
diction.
118 CHAPTER 8. RELATIONAL MARKOV NETWORKS
Maximum margin estimation
For maximummargin estimation, we used approximate LP inference inside the maxmargin
QP, using commercial Ilog CPLEX software to solve it. For networks with general poten
tials, we used the untriangulated LP we described in Sec. 5.4. The untriangulated LP
produced fractional solutions for inference on the test data in several settings, which we
rounded independently for each label. For networks with attractive potentials (AMNs), we
used the LP in Sec. 7.2, which always produced integral solutions on test data.
8.4 Experiments
We tried out our framework on the WebKB dataset [Craven et al., 1998], which is an in
stance of our hypertext example. The data set contains webpages from four different Com
puter Science departments: Cornell, Texas, Washington and Wisconsin. Each page has a
label attribute, representing the type of webpage which is one of course, faculty, student,
project or other. The data set is problematic in that the category other is a grabbag of
pages of many different types. The number of pages classiﬁed as other is quite large,
so that a baseline algorithm that simply always selected other as the label would get an
average accuracy of 75%. We could restrict attention to just the pages with the four other
labels, but in a relational classiﬁcation setting, the deleted webpages might be useful in
terms of their interactions with other webpages. Hence, we compromised by eliminating
all other pages with fewer than three outlinks, making the number of other pages com
mensurate with the other categories. The resulting category distribution is: course (237),
faculty (148), other (332), researchproject (82) and student (542). The number of remain
ing pages for each school are: Cornell (280), Texas (292), Washington (315) and Wisconsin
(454). The number of links for each school are: Cornell (574), Texas (574), Washington
(728) and Wisconsin (1614).
For each page, we have access to the entire html of the page and the links to other
pages. Our goal is to collectively classify webpages into one of these ﬁve categories. In all
of our experiments, we learn a model from three schools and test the performance of the
learned model on the remaining school, thus evaluating the generalization performance of
8.4. EXPERIMENTS 119
the different models. We used C ∈ [0.1, 10] and took the best setting for all models.
Unfortunately, we cannot directly compare our accuracy results with previous work
because different papers use different subsets of the data and different training/test splits.
However, we compare to standard text classiﬁers such as Naive Bayes, Logistic Regression,
and Support Vector Machines, which have been demonstrated to be successful on this data
set [Joachims, 1999].
8.4.1 Flat models
The simplest approach we tried predicts the categories based on just the text content on
the webpage. The text of the webpage is represented using a set of binary attributes that
indicate the presence of different words on the page. We found that stemming and feature
selection did not provide much beneﬁt and simply pruned words that appeared in fewer
than three documents in each of the three schools in the training data. We also experi
mented with incorporating metadata: words appearing in the title of the page, in anchors
of links to the page and in the last header before a link to the page [Yang et al., 2002].
Note that metadata, although mostly originating from pages linking into the considered
page, are easily incorporated as features, i.e. the resulting classiﬁcation task is still ﬂat
featurebased classiﬁcation. Our ﬁrst experimental setup compares three wellknown text
classiﬁers — Naive Bayes, linear support vector machines (Svm), and logistic regression
(Logistic) — using words and metawords. The results, shown in Fig. 8.2, show that the
two discriminative approaches outperformNaive Bayes. Logistic and Svmgive very sim
ilar results. The average error over the 4 schools was reduced by around 4% by introducing
the metadata attributes.
Incorporating metadata gives a signiﬁcant improvement, but we can take additional
advantage of the correlation in labels of related pages by classifying them collectively. We
want to capture these correlations in our model and use them for transmitting informa
tion between linked pages to provide more accurate classiﬁcation. We experimented with
several relational models.
120 CHAPTER 8. RELATIONAL MARKOV NETWORKS
0
0.05
0.1
0.15
0.2
0.25
0.3
0.35
NaïveBayes Svm Logistic
T
e
s
t
E
r
r
o
r
Words Words+Meta
Figure 8.2: Comparison of Naive Bayes, Svm, and Logistic on WebKB, with and without
metadata features. (Only averages over the 4 schools are shown here.)
8.4.2 Link model
Our ﬁrst model captures direct correlations between labels of linked pages. These corre
lations are very common in our data: courses and research projects almost never link to
each other; faculty rarely link to each other; students have links to all categories but mostly
courses. The Link model, shown in Fig. 8.1, captures this correlation through links: in
addition to the local bag of words and metadata attributes, we introduce a relational clique
template over the labels of two pages that are linked.We train this model using maximum
conditional likelihood (labels given the words and the links) and maximum margin.
We also compare to a directed graphical model to contrast discriminative and genera
tive models of relational structure. The ExistsML model is a (partially) generative model
proposed by Getoor et al. [2001]. For each page, a logistic regression model predicts
the page label given the words and metafeatures. Then a simple generative model speci
ﬁes a probability distribution over the existence of links between pages conditioned on both
pages’ labels. Concretely, we learn the probability of existence of a link between two pages
given their labels. Note that this model does not require inference during learning. Max
imum likelihood estimation (with regularization) of the generative component is closed
8.4. EXPERIMENTS 121
0%
5%
10%
15%
20%
25%
30%
Cor Tex Was Wis Average
E
r
r
o
r
ExistsML
SVM
LinkML
LinkMM
Figure 8.3: Comparison of ﬂat versus collective classiﬁcation on WebKB: SVM, Exists
model with logistic regression and the Link model estimated using the maximum likelihood
(ML) and the maximum margin (MM) criteria.
form given appropriate cooccurrence counts of linked pages’ labels. However, the predic
tion phase is much more expensive, since the resulting graphical model includes edges not
only for the existing hyperlinks, but also those that do not exist. Intuitively, observing the
link structure directly correlates all page labels in a website, linked or not. By contrast,
the Link model avoids this problem by only modeling the conditional distribution given the
existing links.
Fig. 8.3 shows a gain in accuracy from SVMs to the Link model by using the corre
lations between labels of linked web pages. There is also very signiﬁcant additional gain
by using maximum margin training: the error rate of LinkMM is 40% lower than that of
LinkML, and 51% lower than multiclass SVMs. The Exists model doesn’t perform very
well in comparison. This can be attributed to the simplicity of the generative model and the
difﬁculty of the resulting inference problem.
8.4.3 Cocite model
The second relational model uses the insight that a webpage often has internal structure
that allows it to be broken up into sections. For example, a faculty webpage might have
122 CHAPTER 8. RELATIONAL MARKOV NETWORKS
0%
5%
10%
15%
20%
25%
Cor Tex Was Wis Average
E
r
r
o
r
SVM
CociteML
CociteMM
Figure 8.4: Comparison of Naive Bayes, Svm, and Logistic on WebKB, with and without
metadata features. (Only averages over the 4 schools are shown here.)
one section that discusses research, with a list of links to all of the projects of the faculty
member, a second section might contain links to the courses taught by the faculty member,
and a third to his advisees. We can view a section of a webpage as a ﬁnegrained version of
Kleinberg’s hub [Kleinberg, 1999] (a page that contains a lot of links to pages of particular
category). Intuitively, if two pages are cocited, or linked to from the same section, they are
likely to be on similar topics. Note that we expect the correlation between the labels in this
case to be positive, so we can use AMNtype potentials in the maxmargin estimation. The
Cocite model captures this type of correlation.
To take advantage of this trend, we need to enrich our schema by adding the attribute
Section to Link to refer to the section number it appears in. We deﬁned a section as a
sequence of three or more links that have the same path to the root in the html parse tree.
In the RMN, we have a relational clique template deﬁned by:
SELECT doc1.Category, doc2.Category
FROM Doc doc1, Doc doc2, Link link1, Link link2
WHERE link1.From = link2.From and link1.Section = link2.Section and
link1.To = doc1.Key and link2.To = doc2.Key and not doc1.Key = doc2.Key
We compared the performance of SVM, CociteML and CociteMM. The results,
8.5. RELATED WORK 123
shown in Fig. 8.4, also demonstrate signiﬁcant improvements of the relational models over
the SVM. The improvement is present when testing on each of the schools. Again, maxi
mum likelihood trained model CociteML achieves a worse test error than maximum mar
gin CociteMM model, which shows a 30% relative reduction in test error over SVM.
We note that, in our experiments, the learned CociteMM weights never produced frac
tional solutions when used for inference, which suggests that the optimization successfully
avoided problematic parameterizations of the network, even in the case of the nonoptimal
multiclass relaxation.
8.5 Related work
Our RMN representation is most closely related to the work on PRMs [Koller & Pfeffer,
1998]. Later work showed how to efﬁciently learn model parameters and structure (equiv
alent of clique selection in Markov networks) from data [Friedman et al., 1999]. Getoor
et al. [2002] propose several generative models of relational structure. Their approach
easily captures the dependence of link existence on attributes of entities. However there
are many patterns that we are difﬁcult to model in PRMs, in particular those that involve
several links at a time. We give some examples here.
One useful type of pattern type is a similarity template, where objects that share a cer
tain graphbased property are more likely to have the same label. Consider, for example,
a professor X and two other entities Y and Z. If X’s webpage mentions Y and Z in the
same context, it is likely that the XY relation and the YZ relation are of the same type; for
example, if Y is Professor X’s advisee, then probably so is Z. Our framework accommo
dates these patterns easily, by introducing pairwise cliques between the appropriate relation
variables.
Another useful type of subgraph template involves transitivity patterns, where the pres
ence of an AB link and of a BC link increases (or decreases) the likelihood of an AC link.
For example, students often assist in courses taught by their advisor. Note that this type
of interaction cannot be accounted for just using pairwise cliques. By introducing cliques
over triples of relations, we can capture such patterns as well. We can incorporate even
more complicated patterns, but of course we are limited by the ability of belief propagation
124 CHAPTER 8. RELATIONAL MARKOV NETWORKS
to scale up as we introduce larger cliques and tighter loops in the Markov network.
We describe and exploit these patterns in our work on RMNs using maximumlikelihood
estimation [Taskar et al., 2003b]. Attempts to model such pattern in PRMs run into the
constraint that the probabilistic dependency graph (Bayesian network) must be a directed
acyclic graph. For example, for the transitivity pattern, we might consider simply directing
the correlation edges between link existence variables arbitrarily. However, it is not clear
how to parameterize a link existence variable for a link that is involved in multiple triangles.
The structure of the relational graph has been used extensively to infer importance in
scientiﬁc publications [Egghe & Rousseau, 1990] and hypertext [Kleinberg, 1999]. Sev
eral recent papers have proposed algorithms that use the link graph to aid classiﬁcation.
Chakrabarti et al. [1998] use systempredicted labels of linked documents to iteratively
relabel each document in the test set, achieving a signiﬁcant improvement compared to a
baseline of using the text in each document alone. A similar approach was used by Neville
and Jensen [2000] in a different domain. Slattery and Mitchell [2000] tried to identify di
rectory (or hub) pages that commonly list pages of the same topic, and used these pages to
improve classiﬁcation of university webpages. However, none of these approaches provide
a coherent model for the correlations between linked webpages, applying combinations of
classiﬁers in a procedural way, with no formal justiﬁcation.
8.6 Conclusion
In this chapter, we propose a new approach for classiﬁcation in relational domains. Our ap
proach provides a coherent foundation for the process of collective classiﬁcation, where we
want to classify multiple entities, exploiting the interactions between their labels. We have
shown that we can exploit a very rich set of relational patterns in classiﬁcation, signiﬁcantly
improving the classiﬁcation accuracy over standard ﬂat classiﬁcation.
In some cases, we can incorporate relational features into standard ﬂat classiﬁcation.
For example, when classifying papers into topics, it is possible to simply view the presence
of particular citations as atomic features. However, this approach is limited in cases where
some or even all of the relational features that occur in the test data are not observed in
the training data. In our WebKB example, there is no overlap between the webpages in the
8.6. CONCLUSION 125
different schools, so we cannot learn anything from the training data about the signiﬁcance
of a hyperlink to/from a particular webpage in the test data. Incorporating basic features
(e.g., words) from the related entities can aid in classiﬁcation, but cannot exploit the strong
correlation between the labels of related entities that RMNs capture.
Hypertext is the most easily available source of structured data, however, RMNs are
generally applicable to any relational domain. The results in this chapter represent only
a subset of the domains we have worked on (see [Taskar et al., 2003b]). In particular,
social networks provide extensive information about interactions among people and orga
nizations. RMNs offer a principled method for learning to predict communities of and
hierarchical structure between people and organizations based on both the local attributes
and the patterns of static and dynamic interaction. Given the wealth of possible patterns, it
is particularly interesting to explore the problem of inducing them automatically.
126 CHAPTER 8. RELATIONAL MARKOV NETWORKS
Part III
Broader applications: parsing,
matching, clustering
127
Chapter 9
Context free grammars
We present a novel discriminative approach to parsing using structured maxmargin crite
rion based on the decomposition properties of context free grammars. We show that this
framework allows highaccuracy parsing in cubic time by exploiting novel kinds of lexical
information. Our models can condition on arbitrary features of input sentences, thus incor
porating an important kind of lexical information not usually used by conventional parsers.
We show experimental evidence of the model’s improved performance over a natural base
line model and a lexicalized probabilistic contextfree grammar.
9.1 Context free grammar model
CFGs are one of the primary formalisms for capturing the recursive structure of syntactic
constructions, although many others have also been proposed [Manning & Sch¨ utze, 1999].
For clarity of presentation, we restrict our grammars to be in Chomsky normal form as
in Sec. 3.4. The nonterminal symbols correspond to syntactic categories such as noun
phrase (NP) or verbal phrase (VP). The terminal symbols are usually words of the sen
tence. However, in the discriminative framework that we adopt, we are not concerned with
deﬁning a distribution over sequences of words (language model). Instead, we condition
on the words in a sentence to produce a model of the syntactic structure. Terminal sym
bols for our purposes are partofspeech tags like nouns (NN), verbs (VBD), determiners
(DT). For example, Fig. 9.1(a) shows a parse tree for the sentence The screen was a sea of
128
9.1. CONTEXT FREE GRAMMAR MODEL 129
red. The set of symbols we use is based on the Penn Treebank [Marcus et al., 1993]. The
nonterminal symbols with bars (for example, DT, NN, VBD) are added to conform to the
CNF restrictions. For convenience, we repeat our deﬁnition of a CFG from Sec. 3.4 here:
Deﬁnition 9.1.1 (CFG) A CFG ( consists of:
◦ A set of nonterminal symbols, ^
◦ A designated set of start symbols, ^
S
⊆ ^
◦ A set of terminal symbols, T
◦ A set of productions, T = ¦T
B
, T
U
¦, divided into
Binary productions, T
B
= ¦A →B C : A, B, C ∈ ^¦ and
Unary productions, T
U
= ¦A → D : A ∈ ^, D ∈ T ¦.
A CFG deﬁnes a set of valid parse trees in a natural manner:
Deﬁnition 9.1.2 (CFG tree) A CFG tree is a labeled directed tree, where the set of valid
labels of the internal nodes other than the root is ^ and the set of valid labels for the leaves
is T . The root’s label set is ^
S
. Additionally, each preleaf node has a single child and
this pair of nodes can be labeled as A and D, respectively, if and only if there is a unary
production A → D ∈ T
U
. All other internal nodes have two children, left and right, and
this triple of nodes can be labeled as A, B and C, respectively, if and only if there is a
binary production A →B C ∈ T
B
.
In general, there are exponentially many parse trees that produce a sentence of length n.
This tree representation seems quite different from the graphical models we have been
considering thus far. However, we can use an equivalent representation that essentially
encodes a tree as an assignment to a set of appropriate variables. For each span starting
with s and an ending with e, we introduce a variable Y
s,e
taking values in ^∪⊥to represent
the label of the subtree that exactly covers, or dominates, the words of the sentence from
s to e. The value ⊥ is assigned if no subtree dominates the span. Indices s and e refer to
positions between words, rather than to words themselves, hence 0 ≤ s < e ≤ n for a
sentence of length n. The “top” symbol Y
0,n
is constrained to be in ^
S
, since it represents
130 CHAPTER 9. CONTEXT FREE GRAMMARS
(a) (b)
Figure 9.1: Two representations of a binary parse tree: (a) nested tree structure, and (b)
grid of labeled spans. The row and column number are the beginning and end of the span,
respectively. Empty squares correspond to nonconstituent spans. The gray squares on the
diagonal represent partofspeech tags.
the starting symbol of the sentence. We also introduce variables Y
s,s
taking values in T to
represent the terminal symbol (partofspeech) between s and s +1. If Y
s,e
,= ⊥, it is often
called a constituent. Fig. 9.1(b) shows the representation of the tree in Fig. 9.1(a) as a grid
where each square corresponds to Y
s,e
. The row and column number in the grid correspond
to the beginning and end of the span, respectively. Empty squares correspond to ⊥ values.
The gray squares on the diagonal represent the terminal variables. For example, the ﬁgure
shows Y
0,0
= DT, Y
6,6
= NN, Y
3,5
= NP and Y
1,4
= ⊥.
While any parse tree corresponds to an assignment to this set of variables in a straight
forward manner, the converse is not true: there are assignments that do not correspond
to valid parse trees. In order to characterize the set of valid assignments ¸, consider the
9.1. CONTEXT FREE GRAMMAR MODEL 131
constraints that hold for a valid assignment y:
1I(y
s,e
= A) =
A→B C∈P
B
s<m<e
1I(y
s,m,e
= (A, B, C)), 0 ≤ s < e ≤ n, ∀A ∈ ^; (9.1)
1I(y
s,e
= A) =
B→A C∈P
B
0≤s
<s
1I(y
s
,s,e
= (B, A, C))
+
B→C A∈P
B
e<e
≤n
1I(y
s,e,e
= (B, C, A)), 0 ≤ s < e ≤ n, ∀A ∈ ^; (9.2)
1I(y
s,s+1
= A) =
A→D∈1
U
1I(y
s,s,s+1
= (A, D)), 0 ≤ s < n, ∀A ∈ ^; (9.3)
1I(y
s,s
= D) =
A→D∈1
U
1I(y
s,s,s+1
= (A, D)), 0 ≤ s < n, ∀D ∈ T . (9.4)
The notation y
s,m,e
= (A, B, C) abbreviates y
s,e
= A ∧ y
s,m
= B ∧ y
m,e
= C and
y
s,s,s+1
= (A, D) abbreviates y
s,s+1
= A ∧ y
s,s
= D. The ﬁrst set of constraints (9.1)
holds because if the span from s to e is dominated by a subtree starting with A (that is,
y
s,e
= A), then there must be a unique production starting with A and some split point m,
s < m < e, that produces that subtree. Conversely, if y
s,e
,= A, no productions start with
A and cover s to e. The second set of constraints (9.2) holds because that if the span from
s to e is dominated by a subtree starting with A (y
s,e
= A), then there must be a (unique)
production that generated it: either starting before s or after e. Similarly, the third and
fourth set of constraints (9.3 and 9.4) hold since the terminals are generated using valid
unary productions. We denote the set of assignments y satisfying (9.19.4) as ¸. In fact
the converse is true as well:
Theorem 9.1.3 If y ∈ ¸, then y represents a valid CFG tree.
Proof sketch: It is straightforward to construct a parse tree from y ∈ ¸ in a topdown
manner. Starting from the root symbol, y
0,n
, the ﬁrst set of constraints (9.1) ensures that a
unique production spans 0 to n, say splitting at m and specifying the values for y
0,m
and
y
m,n
. The second set of constraints (9.2) ensures that all other spans y
0,m
and y
m
,n
, for
m
t
,= m are labeled by ⊥. Recursing on the two subtrees, y
0,m
and y
m,n
, will produce the
rest of the tree down to the preterminals. The last two sets of constraints (9.3 and 9.4)
132 CHAPTER 9. CONTEXT FREE GRAMMARS
ensure that the terminals are generated by an appropriate unary productions from the pre
terminals.
9.2 Context free parsing
A standard approach to parsing is to use a CFG to deﬁne a probability distribution over
parse trees. This can be done simply by assigning a probability to each production and
making sure that the sum of probabilities of all productions starting with each symbol is 1:
B,C:A→B C∈1
B
P(A →B C) = 1,
D:A→D∈1
U
P(A →D) = 1, ∀A ∈ ^.
The probability of a tree is simply the product of probabilities of the productions used in
the tree. More generally, a weighted CFG assigns a score to each production (this score
may depend on the position of the production s, m, e) such that the total score of a tree is
the sum of the score of all the productions used:
S(y) =
0≤s<m<e≤n
S
s,m,e
(y
s,m,e
) +
0≤s<n
S
s,s+1
(y
s,s+1
),
where S
s,m,e
(y
s,m,e
) = 0 if (y
s,e
= ⊥ ∨ y
s,m
= ⊥ ∨ y
m,e
= ⊥). If the production scores
are production log probabilities, then the tree score is the tree log probability. However,
weighted CFGs do not have the local normalization constraints Eq. (9.5).
We can use a Viterbistyle dynamic programming algorithm called CKY to compute
the highest score parse tree in O([T[n
3
) time [Younger, 1967; Manning & Sch¨ utze, 1999].
The algorithm computes the highest score of any subtree starting with a symbol over each
span 0 ≤ s < e ≤ n recursively:
S
∗
s,s+1
(A) = max
A→D∈1
U
S
s,s+1
(A, D), 0 ≤ s < n, ∀A ∈ ^; (9.5)
S
∗
s,e
(A) = max
A→B C∈P
B
s<m<e
S
s,m,e
(A, B, C) + S
∗
s,m
(B) + S
∗
m,e
(C), 0 ≤ s < e ≤ n, ∀A ∈ ^.
The highest scoring tree has score max
A∈A
S
S
∗
0,n
(A). Using the arg max’s of the max’s in
9.3. DISCRIMINATIVE PARSING MODELS 133
the computation of S
∗
, we can backtrace the highest scoring tree itself. We assume that
score ties are broken in a predetermined way, say according to some lexicographic order of
the symbols.
9.3 Discriminative parsing models
We cast parsing as a structured classiﬁcation task, where we want to learn a function h :
A → ¸, where A is a set of sentences, and ¸ is a set of valid parse trees according to a
ﬁxed CFG grammar.
The functions we consider take the following linear discriminant form:
h
w
(x) = arg max
y
w
¯
f (x, y),
where w ∈ IR
d
and f is a basis function representation of a sentence and parse tree pair
f : A ¸ → IR
d
. We assume that the basis functions decompose with the CFG structure:
f (x, y) =
0≤s≤e≤n
f (x
s,e
, y
s,e
) +
0≤s≤m<e≤n
f (x
s,m,e
, y
s,m,e
),
where n is the length of the sentence x and x
s,e
and x
s,m,e
are the relevant subsets of
the sentence the basis functions depend on. To simplify notation, we introduce the set of
indices, (, which includes both spans and span triplets:
( = ¦(s, m) : 0 ≤ s ≤ e ≤ n¦ ∪ ¦(s, m, e) : 0 ≤ s ≤ m < e ≤ n¦.
Hence, f (x, y) =
c∈(
f (x
c
, y
c
).
Note that this class of discriminants includes PCFG models, where the basis func
tions consist of the counts of the productions used in the parse, and the parameters w are
the logprobabilities of those productions. For example, f could include functions which
identify the production used together with features of the words at positions s, m, e, and
neighboring positions in the sentence x (e.g. f(x
s,m,e
, y
s,m,e
) = 1I(y
s,m,e
= S, NP, VP) ∧
m
th
word(x) = was)). We could also include functions that identify the label of the span
134 CHAPTER 9. CONTEXT FREE GRAMMARS
from s to e together with features of the word (e.g. f(x
s,m
, y
s,m
) = 1I(y
s,m
= NP) ∧
s
th
word(x) = the)).
9.3.1 Maximum likelihood estimation
The traditional method of estimating the parameters of PCFGs assumes a generative model
that deﬁnes P(x, y) by assigning normalized probabilities to CFG productions. We then
maximize the joint loglikelihood
i
log P(x
(i)
, y
(i)
) (with some regularization). We com
pare to such a generative grammar of Collins [1999] in our experiments.
A alternative probabilistic approach is to estimate the parameters discriminatively by
maximizing conditional loglikelihood. For example, the maximumentropy approach [John
son, 2001] deﬁnes a conditional loglinear model:
P
w
(y [ x) =
1
Z
w
(x)
exp¦w
¯
f (x, y)¦,
where Z
w
(x) =
y
exp¦w
¯
f (x, y)¦, and maximizes the conditional loglikelihood of
the sample,
i
log P(y
(i)
[ y
(i)
), (with some regularization). The same assumption that
the basis functions decompose as sums of local functions over spans and productions is
typically made in such models. Hence, as in Markov networks, the gradient depends
on the expectations of the basis functions, which can be computed in O([T[n
3
) time by
dynamic programming algorithm called insideoutside, which is similar to the CKY al
gorithm. However, computing the expectations over trees is actually more expensive in
practice than ﬁnding the best tree for several reasons. CKY works entirely in the logspace,
while insideoutside needs to compute actual probabilities. Branchandprune techniques,
which save a lot of useless computation, are only applicable in CKY.
A typical method for ﬁnding the parameters is to use Conjugate Gradients or LBFGS
methods [Nocedal & Wright, 1999; Boyd & Vandenberghe, 2004], which repeatedly com
pute these expectations to calculate the gradient. Clark and Curran [2004] report experi
ments involving 479 iterations of training for one model, and 1550 iterations for another
using similar methods.
9.3. DISCRIMINATIVE PARSING MODELS 135
9.3.2 Maximum margin estimation
We assume that loss function also decomposes with the CFG structure:
(x, y, ˆ y) =
0≤s≤e≤n
(x
s,e
, y
s,e
, ˆ y
s,e
) +
0≤s≤m<e≤n
(x
s,m,e
, y
s,m,e
, ˆ y
s,m,e
) =
c∈(
(x
c
, y
c
, ˆ y
c
).
One approach would be to deﬁne (x
s,e
, y
s,e
, ˆ y
s,e
) = 1I(y
s,e
,= ˆ y
s,e
). This would lead to
(x, y, ˆ y) tracking the number of “constituent errors” in ˆ y. Another, more strict deﬁnition
would be to deﬁne (x
s,m,e
, y
s,m,e
, ˆ y
s,m,e
) = 1I(y
s,m,e
,= ˆ y
s,m,e
). This deﬁnition would lead
to (x, y, ˆ y) being the number of productions in ˆ y which are not seen in y. The constituent
loss function does not exactly correspond to the standard scoring metrics, such as F
1
or
crossing brackets, but shares the sensitivity to the number of differences between trees. We
have not thoroughly investigated the exact interplay between the various loss choices and
the various parsing metrics. We used the constituent loss in our experiments.
As in the maxmargin estimation for Markov networks, we can formulate an exponen
tial size QP:
min
1
2
[[w[[
2
+ C
i
ξ
i
(9.6)
s.t. w
¯
∆f
i
(y) ≥
i
(y) −ξ
i
∀i, y,
where ∆f
i
(y) = f (x
(i)
, y
(i)
) −f (x
(i)
, y), and
i
(y) = (x
(i)
, y
(i)
, y).
The dual of Eq. (9.6) (after normalizing by C) is given by:
max
i,y
α
i
(y)
i
(y) −
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,y
α
i
(y)∆f
i
(y)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
(9.7)
s.t.
y
α
i
(y) = 1, ∀i; α
i
(y) ≥ 0, ∀i, y.
Both of the above formulations are exponential (in the number of variables or con
straints) in the lengths (n
i
’s) of the sentences. But we can exploit the contextfree structure
of the basis functions and the loss to deﬁne a polynomialsize dual formulation in terms of
136 CHAPTER 9. CONTEXT FREE GRAMMARS
marginal variables µ
i
(y):
µ
i,s,e
(A) ≡
y:y
s,e
=A
α
i
(y), 0 ≤ s ≤ e ≤ n, ∀A ∈ ^;
µ
i,s,s
(D) ≡
y:y
s,s
=D
α
i
(y), 0 ≤ s ≤ e ≤ n, ∀D ∈ T ;
µ
i,s,m,e
(A, B, C) ≡
y:y
s,m,e
=(A,B,C)
α
i
(y), 0 ≤ s < m < e ≤ n, ∀A →B C ∈ T
B
,
µ
i,s,s,s+1
(A, D) ≡
y:y
s,s,s+1
=(A,D)
α
i
(y), 0 ≤ s < n, ∀A →D ∈ T
U
.
There are O([T
B
[n
3
i
+ [T
U
[n
i
) such variables for each sentence of length n
i
, instead of
exponentially many α
i
variables. We can now express the objective function in terms of
the marginals. Using these variables, the ﬁrst set of terms in the objective becomes:
i,y
α
i
(y)
i
(y) =
i,y
α
i
(y)
c∈(
(i)
i,c
(y
c
) =
i,c∈(
(i)
,y
c
µ
i,c
(y
c
)
i,c
(y
c
).
Similarly, the second set of terms (inside the 2norm) becomes:
i,y
α
i
(y)∆f
i
(y) =
i,y
α
i
(y)
c∈(
(i)
∆f
i,c
(y
c
) =
i,c∈(
(i)
,y
c
µ
i,c
(y
c
)∆f
i,c
(y
c
).
As in M
3
Ns, we must characterize the set of marginals µ that corresponds to valid
α. The constraints on µ are essentially based on the those that deﬁne ¸ in (9.19.4). In
addition, we require that the marginals over the root nodes, µ
i,0,n
i
(y
0,n
i
), sums to 1 over the
possible start symbols ^
S
.
9.3. DISCRIMINATIVE PARSING MODELS 137
Putting the pieces together, the factored dual is:
max
i,c∈(
(i)
µ
i,c
(y
c
)
i,c
(y
c
) + C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,c∈(
(i)
µ
i,c
(y
c
)∆f
i,c
(y
c
)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
(9.8)
s.t.
A∈A
S
µ
i,0,n
i
(A) = 1, ∀i; µ
i,c
(y
c
) ≥ 0; ∀i, ∀c ∈ (
(i)
;
µ
i,s,e
(A) =
A→B C∈P
B
s<m<e
µ
i,s,m,e
(A, B, C), ∀i, 0 ≤ s < e ≤ n
i
, ∀A ∈ ^;
µ
i,s,e
(A) =
B→A C∈P
B
0≤s
<s
µ
i,s
,s,e
(B, A, C)
+
B→C A∈P
B
e<e
≤n
i
µ
i,s,e,e
(B, C, A), ∀i, 0 ≤ s < e ≤ n
i
, ∀A ∈ ^;
µ
i,s,s+1
(A) =
A→D∈1
U
µ
i,s,s,s+1
(A, D), ∀i, 0 ≤ s < n
i
, ∀A ∈ ^;
µ
i,s,s
(D) =
A→D∈1
U
µ
i,s,s,s+1
(A, D), ∀i, 0 ≤ s < n
i
, ∀D ∈ T .
The constraints on µ is necessary, since they must correspond to marginals of a distri
bution over trees. They are also sufﬁcient:
Theorem 9.3.1 A set of marginals µ
i
(y) satisfying the constraints in Eq. (9.8) corresponds
to a valid distribution over the legal parse trees y ∈ ¸
(i)
. A consistent distribution α
i
(y)
is given by
α
i
(y) = µ
i,0,n
i
(y
0,n
i
)
0≤s≤m<e≤n
i
µ
i,s,m,e
(y
s,m,e
)
µ
i,s,e
(y
s,e
)
,
where 0/0 = 0 by convention.
Proof sketch: The proof follows from insideoutside probability relations [Manning &
Sch¨ utze, 1999]. The ﬁrst term is a valid distribution of starting symbols. Each
µ
i,s,m,e
(y
s,m,e
)
µ
i,s,e
(y
s,e
)
term for m > s corresponds to a conditional distribution over binary productions (y
s,e
→
y
s,m
y
m,e
) that are guaranteed to sum to 1 over split points m and possible productions.
Similarly, each
µ
i,s,s,s+1
(y
s,s,s+1
)
µ
i,s,s+1
(y
s,s+1
)
term for corresponds to a conditional distribution over
138 CHAPTER 9. CONTEXT FREE GRAMMARS
unary productions (y
s,s+1
→ y
s,s
) that are guaranteed to sum to 1 over possible produc
tions. Hence, we have deﬁned a kind of PCFG (where production probabilities depend on
the location of the symbol), which induces a valid distribution α
i
over trees. It straightfor
ward to verify that this distribution has marginals µ
i
.
9.4 Structured SMO for CFGs
We trained our maxmargin models using the Structured SMOalgorithmwith blockcoordinate
descent adopted from graphical models (see Sec. 6.1). The CKY algorithm computes sim
ilar maxmarginals in the course of computing the best tree as does Viterbi in Markov
networks.
´ v
i,c
(y
c
) = max
y∼y
c
[w
¯
f
i
(y) +
i
(y)], ´ α
i,c
(y
c
) = max
y∼y
c
α
i
(y).
We also deﬁne ´ v
i,c
(y
c
) = max
y
c
,=y
c
´ v
i,c
(y
t
c
) = max
y,∼y
c
[w
¯
f
i
(y) +
i
(y)]. Note that we
do not explicitly represent α
i
(y), but we can reconstruct the maximumentropy one from
the marginals µ
i
as in Theorem 9.3.1.
We again express the KKT conditions in terms of the maxmarginals for each span and
span triple c ∈ (
(i)
and its values y
c
:
´ α
i,c
(y
c
) = 0 ⇒ ´ v
i,c
(y
c
) ≤ ´ v
i,c
(y
c
); ´ α
i,c
(y
c
) > 0 ⇒ ´ v
i,c
(y
c
) ≥ ´ v
i,c
(y
c
). (9.9)
The algorithm cycles through the training sentences, runs CKY to compute the max
marginals and performs an SMO update on the violated constraints. We typically ﬁnd that
2040 iterations through the data are sufﬁcient for convergence in terms of the objective
function improvements.
9.5 Experiments
We used the Penn English Treebank for all of our experiments. We report results here for
each model and setting trained and tested on only the sentences of length ≤15 words. Aside
9.5. EXPERIMENTS 139
from the length restriction, we used the standard splits: sections 221 for training (9753
sentences), 22 for development (603 sentences), and 23 for ﬁnal testing (421 sentences).
As a baseline, we trained a CNF transformation of the unlexicalized model of Klein and
Manning [2003] on this data. The resulting grammar had 3975 nonterminal symbols and
contained two kinds of productions: binary nonterminal rewrites and tagword rewrites.
Unary rewrites were compiled into a single compound symbol, so for example a subject
gapped sentence would have label like S+VP. These symbols were expanded back into
their source unary chain before parses were evaluated. The scores for the binary rewrites
were estimated using unsmoothed relative frequency estimators. The tagging rewrites were
estimated with a smoothed model of P(w[t), also using the model from Klein and Manning
[2003]. In particular, Table 9.2 shows the performance of this model (GENERATIVE): 87.99
F
1
on the test set.
For the BASIC maxmargin model, we used exactly the same set of allowed rewrites
(and therefore the same set of candidate parses) as in the generative case, but estimated
their weights using the maxmargin formulation with a loss that counts the number of
wrong spans. Tagword production weights were ﬁxed to be the log of the generative
P(w[t) model. That is, the only change between GENERATIVE and BASIC is the use of the
discriminative maximummargin criterion in place of the generative maximum likelihood
one for learning production weights. This change alone results in a small improvement
(88.20 vs. 87.99 F
1
).
On top of the basic model, we ﬁrst added lexical features of each span; this gave a
LEXICAL model. For a span ¸s, e) of a sentence x, the base lexical features were:
◦ x
s
, the ﬁrst word in the span
◦ x
s−1
, the preceding adjacent word
◦ x
e−1
, the last word in the span
◦ x
e
, the following adjacent word
◦ ¸x
s−1
, x
s
)
◦ ¸x
e−1
, x
e
)
◦ x
s+1
for spans of length 3
140 CHAPTER 9. CONTEXT FREE GRAMMARS
Model P R F
1
GENERATIVE 87.70 88.06 87.88
BASIC 87.51 88.44 87.98
LEXICAL 88.15 88.62 88.39
LEXICAL+AUX 89.74 90.22 89.98
Table 9.1: Development set results of the various models when trained and tested on Penn
treebank sentences of length ≤ 15.
Model P R F
1
GENERATIVE 88.25 87.73 87.99
BASIC 88.08 88.31 88.20
LEXICAL 88.55 88.34 88.44
LEXICAL+AUX 89.14 89.10 89.12
COLLINS 99 89.18 88.20 88.69
Table 9.2: Test set results of the various models when trained and tested on Penn treebank
sentences of length ≤ 15.
These base features were conjoined with the span length for spans of length 3 and below,
since short spans have highly distinct behaviors (see the examples below). The features are
lexical in the sense than they allow speciﬁc words and word pairs to inﬂuence the parse
scores, but are distinct from traditional lexical features in several ways. First, there is no
notion of headword here, nor is there any modeling of wordtoword attachment. Rather,
these features pick up on lexical trends in constituent boundaries, for example the trend
that in the sentence The screen was a sea of red., the (length 2) span between the word was
and the word of is unlikely to be a constituent. These nonhead lexical features capture a
potentially very different source of constraint on tree structures than headargument pairs,
one having to do more with linear syntactic preferences than lexical selection. Regardless
of the relative merit of the two kinds of information, one clear advantage of the present
approach is that inference in the resulting model remains cubic (as opposed to O(n
5
)),
since the dynamic program need not track items with distinguished headwords. With the
addition of these features, the accuracy moved past the generative baseline, to 88.44.
9.5. EXPERIMENTS 141
As a concrete (and particularly clean) example of how these features can sway a de
cision, consider the sentence The Egyptian president said he would visit Libya today to
resume the talks. The generative model incorrectly considers Libya today to be a base NP.
However, this analysis is counter to the trend of today to be a oneword constituent. Two
features relevant to this trend are: (CONSTITUENT ∧ ﬁrstword = today ∧ length = 1) and
(CONSTITUENT ∧ lastword = today ∧ length = 1). These features represent the preference
of the word today for being the ﬁrst and last word in constituent spans of length 1.
1
In the
LEXICAL model, these features have quite large positive weights: 0.62 each. As a result,
this model makes this parse decision correctly.
Another kind of feature that can usefully be incorporated into the classiﬁcation process
is the output of other, auxiliary classiﬁers. For this kind of feature, one must take care
that its reliability on the training not be vastly greater than its reliability on the test set.
Otherwise, its weight will be artiﬁcially (and detrimentally) high. To ensure that such
features are as noisy on the training data as the test data, we split the training into two
folds. We then trained the auxiliary classiﬁers on each fold, and using their predictions as
features on the other fold. The auxiliary classiﬁers were then retrained on the entire training
set, and their predictions used as features on the development and test sets.
We used two such auxiliary classiﬁers, giving a prediction feature for each span (these
classiﬁers predicted only the presence or absence of a bracket over that span, not bracket
labels). The ﬁrst feature was the prediction of the generative baseline; this feature added
little information, but made the learning phase faster. The second feature was the output
of a ﬂat classiﬁer which was trained to predict whether single spans, in isolation, were
constituents or not, based on a bundle of features including the list above, but also the
following: the preceding, ﬁrst, last, and following tag in the span, pairs of tags such as
precedingﬁrst, lastfollowing, precedingfollowing, ﬁrstlast, and the entire tag sequence.
Tag features on the test sets were taken from a pretagging of the sentence by the tagger
described in [Toutanova et al., 2003].While the ﬂat classiﬁer alone was quite poor (P 78.77
/ R 63.94 / F
1
70.58), the resulting maxmargin model (LEXICAL+AUX) scored 89.12 F
1
.
To situate these numbers with respect to other models, the parser in [Collins, 1999],which
1
In this length 1 case, these are the same feature. Note also that the features are conjoined with only one
generic label class “constituent” rather than speciﬁc constituent types.
142 CHAPTER 9. CONTEXT FREE GRAMMARS
is generative, lexicalized, and intricately smoothed scores 88.69 over the same train/test
conﬁguration.
9.6 Related work
A number of recent papers have considered discriminative approaches for natural language
parsing [Johnson et al., 1999; Collins, 2000; Johnson, 2001; Geman & Johnson, 2002;
Miyao & Tsujii, 2002; Clark & Curran, 2004; Kaplan et al., 2004; Collins, 2004]. Broadly
speaking, these approaches fall into two categories, reranking and dynamic programming
approaches. In reranking methods [Johnson et al., 1999; Collins, 2000; Shen et al., 2003],
an initial parser is used to generate a number of candidate parses. A discriminative model
is then used to choose between these candidates. In dynamic programming methods, a
large number of candidate parse trees are represented compactly in a parse tree forest or
chart. Given sufﬁciently “local” features, the decoding and parameter estimation problems
can be solved using dynamic programming algorithms. For example, several approaches
[Johnson, 2001; Geman & Johnson, 2002; Miyao & Tsujii, 2002; Clark & Curran, 2004;
Kaplan et al., 2004] are based on conditional loglinear (maximum entropy) models, where
variants of the insideoutside algorithm can be used to efﬁciently calculate gradients of the
loglikelihood function, despite the exponential number of trees represented by the parse
forest.
The method we presented has several compelling advantages. Unlike reranking meth
ods, which consider only a prepruned selection of “good” parses, our method is an end
toend discriminative model over the full space of parses. This distinction can be very
signiﬁcant, as the set of nbest parses often does not contain the true parse. For example,
in the work of Collins [2000], 41% of the correct parses were not in the candidate pool of
∼30best parses. Unlike previous dynamic programming approaches, which were based on
maximum entropy estimation, our method incorporates an articulated loss function which
penalizes larger tree discrepancies more severely than smaller ones.
Moreover, the structured SMO we use requires only the calculation of Viterbi trees,
rather than expectations over all trees (for example using the insideoutside algorithm).
9.7. CONCLUSION 143
This allows a range of optimizations that prune the space of parses (without making ap
proximations) not possible for maximum likelihood approaches which must extract basis
function expectations from the entire set of parses. In our experiments, 2040 iterations
were generally required for convergence (except the BASIC model, which took about 100
iterations.)
9.7 Conclusion
We have presented a maximummargin approach to parsing, which allows a discriminative
SVMlike objective to be applied to the parsing problem. Our framework permits the use
of a rich variety of input features, while still decomposing in a way that exploits the shared
substructure of parse trees in the standard way.
It is worth considering the cost of this kind of method. At training time, discriminative
methods are inherently expensive, since they all involve iteratively checking current model
performance on the training set, which means parsing the training set (usually many times).
Generative approaches are vastly cheaper to train, since they must only collect counts from
the training set.
On the other hand, the maxmargin approach does have the potential to incorporate
many new kinds of features over the input, and the current feature set allows limited lexi
calization in cubic time, unlike other lexicalized models (including the Collins model which
it outperforms in the present limited experiments). This tradeoff between the complexity,
accuracy and efﬁciency of a parsing model is an important area of future research.
Chapter 10
Matchings
We address the problem of learning to match: given a set of input graphs and corresponding
matchings, ﬁnd a parameterized edge scoring function such that the correct matchings have
the highest score. Bipartite matchings are used in many ﬁelds, for example, to ﬁnd marker
correspondences in vision problems, to map words of a sentence in one language to another,
to identify functional genetic analogues in different organisms. We have shown a compact
maxmargin formulation for bipartite matchings in Ch. 4. In this chapter, we focus on a
more complex problem of nonbipartite matchings. We motivate this problem using an
application in computational biology, disulﬁde connectivity prediction, but nonbipartite
matchings can be used for many other tasks.
Identifying disulﬁde bridges formed by cysteine residues is critical in determining the
structure of proteins. Recently proposed models have formulated this prediction task as a
maximum weight perfect matching problem in a graph containing cysteines as nodes with
edge weights measuring the attraction strength of the potential bridges. We exploit combi
natorial properties of the perfect matching problem to deﬁne a compact, convex, quadratic
program. We use kernels to efﬁciently learn very rich (infact, inﬁnitedimensional) mod
els and present experiments on standard protein databases, showing that our framework
achieves stateoftheart performance on the task.
Throughout this chapter, we use the problem of disulﬁde connectivity prediction as an
example. We provide some background on this problem.
144
10.1. DISULFIDE CONNECTIVITY PREDICTION 145
10.1 Disulﬁde connectivity prediction
Proteins containing cysteine residues form intrachain covalent bonds known as disulﬁde
bridges. Such bonds are a very important feature of protein structure since they enhance
conformational stability by reducing the number of conﬁgurational states and decreasing
the entropic cost of folding a protein into its native state [Matsumura et al., 1989]. They do
so mostly by imposing strict structural constraints due to the resulting links between distant
regions of the protein sequence [Harrison & Sternberg, 1994].
Knowledge of the exact disulﬁde bonding pattern in a protein provides information
about protein structure and possibly its function and evolution. Furthermore, since the
disulﬁde connectivity pattern imposes structure constraints, it can be used to reduce the
search space in both protein folding prediction as well as protein 3D structure prediction.
Thus, the development of efﬁcient, scalable and accurate methods for the prediction of
disulﬁde bonds has numerous practical applications.
Recently, there has been increased interest in applying computational techniques to
the task of predicting the intrachain disulﬁde connectivity [Fariselli & Casadio, 2001;
Fariselli et al., 2002; Vullo & Frasconi, 2004; Klepeis & Floudas, 2003; Baldi et al., 2004].
Since a sequence may contain any number of cysteine residues, which may or may not
participate in disulﬁde bonds, the task of predicting the connectivity pattern is typically
decomposed into two subproblems: predicting the bonding state of each cysteine in the
sequence, and predicting the exact connectivity among bonded cysteines. Alternatively,
there are methods [Baldi et al., 2004] that predict the connectivity pattern without knowing
the bonding state of each cysteine
1
.
We predict the connectivity pattern by ﬁnding the maximum weighted matching in a
graph in which each vertex represents a cysteine residue, and each edge represents the
“attraction strength” between the cysteines it connects [Fariselli & Casadio, 2001]. We
parameterize the this attraction strength via a linear combination of features, which can
include the protein sequence around the two residues, evolutionary information in the form
of multiple alignment proﬁles, secondary structure or solvent accessibility information, etc.
1
We thank Pierre Baldi and Jianlin Cheng for introducing us to the problem of disulﬁde connectivity
prediction and providing us with preliminary draft of their paper and results of their model, as well as the
protein datasets.
146 CHAPTER 10. MATCHINGS
10.2 Learning to match
Formally, we seek a function h : A → ¸ that maps inputs x ∈ A to output matchings
y ∈ ¸, for example, A is the space of protein sequences and ¸ is the space of matchings
of their cysteines. The space of matchings ¸ is very large, in fact, superexponential in
the number of nodes in a graph. However, ¸ has interesting and complex combinatorial
structure which we exploit to learn h efﬁciently.
The training data consists of m examples S = ¦(x
(i)
, y
(i)
)¦
m
i=1
of input graphs and
output matchings. We assume that the input x deﬁnes the space of possible matchings
using some deterministic procedure. For example, given a protein sequence, we construct
a complete graph where each node corresponds to a cysteine. We represent each possible
edge between nodes j and k (j < k) in example i using a binary variable y
(i)
jk
. For simplicity,
we assume complete graphs, but very little needs to be changed to handle sparse graphs.
If example i has L
i
nodes, then there are L
i
(L
i
− 1)/2 edge variables, so y
(i)
is a
binary vector of dimension L
i
(L
i
− 1)/2. In a perfect matching, each node is connected
exactly one other node. In nonperfect matchings, each node is connected to at most one
other node. Let n
i
= L
i
/2, then for complete graphs with even number of vertices L
i
, the
number of possible perfect matchings is
(2n
i
)!
2
n
i n
i
!
(which is Ω((
n
i
2
)
n
i
), superexponential in
n
i
). For example, 1ANS protein in Fig. 10.1 has 6 cysteines (nodes), 15 potential bonds
(edges) and 15 possible perfect matchings.
Our hypothesis class is maximum weight matchings:
h
s
(x) = arg max
y∈¸
jk
s
jk
(x)y
jk
, (10.1)
For disulﬁde connectivity prediction, this model was used by Fariselli and Casadio [2001].
Their model assigns an attraction strength s
jk
(x) to each pair of cysteines, calculated by
assuming that all residues in the local neighborhoods of the two cysteines make contact,
and summing contact potentials for pairs of residues. We consider a simple but very general
class of attraction scoring functions deﬁned by a weighted combination of features or basis
functions:
s
jk
(x) =
d
w
d
f
d
(x
jk
) = w
¯
f (x
jk
), (10.2)
10.2. LEARNING TO MATCH 147
1
2 3
4
5 6
1
2 3
4
5 6
RSCCPCYWGGCPWGQNCYPEGCSGPKV
1234 56
Figure 10.1: PDB protein 1ANS: amino acid sequence, 3D structure, and graph of potential
disulﬁde bonds. Actual disulﬁde connectivity is shown in yellow in the 3D model and the
graph of potential bonds.
where x
jk
is the portion of the input x that directly relates to nodes j and k, f
d
(x
jk
) is
a realvalued basis function and w
d
∈ IR. For example, the basis functions can represent
arbitrary information about the two cysteine neighborhoods: the identity of the residues
at speciﬁc positions around the two cysteines, or the predicted secondary structure in the
neighborhood of each cysteine. We assume that the user provides the basis functions, and
that our goal is to learn the weights w, for the model:
h
w
(x) = arg max
y∈¸
jk
w
¯
f (x
jk
)y
jk
. (10.3)
Below, we will abbreviate w
¯
f (x, y) ≡
jk
w
¯
f (x
jk
)y
jk
, and w
¯
f
i
(y) ≡ w
¯
f (x
(i)
, y),
The naive formulation of the maxmargin estimation, which enumerates all perfect
matchings for each example i, is:
min
1
2
[[w[[
2
s.t. w
¯
f
i
(y
(i)
) ≥ w
¯
f
i
(y) +
i
(y), ∀i, ∀y ∈ ¸
(i)
. (10.4)
The number of constraints in this formulation is superexponential in the number of nodes
in each example. In the following sections we present two maxmargin formulations,
ﬁrst with an exponential set of constraints (Sec. 10.3), and then with a polynomial one
(Sec. 10.4).
148 CHAPTER 10. MATCHINGS
10.3 Minmax formulation
Using the minmax formulation from Ch. 4, we have a single max constraint for each i:
min
1
2
[[w[[
2
s.t. w
¯
f
i
(y
(i)
) ≥ max
y∈¸
(i)
[w
¯
f
i
(y) +
i
(y)], ∀i. (10.5)
The key to solving this problem efﬁciently is the lossaugmented inference
max
y∈¸
(i) [w
¯
f
i
(y) +
i
(y)]. Under the assumption of Hamming distance loss (or any loss
function that can be written as a sum of terms corresponding to edges), this maximization
is equivalent (up to a constant term) to a maximum weighted matching problem. Note that
since the y variables are binary, the Hamming distance between y
(i)
and y can be written
as (1 − y)
¯
y
(i)
+ (1 − y
(i)
)
¯
y = 1
¯
y
(i)
+ (1 − 2y
(i)
)
¯
y. Hence, the maximum weight
matching where edge jk has weight w
¯
f (x
(i)
jk
)+(1−2y
(i)
jk
) (plus the constant 1
¯
y
(i)
) gives
the value of max
y∈¸
(i) [w
¯
f
i
(y) +
i
(y)].
This problem can be solved in O(L
3
) time [Gabow, 1973; Lawler, 1976]. It can also be
solved as a linear program, where we introduce continuous variables µ
i,jk
instead of binary
variables y
(i)
jk
.
max
jk
µ
i,jk
[w
¯
f (x
(i)
jk
) + (1 −2y
(i)
jk
)] (10.6)
s.t. µ
i,jk
≥ 0, 1 ≤ j < k ≤ L
i
;
k
µ
i,jk
≤ 1, 1 ≤ j ≤ L
i
;
j,k∈V
µ
i,jk
≤
1
2
([V [ −1), V ⊆ ¦1, . . . , L
i
¦, [V [ ≥ 3 and odd.
The constraints
k
µ
i,jk
≤ 1 require that the number of bonds incident on a node is less
or equal to one. For perfect matchings, these constraints are changed to
k
µ
i,jk
= 1 to
ensure exactly one bond. The subset constraints (in the last line of Eq. (10.6)) ensure that
solutions to the LP are integral [Edmonds, 1965]. Note that we have an exponential number
of constraints (O(2
(L
i
−1)
)), but this number is asymptotically smaller than the number of
possible matchings . It is an open problem to derive a polynomial sized LP formulation for
perfect matchings [Schrijver, 2003].
10.3. MINMAX FORMULATION 149
We can write the lossaugmented inference problem in terms of the LP in Eq. (10.6):
max
y∈¸
(i)
[w
¯
f
i
(y) +
i
(y)] = d
i
+ max
A
i
µ
i
≤b
i
µ
i
≥0
µ
¯
i
[F
i
w+c
i
],
where: d
i
= 1
¯
y
(i)
; µ
i
is a vector of length L
i
(L
i
− 1)/2 indexed by bond jk; A
i
and b
i
are the appropriate constraint coefﬁcient matrix and right hand side vector, respectively. F
i
is a matrix of basis function coefﬁcients such that the component jk of the vector F
i
w is
w
¯
f (x
(i)
jk
) and c
i
= (1 − 2y
(i)
). Note that the dependence on w is linear and occurs only
in the objective of the LP.
The dual of the LP in Eq. (10.6) is
min λ
¯
i
b
i
s.t. A
¯
i
λ
i
≥ F
i
w+c
i
; λ
i
≥ 0. (10.7)
We plug it into Eq. (10.5) and combine the minimization over λ with minimization over w.
min
1
2
[[w[[
2
(10.8)
s.t. w
¯
f
i
(y
(i)
) ≥ d
i
+ λ
¯
i
b
i
, ∀i;
A
¯
i
λ
i
≥ F
i
w+c
i
, ∀i;
λ
i
≥ 0, ∀i.
In case that our basis functions are not rich enough to predict the training data perfectly,
we can introduce a slack variable ξ
i
for each example i to allow violations of the constraints
and minimize the sum of the violations:
min
1
2
[[w[[
2
+ C
i
ξ
i
(10.9)
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥ d
i
+ λ
¯
i
b
i
, ∀i;
A
¯
i
λ
i
≥ F
i
w+c
i
, ∀i;
λ
i
≥ 0, ∀i; ξ
i
≥ 0, ∀i.
The parameter C allows the user to trade off violations of the constraints with ﬁt to the
150 CHAPTER 10. MATCHINGS
0
5
10
15
20
25
30
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
NumberofBonds
L
o
g

N
u
m
b
e
r
o
f
C
o
n
s
t
r
a
i
n
t
s
PerfectMatchings
Minmax
Certificate
Figure 10.2: Log of the number of QP constraints (yaxis) vs. number of bonds (xaxis) in
the three formulations (perfect matching enumeration, minmax and certiﬁcate).
data.
Our formulation is a linearlyconstrained quadratic program, albeit with an exponen
tial number of constraints. In the next section, we develop an equivalent polynomial size
formulation.
10.4 Certiﬁcate formulation
Rather than solving the lossaugmented inference problem explicitly, we can focus on ﬁnd
ing a compact certiﬁcate of optimality that guarantees that y
(i)
= arg max
y
[w
¯
f
i
(y) +
i
(y)]. We consider perfect matchings and then provide a reduction for the nonperfect
case. Let M be a perfect matching for a complete undirected graph G = (V, E). In an
alternating cycle/path in G with respect to M, the edges alternate between those that be
long to M and those that do not. An alternating cycle is augmenting with respect to M if
the score of the edges in the matching M is smaller that the score of the edges not in the
matching M.
Theorem 10.4.1 [Edmonds, 1965] A perfect matching M is a maximum weight perfect
matching if and only if there are no augmenting alternating cycles.
10.4. CERTIFICATE FORMULATION 151
The number of alternating cycles is exponential in the number of vertices, so simply enu
merating all of them will not do. Instead, we can rule out such cycles by considering
shortest paths.
We begin by negating the score of those edges not in M. In the discussion below we
assume that each edge score s
jk
has been modiﬁed this way. We also refer to the score s
jk
as the length of the edge jk. An alternating cycle is augmenting if and only if its length is
negative. A condition ruling out negative length alternating cycles can be stated succinctly
using a kind of distance function. Pick an arbitrary root node r. Let d
e
j
, with j ∈ V ,
e ∈ ¦0, 1¦, denote the length of the shortest distance alternating path from r to j, where
e = 1 if the last edge of the path is in M, 0 otherwise. These shortest distances are well
deﬁned if and only if there are no negative alternating cycles. The following constraints
capture this distance function.
s
jk
≥ d
0
k
−d
1
j
, s
jk
≥ d
0
j
−d
1
k
, ∀ jk / ∈ M; (10.10)
s
jk
≥ d
1
k
−d
0
j
, s
jk
≥ d
1
j
−d
0
k
, ∀ jk ∈ M.
Theorem 10.4.2 There exists a distance function ¦d
e
j
¦ satisfying the constraints in
Eq. (10.10) if and only if no augmenting alternating cycles exist.
Proof.
(If) Suppose there are no augmenting alternating cycles. Since any alternating paths
from r to j can be shortened (or left the same length) by removing the cycles they contain,
the two shortest paths to j (one ending with Medge and one not) contain no cycles. Then
let d
0
j
and d
1
j
be the length of those paths, for all j (for j = r, set d
0
r
= d
1
r
= 0). Then for
any jk (or kj) in M, the shortest path to j ending with an edge not in M plus the edge jk
(or kj) is an alternating path to k ending with an edge in M. This path is longer or same
length as the shortest path to k ending with an edge in M: s
jk
+d
0
j
≥ d
1
k
(or s
kj
+d
0
j
≥ d
1
k
),
so the constraint is satisﬁed. Similarly for jk, kj / ∈ M.
(Only if) Suppose a distance function ¦d
e
j
¦ satisﬁes the constraints in Eq. (10.10). Con
sider an alternating cycle C. We renumber the nodes such that the cycle passes through
nodes 1, 2, . . . , l and the ﬁrst edge, (1, 2), is in M. The length of the path is s(C) =
s
1,l
+
l−1
j=1
s
j,j+1
. For each odd j, the edge (j, j + 1) is in M, so s
j,j+1
≥ d
1
j+1
−d
0
j
. For
152 CHAPTER 10. MATCHINGS
even j, the edge (j, j + 1) is not in M, so s
j,j+1
≥ d
0
j+1
−d
1
j
. Finally, the last edge, (1, l),
is not in M, so s
1,l
≥ d
0
1
−d
1
l
. Summing the edges, we have:
s(C) ≥ d
0
1
−d
1
l
+
l−1
j=1,odd
[d
1
j+1
−d
0
j
] +
l−1
j=2,even
[d
0
j+1
−d
1
j
] = 0.
Hence all alternating cycles have nonnegative length.
In our learning formulation we have the lossaugmented edge weights s
(i)
jk
= (2y
(i)
jk
−
1)(w
¯
f (x
jk
)+1−2y
(i)
jk
). Let d
i
be a vector of distance variables d
e
j
, H
i
and G
i
be matrices
of coefﬁcients and q
i
be a vector such that H
i
w + G
i
d
i
≥ q
i
represents the constraints
in Eq. (10.10) for example i. Then the following joint convex programin wand d computes
the maxmargin parameters:
min
1
2
[[w[[
2
(10.11)
s.t. H
i
w+G
i
d
i
≥ q
i
, ∀i.
Once again, in case that our basis functions are not rich enough to predict the training data
perfectly, we can introduce a slack variable vector ξ
i
to allow violations of the constraints.
The case of nonperfect matchings can be handled by a reduction to perfect matchings
as follows [Schrijver, 2003]. We create a new graph by making a copy of the nodes and
the edges and adding edges between each node and the corresponding node in the copy.
We extend the matching by replicating its edges in the copy and for each unmatched node,
introduce an edge to its copy. We deﬁne f (x
jk
) ≡ 0 for edges between the original and
the copy. Perfect matchings in this graph projected onto the original graph correspond to
nonperfect matchings in the original graph.
The comparison between the lognumber of constraints for our three equivalent QP
formulations (enumeration of all perfect matchings, minmax and certiﬁcate) is shown
in Fig. 10.2. The xaxis is the number of edges in the matching (number of nodes divided
by two).
10.5. KERNELS 153
10.5 Kernels
Instead of directly optimizing the primal problem in Eq. (10.8), we can work with its dual.
Each training example i has L
i
(L
i
− 1)/2 dual variables, and α
(i)
jk
is the dual variable
associated with the features corresponding to the edge jk. Let α
(i)
be the vector of dual
variables for example i. The dual quadratic optimization problem has the form:
max
i
c
¯
i
α
(i)
−
1
2
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i
jk∈E
(i)
__
Cy
(i)
jk
−α
(i)
jk
_
f (x
(i)
jk
)
_
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
(10.12)
s.t. A
i
α
(i)
≤ Cb
i
, ∀i.
α
(i)
≥ 0, ∀i.
The only occurrence of feature vectors is in the expansion of the squarednorm term in the
objective:
i,j
kl∈E
(i)
mn∈E
(j)
_
Cy
(i)
jk
−α
(i)
jk
_
f (x
(i)
kl
)
¯
f (x
(j)
mn
)
_
Cy
(j)
jk
−α
(j)
jk
_
(10.13)
Therefore, we can apply the kernel trick and let f (x
(i)
kl
)
¯
f (x
(j)
mn
) = K(x
(i)
kl
, x
(j)
mn
). Thus, we
can efﬁciently map the original features f (x
jk
) to a highdimensional space. The primal
and dual solutions are related by:
w =
i
jk
(Cy
(i)
jk
−α
(i)
jk
)f (x
(i)
jk
) (10.14)
Eq. (10.14) can be used to compute the attraction strength s
jk
(x) in a kernelized manner at
prediction time. The polynomialsized representation in Eq. (10.11) is similarly kerneliz
able.
154 CHAPTER 10. MATCHINGS
10.6 Experiments
We assess the performance of our method on two datasets containing sequences with ex
perimentally veriﬁed bonding patterns: DIPRO2 and SP39. The DIPRO2 dataset
2
was
compiled and made publicly available by Baldi et al. [2004]. It consists of all proteins
from PDB [Berman et al., 2000], as of May 2004, which contain intrachain disulﬁde
bonds. After redundance reduction there are a total of 1018 sequences. In addition, the
sequences are annotated with secondary structure and solvent accessibility information de
rived from the DSSP database [Kabsch & Sander, 1983]. The SP39 dataset is extracted
from the SwissProt database of proteins [Bairoch & Apweiler, 2000], release 39. It con
tains only sequences with experimentally veriﬁed disulﬁde bridges, and has a total of 726
proteins. The same dataset was used in earlier work [Baldi et al., 2004; Vullo & Frasconi,
2004; Fariselli & Casadio, 2001], and we have followed the same procedure for extracting
sequences from the database.
Even though our method is applicable to both sequences with a high number of bonds
or sequences in which the bonding state of cysteine residues is unknown, we report results
for the case where the bonding state is known, and the number of bonds is between 2 and
5 (since the case of 1 bond is trivial). The DIPRO2 contains 567 such sequences, and only
53 sequences with a higher number of bonds, so we are able to perform learning on over
90% of all proteins. There are 430 proteins with 2 and 3 bonds and 137 with 4 and 5 bonds.
SP39 contains 446 sequences containing between 2 and 5 bonds.
In order to avoid biases during testing, we adopt the same dataset splitting procedure
as the one used in previous work [Fariselli & Casadio, 2001; Vullo & Frasconi, 2004;
Baldi et al., 2004]. We split SP39 into 4 different subsets, with the constraint that pro
teins no proteins with sequence similarity of more than 30% belong to different subsets.
Sequence similarity was derived using an allagainstall rigorous SmithWaterman local
pairwise alignment [Smith & Waterman, 1981] (with the BLOSUM65 scoring matrix, gap
penalty 12 and gap extension 4). Pairs of chains whose alignment is less than 30 residues
were considered unrelated. The DIPRO2 dataset was split similarly into 5 folds, although
the procedure had less effect due to the redundance reduction applied by the authors of the
2
http://contact.ics.uci.edu/bridge.html
10.6. EXPERIMENTS 155
dataset.
Models
The experimental results we report use the dual formulation of Sec. 10.5 and an RBF kernel
K(x
jk
, x
lm
) = exp(
x
jk
−x
lm

2
γ
), with γ ∈ [0.1, 10]. We use the exponential sized represen
tation of Sec. 10.3 since for the case of proteins containing between two and ﬁve bonds, it
is more efﬁcient due to the low constants in the exponential problem size. We used com
mercial QP software (CPLEX) to train our models. Training time took around 70 minutes
for 450 examples, using a sequential optimization procedure which solves QP subproblems
associated with blocks of training examples. We are currently working on an implemen
tation of the certiﬁcate formulation Sec. 10.4 to handle longer sequences and nonperfect
matchings (when bonding state is unknown). Below, we describe several models we used.
The features we experimented with were all based on the local regions around candidate
cysteine pairs. For each pair of candidate cysteines ¦j, k¦, where j < k, we extract the
aminoacid sequence in windows of size n centered at j and k. As in Baldi et al. [2004],
we augment the features of each model with the number of residues between j and k. The
models below use windows of size n = 9.
The ﬁrst model, SEQUENCE, uses the features described above: for each window, the
actual sequence is expanded to a 20 n binary vector, in which the entries denote whether
or not a particular amino acid occurs at the particular position. For example, the 21st entry
in the vector represents whether or not the aminoacid Alanine occurs at position 2 of the
local window, counting from the left end of the window. The ﬁnal set of features for each
¦j, k¦ pair of cysteines is simply the two local windows concatenated together, augmented
with the linear distance between the cysteine residues.
The second model, PROFILE, is the same as SEQUENCE, except that instead of us
ing the actual protein sequence, we use multiple sequence alignment proﬁle information.
Multiple alignments were computed by running PSIBLAST using default settings to align
the sequence with all sequences in the NR database [Altschul et al., 1997]. Thus, the in
put at each position of a local window is the frequency of occurrence of each of the 20
aminoacids in the alignments.
156 CHAPTER 10. MATCHINGS
K PROFILE DAGRNN
2 0.75 / 0.75 0.74 / 0.74
3 0.60 / 0.48 0.61 / 0.51
4 0.46 / 0.24 0.44 / 0.27
5 0.43 / 0.16 0.41 / 0.11
K SEQUENCE PROFILE PROFILESS
2 0.70 / 0.70 0.73 / 0.73 0.79 / 0.79
3 0.62 / 0.52 0.67 / 0.59 0.74 / 0.69
4 0.44 / 0.21 0.59 / 0.44 0.70 / 0.56
5 0.29 / 0.06 0.43 / 0.17 0.62 / 0.27
(a) (b)
Table 10.1: Numbers indicate Precision / Accuracy. (a) Performance of PROFILE model
on SP39 vs. preliminary results of the DAGRNN model [Baldi et al., 2004] which repre
sent the best currently published results. In each row, the best performance is in bold. (b)
Performance of SEQUENCE, PROFILE, PROFILESS models on the DIPRO2 dataset.
The third model, PROFILESS, augments the PROFILE model with secondary structure
and solventaccessibility information. The DSSP program produces 8 types of secondary
structure, so we augment each local window of size n with an additional length 8 n
binary vector, as well as a length n binary vector representing the solvent accessibility at
each position.
Results and discussion
We evaluate our algorithm using two metrics: accuracy and precision. The accuracy mea
sure counts how many full connectivity patterns were predicted correctly, whereas preci
sion measures the number of correctly predicted bonds as a fraction of the total number of
possible bonds.
The ﬁrst set of experiments compares our model to preliminary results reported in Baldi
et al. [2004], which represent the current topperforming system. We perform 4fold cross
validation on SP39 in order to replicate their setup. As Table 10.1 shows, the PROFILE
model achieves comparable results, with similar or better levels of precision for all bond
numbers, and slightly lower accuracies for the case of 2 and 3 bonds.
In another experiment, we show the performance gained by using multiple alignment
information by comparing the results of the SEQUENCE model with the PROFILE. As we
can see from Table 10.1(b), the evolutionary information captured by the aminoacid align
ment frequencies plays an important role in increasing the performance of the algorithm.
10.7. RELATED WORK 157
2 and 3 bonds
20%
30%
40%
50%
60%
70%
80%
90%
100%
100 150 200 250 300 350 400 450
Training Set Size
Accuracy (2 Bonds)
Precision (3 Bonds)
Accuracy (3 Bonds)
4 and 5 bonds
5%
15%
25%
35%
45%
55%
65%
75%
85%
100 150 200 250 300 350 400 450
Training Set Size
Precision (4 Bonds)
Accuracy (4 Bonds)
Precision (5 Bonds)
Accuracy (5 Bonds)
(a) (b)
Figure 10.3: Performance of PROFILE model as training set size changes for proteins with
(a) 2 and 3 bonds (b) 4 and 5 bonds.
The same phenomenon is observed by Vullo and Frasconi [2004] in their comparison of
sequence and proﬁlebased models.
As a ﬁnal experiment, we examine the role that secondary structure and solventaccessibility
information plays in the model PROFILESS. Table 10.1(b) shows that the gains are sig
niﬁcant, especially for sequences with 3 and 4 bonds. This highlights the importance of
developing even richer features, perhaps through more complex kernels.
Fig. 10.3 shows the performance of the PROFILE model as training set size grows. We
can see that for sequences of all bond numbers, both accuracy and precision increase as the
amount of data grows. The trend is more pronounced for sequences with 4 and 5 bonds
because they are sparsely distributed in the dataset. Such behavior is very promising, since
it validates the applicability of our algorithm as the availability of highquality disulﬁde
bridge annotations increases with time.
10.7 Related work
The problem of inverse perfect matching has been studied by Liu and Zhang [2003] in
the inverse combinatorial optimization framework we describe in Sec. 4.3: Given a set of
nominal weights w
0
and a perfect matching M, which is not a maximum one with respect
to w
0
, ﬁnd a new weight vector w that makes M optimal and minimizes [[w
0
− w[[
p
for p = 1, ∞. They do not provide a compact optimization problem for this related but
158 CHAPTER 10. MATCHINGS
different task, relying instead on the ellipsoid method with constraint generation.
The problem of disulﬁde bond prediction ﬁrst received comprehensive computational
treatment in Fariselli and Casadio [2001]. They modeled the prediction problem as ﬁnding
a perfect matching in a weighted graph where vertices represent bonded cysteine residues,
and edge weights correspond to attraction strength. The problem of learning the edge
weights was addressed using a simulated annealing procedure. Their method is only ap
plicable to the case when bonding state is known. In Fariselli et al. [2002], the authors
switch to using a neural network for learning edge weights and achieve better performance,
especially for the case of 2 and 3 disulﬁde bonds.
The method in Vullo and Frasconi [2004] takes a different approach to the problem. It
scores candidate connectivity patterns according to their similarity with respect to the cor
rect pattern, and uses a recursive neural network architecture [Frasconi et al., 1998] to score
candidate patterns. At prediction time the pattern scores are used to perform an exhaustive
search on the space of all matchings. The method is computationally limited to sequences
of 2 to 5 bonds. It also uses multiple alignment proﬁle information and demonstrates its
beneﬁts over sequence information.
In Baldi et al. [2004], the authors achieve the current stateoftheart performance on
the task. Their method uses Directed Acyclic Graph Recursive Neural Networks [Baldi
& Pollastri, 2003] to predict bonding probabilities between cysteine pairs. The prediction
problem is solved using a weighted graph matching based on these probabilities. Their
method performs better than the one in Vullo and Frasconi [2004] and is also the only
one which can cope with sequences with more than 5 bonds. It also improves on previous
methods by not assuming knowledge of bonding state.
A different approach to predicting disulﬁde bridges is reported in Klepeis and Floudas
[2003], where bond prediction occurs as part of predicting βsheet topology in proteins.
Residuetoresidue contacts (which include disulphide bridges) are predicted by solving a
series of constrained integer programming problems. Interestingly, the approach can be
used to predict disulﬁde bonds with no knowledge of bonding state, but the results are not
comparable with those in other publications.
The task of predicting whether or not a cysteine is bonded has also been addressed using
a variety of machine learning techniques including neural networks, SVMs, and HMMs
10.8. CONCLUSION 159
[Fariselli et al., 1999; Fiser & Simon, 2000; Martelli et al., 2002; Frasconi et al., 2002;
Ceroni et al., 2003] Currently the top performing systems have accuracies around 85%.
10.8 Conclusion
In this chapter, we derive a compact convex quadratic program for the problem of learning
to match. Our approach learns a parameterized scoring function that reproduces the ob
served matchings in a training set. We present two formulations: one which is based on a
linear programming approach to matching, requiring an exponential number of constraints,
and one which develops a certiﬁcate of matching optimality for a compact polynomialsized
representation. We apply our framework to the task of disulﬁde connectivity prediction, for
mulated as a weighted matching problem. Our experimental results show that the method
can achieve performance comparable to current topperforming systems. Furthermore, the
use of kernels makes it easy to incorporate rich sets of features such as secondary structure
information, or extended local neighborhoods of the protein sequence. In the future, it will
be worthwhile to examine how other kernels, such as convolution kernels for protein se
quences, will affect performance. We also hope to explore the more challenging problem
of disulﬁde connectivity prediction when the bonding state of cysteines is unknown. While
we have developed the framework to handle that task, it remains to experimentally deter
mine how well the method performs, especially in comparison to existing methods [Baldi
et al., 2004], which have already addressed the more challenging setting.
Chapter 11
Correlation clustering
Data can often be grouped in many different reasonable clusterings. For example, one user
may organize her email messages by project and time, another by sender and topic. Images
can be segmented by hue or object boundaries. For a given application, there might be
only one of these clusterings that is desirable. Learning to cluster considers the problem of
ﬁnding desirable clusterings on new data, given example desirable clusterings on training
data.
We focus on correlation clustering, a novel clustering method that has recently en
joyed signiﬁcant attention from the theoretical computer science community [Bansal et al.,
2002; Demaine & Immorlica, 2003; Emanuel & Fiat, 2003]. It is formulated as a vertex
partitioning problem: Given a graph with realvalued edge scores (both positive and neg
ative), partition the vertices into clusters to maximize the score of intracluster edges, and
minimize the weight of intercluster edges. Positive edge weights represent correlations be
tween vertices, encouraging those vertices to belong to a common cluster; negative weights
encourage the vertices to belong to different clusters. Unlike most clustering formulations,
correlation clustering does not require the user to specify the number of clusters nor a dis
tance threshold for clustering; both of these parameters are effectively chosen to be the best
possible by the problem deﬁnition. These properties make correlation clustering a promis
ing approach to many clustering problems; in machine learning, it has been successfully
applied to coreference resolution for proper nouns [McCallum & Wellner, 2003].
Recently, several algorithms based on linear programming and positivesemideﬁnite
160
11.1. CLUSTERING FORMULATION 161
programming relaxations have been proposed to approximately solve this problem. In this
chapter, we employ these relaxations to derive a maxmargin formulation for learning the
edge scores for correlation clustering from clustered training data. We formulate the ap
proximate learning problem as a compact convex program with quadratic objective and
linear or positivesemideﬁnite constraints. Experiments on synthetic and realworld data
show the ability of the algorithm to learn an appropriate clustering metric for a variety of
desired clusterings.
11.1 Clustering formulation
An instance of correlation clustering is speciﬁed by an undirected graph ( = (1, c) with
N nodes and edge score s
jk
for each jk in c, (j < k). We assume that the graph is fully
connected (if it is not, we can make it fully connected by adding appropriate edges jk with
s
jk
= 0). We deﬁne binary variables y
jk
, one for each edge jk, that represent whether node
j and k belong to the same cluster. Let ¸ be the space of assignments y that deﬁne legal
partitions. For notational convenience, we introduce both y
jk
and y
kj
variables, which will
be constrained to have the same value. We also introduce y
jj
variables, and ﬁx them to
have value 1 and set s
jj
= 0.
Bansal et al. [2002] consider two related problems:
max
y∈¸
jk:s
jk
>0
s
jk
y
jk
−
jk:s
jk
<0
s
jk
(1 −y
jk
); (MAXAGREE)
min
y∈¸
jk:s
jk
>0
s
jk
(1 −y
jk
) −
jk:s
jk
<0
s
jk
y
jk
; (MINDISAGREE)
The motivation for the names of the two problems comes from separating the set of edges
into positive weight edges and negative weight edges. The best score is obviously achieved
by including all the positive and excluding all the negative edges, but this will not generally
produce a valid partition. In MAXAGREE, we maximize the “agreement” of the partition
with the positive/negative designations: the weight of the positive included edges minus
the weight of negative excluded edges. In MINDISAGREE, we minimize the disagreement:
the weight of positive excluded edges minus the weight of negative included edges. In
162 CHAPTER 11. CORRELATION CLUSTERING
particular, let
s
∗
= max
y∈¸
s
jk
y
jk
; s
−
=
jk:s
jk
<0
s
jk
; s
+
=
jk:s
jk
>0
s
jk
.
Then the value of MAXAGREE is s
∗
− s
−
and the value of MINDISAGREE s
+
− s
∗
. The
optimal partition for the two problems is of course the same (if it is unique). Bansal
et al. [2002] show that both of these problems are NPhard (but have different approxi
mation hardness). We will concentrate on the maximization version, MAXAGREE. Several
approximation algorithms have been developed based on Linear and Semideﬁnite Program
ming [Charikar et al., 2003; Demaine & Immorlica, 2003; Emanuel & Fiat, 2003], which
we consider in the next sections.
11.1.1 Linear programming relaxation
In order to insure that y deﬁnes a partition, it is sufﬁcient to enforce a kind of triangle
inequality for each triple of nodes j < k < l:
y
jk
+ y
kl
≤ y
jl
+ 1; y
jk
+ y
jl
≤ y
kl
+ 1; y
jl
+ y
kl
≤ y
jk
+ 1. (11.1)
The triangle inequality enforces transitivity: if j and k are in the same cluster (y
jk
= 1)
and k and l are in the same cluster (y
kl
= 1), then j and l will be forced to be in this
cluster (y
jl
= 1). The other two cases are similar. Any symmetric, transitive binary relation
induces a partition of the objects.
With these deﬁnitions, we can express the MAXAGREE problem as an integer linear
program (ignoring the constant −s
−
):
max
jk
s
jk
y
jk
(11.2)
s.t. y
jk
+ y
kl
≤ y
lj
+ 1, ∀j, k, l; y
jj
= 1, ∀j; y
jk
∈ ¦0, 1¦, ∀j, k.
Note that the constraints imply that y
ab
= y
ba
for any two nodes a and b. To see this,
consider the inequalities involving node a and b with j = a, k = b, l = b and j = b, k =
11.1. CLUSTERING FORMULATION 163
a, l = a:
y
ab
+ y
bb
≤ y
ba
+ 1; y
ba
+ y
aa
≤ y
ab
+ 1;
Since y
aa
= y
bb
= 1, we have y
ab
= y
ba
.
The LP relaxation is obtained by replacing the binary variables y
jk
∈ ¦0, 1¦ in Eq. (11.2)
with continuous variables 0 ≤ µ
jk
≤ 1.
µ
jk
+ µ
kl
≤ µ
lj
+ 1, ∀j, k, l; µ
jj
= 1, ∀j; µ
jk
≥ 0, ∀j, k. (11.3)
Note that µ
jk
≤ 1 is implied since the triangle inequality with j = l gives µ
jk
+ µ
kj
≤
µ
jj
+ 1, and since µ
jj
= 1 and µ
jk
= µ
kj
, we have µ
jk
≤ 1.
We are not guaranteed that this relaxation will produce integral solutions. The LP
solution, s
LP
, is an upper bound on the s
∗
. Charikar et al. [2003] show that the integrality
gap of this upper bound is at least 2/3:
s
∗
−s
−
s
LP
−s
−
<
2
3
.
11.1.2 Semideﬁnite programming relaxation
An alternative formulation [Charikar et al., 2003] is the SDP relaxation. Let mat(µ) denote
the variables µ
jk
arranged into a matrix.
max
jk
s
jk
µ
jk
(11.4)
s.t. mat(µ) _ 0; µ
jj
= 1, ∀j; µ
jk
≥ 0, ∀j, k.
In effect, we substituted the triangle inequalities by the semideﬁnite constraint. To motivate
this relaxation, consider any clustering solution. Choose a collection of orthogonal unit
vectors ¦v
1
, . . . , v
K
¦, one for each cluster in the solution. Every vertex j in the cluster
is assigned the unit vector v
j
corresponding to the cluster it is in. If vertices j and k
are in the same cluster, then v
¯
j
v
k
= 1, if not, v
¯
j
v
k
= 0. The score of the clustering
164 CHAPTER 11. CORRELATION CLUSTERING
solution can now be expressed in terms of the dot products v
¯
j
v
k
. In the SDP relaxation
in Eq. (11.4), we have mat(µ) _ 0, which can be decomposed into a sum of outer products
mat(µ) =
j
v
j
v
¯
j
.
The entries µ
jk
correspond to inner products v
¯
j
v
k
. The vectors generating the inner
products are unit vectors by the requirement µ
jj
= 1. However, they do not necessarily
form a set of orthogonal vectors.
The SDP solution, s
SDP
, is also an upper bound on the s
∗
and Charikar et al. [2003]
show that the integrality gap of this upper bound is at least 0.82843:
s
∗
−s
−
s
SDP
−s
−
≤ 0.82843.
11.2 Learning formulation
The score for an edge is commonly derived from the characteristics of the pair of nodes.
Speciﬁcally, we parameterize the score as a weighted combination of basis functions
s
jk
= w
¯
f (x
jk
),
w, f (x
jk
) ∈ IR
n
, where x
jk
is a set of features associated with nodes j and k. In document
clustering, the entries of f
x
jk
might be the words shared by the documents j and k, while if
one is clustering points in IR
n
, features might be distances along different dimensions. We
assume f (x
jj
) = 0 so that s
jj
= 0. Hence we write
w
¯
f (x, y) =
jk
y
jk
w
¯
f (x
jk
).
Furthermore, we assume that the loss function decomposes over the edges, into a sum
of edge losses
i,jk
(y
jk
):
i
(y) =
jk
i,jk
(y
jk
) =
jk
y
jk
i,jk
(1) + (1 −y
jk
)
i,jk
(0) =
i
(0) +
jk
y
jk
i,jk
,
where
i,jk
=
i,jk
(1) −
i,jk
(0). For example, the Hamming loss counts the number of
11.2. LEARNING FORMULATION 165
edges incorrectly cut or uncut by a partition.
H
i
(y) =
jk
1I(y
jk
,= y
(i)
jk
) =
jk
y
(i)
jk
+
jk
y
jk
(1 −2y
(i)
jk
) =
H
i
(0) +
jk
y
jk
i,jk
,
where
i,jk
= 1 −2y
(i)
jk
.
With this assumption, the loss augmented maximization is
i
(0) + max
y∈¸
jk
y
jk
[w
¯
f (x
(i)
jk
) +
i,jk
]. (11.5)
We can now use the LP relaxation in Eq. (11.3) and the SDP relaxation in Eq. (11.4) as
upper bounds on Eq. (11.5). We use these upperbounds in the minmax formulation to
achieve approximate maxmargin estimation.
The dual of the LP based upper bound for example i is
i
(0)+
min
jkl
λ
i,jkl
+
j
z
i,j
(11.6)
s.t.
l
[λ
i,jkl
+ λ
i,ljk
−λ
i,klj
] ≥ w
¯
f (x
(i)
jk
) +
i,jk
, ∀j ,= k;
z
i,j
+
l
[λ
i,jjl
+ λ
i,ljj
−λ
i,jlj
] ≥
i,jj
, ∀j;
λ
i,jkl
≥ 0, ∀j, k, l.
Above, we introduced a dual variable λ
i,jkl
for each triangle inequality and z
i,j
for the
identity on the diagonal. Note the righthandside of the second set of inequalities follows
from the assumption f (x
jj
) = 0.
166 CHAPTER 11. CORRELATION CLUSTERING
Plugging this dual into the minmax formulation, we have:
min
1
2
[[w[[
2
+ C
ξ
i
(11.7)
s.t. w
¯
f (x
(i)
, y
(i)
) + ξ
i
≥
i
(0) +
jkl
λ
i,jkl
+
j
z
i,j
, ∀i;
l
[λ
i,jkl
+ λ
i,ljk
−λ
i,klj
] ≥ w
¯
f (x
(i)
jk
) +
i,jk
, ∀i, ∀j ,= k;
z
i,j
+
l
[λ
i,jjl
+ λ
i,ljj
−λ
i,jlj
] ≥
i,jj
, ∀i, ∀j;
λ
i,jkl
≥ 0, ∀i, ∀j, k, l.
Similarly, the dual of the SDP based upper bound is
i
(0)+
min
j
z
i,j
(11.8)
s.t. −λ
i,jk
≥ w
¯
f (x
(i)
jk
) +
i,jk
, ∀j ,= k;
z
i,j
−λ
i,jj
≥
i,jj
∀j;
mat(λ
i
) _ 0.
Plugging the SDP dual into the minmax formulation, we have:
min
1
2
[[w[[
2
+ C
ξ
i
(11.9)
s.t. w
¯
f (x
(i)
, y
(i)
) + ξ
i
≥
i
(0) +
j
z
i,j
, ∀i;
−λ
i,jk
≥ w
¯
f (x
(i)
jk
) +
i,jk
, ∀i, ∀j ,= k;
z
i,j
−λ
i,jj
≥
i,jj
, ∀i, ∀j;
mat(λ
i
) _ 0, ∀i, ∀j, k, l.
11.3. DUAL FORMULATION AND KERNELS 167
11.3 Dual formulation and kernels
The dual of Eq. (11.7) and Eq. (11.9) provide some insight into the structure of the problem
and enable efﬁcient use of kernels. Here we give the dual of Eq. (11.7):
max
i,jk
µ
i,jk
i,jk
−
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,jk
(y
(i)
jk
−µ
i,jk
)f (x
(i)
jk
)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
s.t. µ
jk
+ µ
kl
≤ µ
lj
+ 1, ∀i, ∀j, k, l; µ
i,jj
= 1, ∀i, ∀j; µ
i,jk
≥ 0, ∀i, ∀j, k.
The dual of Eq. (11.9) is very similar, except that the linear transitivity constraints
µ
jk
+ µ
kl
≤ µ
lj
+ 1, ∀i, ∀j, k, l are replaced by the corresponding mat(µ
i
) _ 0:
max
i,jk
µ
i,jk
i,jk
−
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,jk
(y
(i)
jk
−µ
i,jk
)f (x
(i)
jk
)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
s.t. mat(µ
i
) _ 0, ∀i; µ
i,jj
= 1, ∀i, ∀j; µ
i,jk
≥ 0, ∀i, ∀j, k.
The relation between the primal and dual solution is
w = C
i,jk
(y
(i)
jk
−µ
jk
)f (x
(i)
jk
). (11.10)
One important consequence of this relationship is that the edge parameters are all sup
port vector expansions. The dual objective can be expressed in terms of dotproducts
f (x
jk
)
¯
f (x
lm
). Therefore, we can use kernels K(x
jk
, x
lm
) to deﬁne the space of basis
functions. This kernel looks at two pairs of nodes, (j, k) and (l, m), and measures the
similarity between the relation between the nodes of each pair. If we are clustering points
in Euclidian space, the kernel could be a function of the two segments corresponding to
the pairs of points, for example, a polynomial kernel over their lengths and angle between
them.
168 CHAPTER 11. CORRELATION CLUSTERING
11.4 Experiments
We present experiments on a synthetic problem exploring the effect of irrelevant basis
functions (features), and two real data sets, email clustering and image segmentation.
11.4.1 Irrelevant features
In this section, we explore on a synthetic example how our algorithm deals with irrele
vant features. In particular, we generate data (100 points) from a mixture of two one
dimensional Gaussians, where each mixture component corresponds to a cluster. This ﬁrst
dimension is thus the relevant feature. Then we add noise components in D additional
(irrelevant) dimensions. The noise is independently generated for each dimension, from a
mixture of Gaussians with same difference in means and variance as for the relevant dimen
sion. Figure 11.1(a) shows the projection of a data sample onto the ﬁrst two dimensions
and on two irrelevant dimensions.
Let x
j
denote each point and x
j
[d] denote the dth dimension of the point. We used
a basis function for each dimension f
d
(x
jk
) = e
−(x
j
[d]−x
k
[d])
2
, plus an additional constant
basis function. The training and test data consists of a 100 samples from the model. The
results in Fig. 11.1(b) illustrate the capability of our algorithm to learn to ignore irrelevant
dimensions. The accuracy is the fraction of edges correctly predicted to be between/within
cluster. Random clustering will give an accuracy of 50%. The comparison with kmeans is
simply a baseline to illustrate the effect of the noise on the data.
11.4.2 Email clustering
We also test our approach on the task of clustering email into folders. We gathered the
data from the SRI CALO project.
1
Our dataset consisted of email from seven users (ap
proximately 100 consecutive messages per user), which the users had manually ﬁled into
different folders. The number of folders for each users varied from two to six, with an
average of 34 folders. We are interested in the problem of learning to cluster emails.
1
http://www.ai.sri.com/project/CALO
11.4. EXPERIMENTS 169
−4 −3 −2 −1 0 1 2 3
−4
−3
−2
−1
0
1
2
3
4
−4 −3 −2 −1 0 1 2 3 4
−4
−3
−2
−1
0
1
2
3
4
0.45
0.55
0.65
0.75
0.85
0.95
1 2 4 8 16 32 64 128
#noisedimensions
t
e
s
t
a
c
c
u
r
a
c
y
lcc
kmeans
(a) (b)
Figure 11.1: (a) Projection onto ﬁrst two dimensions (top) and two noise dimensions (bot
tom); (c) Performance on 2 cluster problem as function of the number of irrelevant noise
dimensions. Learning to cluster is the solid line, kmeans the dashed line. Errorbars de
note one standard deviation, averages are over 20 runs. Accuracy is the fraction of edges
correctly predicted to be between/within cluster.
Speciﬁcally, what score function s
jk
causes correlation clustering to give clusters similar
to those that human users had chosen?
To test our learning algorithm, we use each user as a training set in turn, learning the
parameters from the partition of a single user’s mailbox into folders. We then use the
learned parameters to cluster the other users’ mail. The basis functions f (x
jk
) measured the
similarity between the text of the messages, the similarity between the “From:” ﬁeld, “To:”
ﬁeld, and “Cc:” ﬁeld. One feature was used for each common word in the pair of emails
(except words that appeared in more than half the messages, which were deemed “stop
words” and omitted). Also, additional features captured the proportion of shared tokens
for each email ﬁeld, including the from, to, Cc, subject and body ﬁelds. The algorithm
is therefore able to automatically learn the relative importance of certain email ﬁelds to
ﬁling two messages together, as well as importance of meaningful words versus common,
irrelevant ones.
We compare our method to the kmeans clustering algorithm using with the same word
170 CHAPTER 11. CORRELATION CLUSTERING
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
1 2 3 4 5 6 7
User
P
a
i
r
F
1
lcc
kmeans
Figure 11.2: Average Pair F1 measure for clustering user mailboxes.
features, and took the best clustering out of ﬁve tries. We made this comparison somewhat
easy for kmeans by giving it the correct number of clusters k. We also informed our algo
rithm of the number of clusters by uniformly adding a positive weight to the edge weights
to cause it to give the correct number of clusters. We performed a simple binary search on
this additional bias weight parameter to ﬁnd the number of clusters comparable to k. The
results in Fig. 11.2 show the average F1 measure (harmonic mean of precision and recall;
a standard metric in information retrieval [BaezaYates & RibeiroNeto, 1999]) computed
on the pairs of messages that belonged to the same cluster. Our algorithm signiﬁcantly
outperforms kmeans on several users and does worse only for one of the users.
11.4.3 Image segmentation
We also test our approach on the task of image segmentation. We selected images from
the Berkeley Image Segmentation Dataset [Martin et al., 2001] for which two users had
signiﬁcantly different segmentations. For example, Fig. 11.3(a) and (b) show two distinct
segmentations: one very coarse, mostly based of overall hue, and one much ﬁner, based
on the hue and intensity. Depending on the task at hand, we may prefer the ﬁrst over the
second or viceversa. It is precisely this kind of variability in the similarity judgements that
11.4. EXPERIMENTS 171
(a) (b)
Figure 11.3: Two segmentations by different users: training image with (a) coarse segmen
tation and (b) ﬁne segmentation.
we want our algorithm to capture.
In order to segment the image, we ﬁrst divided it contiguous regions of approximately
the same color by running connected components on the pixels. We connected two adjacent
pixels by an edge if their RGB value was the same at a coarse resolution (4 bits per each
of the R,G,B channel). We then selected about a hundred largest regions, which covered
8090% of the pixels. These regions are the objects that our algorithm learns to cluster.
(We then use the learned metric to greedily assign the remaining small regions to the large
adjoining regions.)
There is a rich space of possible features we can use in our models: for each pair
of regions, we can consider their shape, color distribution, distance, presence of edges
between them, etc. In our experiments, we used a fairly simple set of features that are very
easy to compute. For each region, we calculated the bounding box, area and average color
(averaging the pixels in the RGB space). We then computed three distances (one for each
HSV channel), as well as the distance in pixels between the bounding boxes and the area
of the smaller of the two regions. All features were normalized to have zero mean and
variance 1.
We trained two models, one using Fig. 11.3(a) and the other using Fig. 11.3(b) and
172 CHAPTER 11. CORRELATION CLUSTERING
(a) (b) (c)
Figure 11.4: Test image: (a) input; (b) segmentation based on coarse training data (c)
segmentation based on ﬁne training data.
tested on the image in Fig. 11.4(a). The results are shown in Fig. 11.4(b) and (c), respec
tively. Note that mountains, rocks and grass are segmented very coarsely based on hue in
(b) while the segmentation in (c) is more detailed and sensitive to saturation and value of
the colors.
11.5 Related work
The performance of most clustering algorithms depends critically on the distance metric
that they are given for measuring the similarity or dissimilarity between different data
points. Recently, a number of algorithms have been proposed for automatically learning
distance metrics as a preprocessing step for clustering [Xing et al., 2002; BarHillel et al.,
2003]. In contrast to algorithms that learn a metric independently of the algorithm that will
be used to cluster the data, we describe a formulation that tightly integrates metric learning
with the clustering algorithm, tuning one to the other in a joint optimization. Thus, instead
of using an externallydeﬁned criterion for choosing the metric, we will instead seek to
learn a good metric for the clustering algorithm. An example of work in a similar vein is
the algorithm for learning a distance metric for spectral clustering [Bach & Jordan, 2003].
The clustering algorithm essentially uses an eigenvector decomposition of an appropriate
matrix derived from the pairwise afﬁnity matrix, which is more efﬁcient than correlation
clustering, for which we use LP or SDP formulations. However the objective in the learning
11.6. CONCLUSION 173
formulation proposed in Bach and Jordan [2003] is not convex and difﬁcult to optimize.
11.6 Conclusion
We looked at correlation clustering, and how to learn the edge weights from example clus
terings. Our approach ties together the inference and learning algorithm, and attempts
to learn a good metric speciﬁcally for the clustering algorithm.. We showed results on a
synthetic dataset, showcasing robustness to noise dimensions. Experiments on the CALO
email and image segmentation experiments show the potential of the algorithm on real
world data. The main limitation of the correlation clustering is scalability: the number of
constraints ([1[
3
) in the LP relaxation and the size of the positivesemideﬁnite constraint
in the SDP relaxation. It would be very interesting to explore constraint generation or sim
ilar approaches to speed up learning and inference. On the theoretical side, it would be
interesting to work out a PAClike bound for generalization of the learned score metric.
174 CHAPTER 11. CORRELATION CLUSTERING
Part IV
Conclusions and future directions
175
Chapter 12
Conclusions and future directions
This thesis presents a novel statistical estimation framework for structured models based
on the large margin principle underlying support vector machines. The framework results
in several efﬁcient learning formulations for complex prediction tasks. Fundamentally,
we rely on the expressive power of convex optimization problems to compactly capture
inference or solution optimality in structured models. Directly embedding this structure
within the learning formulation produces compact convex problems for efﬁcient estimation
of very complex models. For some of these models, alternative estimation methods are
intractable. We develop theoretical foundations for our approach and show a wide range
of experimental applications, including handwriting recognition, 3D terrain classiﬁcation,
disulﬁde connectivity in protein structure prediction, hypertext categorization, natural lan
guage parsing, email organization and image segmentation.
12.1 Summary of contributions
We view a structured prediction model as a mapping from the space of inputs x ∈ A to
a discrete vector output y ∈ ¸. Essentially, a model deﬁnes a compact, parameterized
scoring function w
¯
f (x, y) and prediction using the model reduces to ﬁnding the highest
scoring output y given the input x. Our class of models has the following linear form:
h
w
(x) = arg max
y: g(x,y)≤0
w
¯
f (x, y),
176
12.1. SUMMARY OF CONTRIBUTIONS 177
where w ∈ IR
n
is the vector of parameters of the model, constraints g(x, y) ∈ IR
k
deﬁne
the space of feasible outputs y given the input x and basis functions f (x, y) ∈ IR
n
represent
salient features of the input/output pair. Although the space of outputs ¦y : g(x, y) ≤ 0¦ is
usually immense, we assume that the inference problem arg max
y : g(x,y)≤0
w
¯
f (x, y) can
be solved (or closely approximated) by an efﬁcient algorithm that exploits the structure of
the constraints g and basis functions f . This deﬁnition covers a broad range of models,
from probabilistic models such as Markov networks and context free grammars to more
unconventional models like weighted graphcuts and matchings.
12.1.1 Structured maximum margin estimation
Given a sample S = ¦(x
(i)
, y
(i)
)¦
m
i=1
, we develop methods for ﬁnding parameters w such
that:
arg max
y∈¸
(i)
w
¯
f (x
(i)
, y) ≈ y
(i)
, ∀i,
where ¸
(i)
= ¦y : g(x
(i)
, y) ≤ 0¦.
The naive formulation
1
uses
i
[¸
(i)
[ linear constraints, which is generally exponential
in the number of variables in each y
(i)
.
min
1
2
[[w[[
2
s.t. w
¯
f
i
(y
(i)
) ≥ w
¯
f
i
(y) +
i
(y), ∀i, ∀y ∈ ¸
(i)
.
We propose two general approaches that transform the above exponential size QP to an
exactly equivalent polynomial size QP in many important classes of models. These formu
lations allow us to ﬁnd globally optimal parameters (with ﬁxed precision) in polynomial
time using standard optimization software. In many models where maximum likelihood
estimation is intractable, we provide exact maximum margin solutions (Ch. 7 and Ch. 10).
1
For simplicity, we omit the slack variables in this summary.
178 CHAPTER 12. CONCLUSIONS AND FUTURE DIRECTIONS
Minmax formulation
We can turn the above problem into an equivalent minmax formulation with i nonlinear
maxconstraints:
min
1
2
[[w[[
2
s.t. w
¯
f
i
(y
(i)
) ≥ max
y∈¸
(i)
[w
¯
f
i
(y) +
i
(y)], ∀i.
The key to solving the estimation problem above efﬁciently is the lossaugmented infer
ence problem max
y∈¸
(i) [w
¯
f
i
(y) +
i
(y)]. Even if max
y∈¸
(i) w
¯
f
i
(y) can be solved in
polynomial time using convex optimization, the form of the loss term
i
(y) is crucial for
the lossaugmented inference to remain tractable. We typically use a natural loss func
tion which is essentially the Hamming distance between y
(i)
and h(x
(i)
): the number of
variables predicted incorrectly.
We show that if we can express the (lossaugmented) inference as a compact convex
optimization problem (e.g., LP, QP, SDP, etc.), we can embed the maximization inside the
minmax formulation to get a compact convex program equivalent to the naive exponential
formulation. We show that this approach leads to exact polynomialsize formulations for
estimation of lowtreewidth Markov networks, associative Markov networks over binary
variables, contextfree grammars, bipartite matchings, and many other models.
Certiﬁcate formulation
There are several important combinatorial problems which allow polynomial time solu
tion yet do not have a compact convex optimization formulation. For example, maximum
weight perfect (nonbipartite) matching and spanning tree problems can be expressed as
linear programs with exponentially many constraints, but no polynomial formulation is
known [Bertsimas & Tsitsiklis, 1997; Schrijver, 2003]. Both of these problems, however,
can be solved in polynomial time using combinatorial algorithms. In some cases, though,
we can ﬁnd a compact certiﬁcate of optimality that guarantees that
y
(i)
= arg max
y
[w
¯
f
i
(y) +
i
(y)].
12.1. SUMMARY OF CONTRIBUTIONS 179
For perfect (nonbipartite) matchings, this certiﬁcate is a condition that ensures there are
no augmenting alternating cycles (see Ch. 10). We can express this condition by deﬁning
an auxiliary distance function on the nodes an a set of linear constraints that are satisﬁed if
and only if there are no negative cycles. This simple set of linear constraints scales linearly
with the number of edges in the graph. Similarly, we can derive a compact certiﬁcate for
the spanning tree problem.
The certiﬁcate formulation relies on the fact that verifying optimality of a solution is
often easier than actually ﬁnding one. This observation allows us to apply our framework
to an even broader range of models with combinatorial structure than the minmax formu
lation.
Maximum margin vs. maximum likelihood
There are several theoretical advantages to our approach in addition to the empirical accu
racy improvements we have shown experimentally. Because our approach only relies on
using the maximum in the model for prediction, and does not require a normalized dis
tribution P(y [ x) over all outputs, maximum margin estimation can be tractable when
maximum likelihood is not. For example, to learn a probabilistic model P(y [ x) over
bipartite matchings using maximum likelihood requires computing the normalizing parti
tion function, which is #Pcomplete [Valiant, 1979; Garey & Johnson, 1979]. By contrast,
maximum margin estimation can be formulated as a compact QP with linear constraints.
Similar results hold for an important subclass of Markov networks and nonbipartite match
ings.
In models that are tractable for both maximum likelihood and maximum margin (such
as lowtreewidth Markov networks, context free grammars, many other problems in which
inference is solvable by dynamic programming), our approach has an additional advantage.
Because of the hingeloss, the solutions to the estimation are relatively sparse in the dual
space (as in SVMs), which makes the use of kernels much more efﬁcient. Maximum like
lihood models with kernels are generally nonsparse and require pruning or greedy support
vector selection methods [Wahba et al., 1993; Zhu & Hastie, 2001; Lafferty et al., 2004;
Altun et al., 2004].
180 CHAPTER 12. CONCLUSIONS AND FUTURE DIRECTIONS
There are, of course, several advantages to maximum likelihood estimation. In appli
cations where probabilistic conﬁdence information is a must, maximum likelihood is much
more appropriate. Also, in training settings with missing data and hidden variables, proba
bilistic interpretation permits the use of wellunderstood algorithms such as EM [Dempster
et al., 1977].
Approximations
In many problems, the maximization problem we are interested in may be NPhard, for
example, we consider MAP inference in large treewidth Markov networks in Ch. 8, multi
way cuts in Ch. 7, graphpartitioning in Ch. 11. Many such problems can be written as
integer programs. Relaxations of such integer programs into LPs, QPs or SDPs often pro
vide excellent approximation algorithms and ﬁt well within our framework, particularly the
minmax formulation. We show empirically that these approximations are very effective in
many applications.
12.1.2 Markov networks: maxmargin, associative, relational
The largest portion of the thesis is devoted to novel estimation algorithms, representational
extensions, generalization analysis and experimental validation for Markov networks.
◦ Lowtreewidth Markov networks
We use a compact LP for MAP inference in Markov networks with sequence and
other lowtreewidth structure to derive an exact, compact, convex learning formu
lation. The dual formulation allows efﬁcient integration of kernels with graphical
models that leverages rich highdimensional representations for accurate prediction
in realworld tasks.
◦ Scalable online algorithm
Although our convex formulation is a QP with linear number of variables and con
straints in the size of the data, for large datasets (millions of examples), it is very
difﬁcult to solve using standard software. We present an efﬁcient algorithm for solv
ing the estimation problem called Structured SMO. Our onlinestyle algorithm uses
12.1. SUMMARY OF CONTRIBUTIONS 181
inference in the model and analytic updates to solve extremely large estimation prob
lems.
◦ Generalization analysis
We analyze the theoretical generalization properties of maxmargin estimation in
Markov networks and derive a novel marginbased bound for structured prediction.
This is the ﬁrst bound to address structured error (e.g., proportion of mislabeled
pixels in an image).
◦ Learning associative Markov networks (AMNs)
We deﬁne an important subclass of Markov networks that captures positive correla
tions present in many domains. This class of networks extends the Potts model [Potts,
1952] often used in computer vision and allows exact MAP inference in the case of
binary variables. We show how to express the inference problem using an LP which
is exact for binary networks. As a result, for associative Markov networks over bi
nary variables, our framework allows exact estimation of networks of arbitrary con
nectivity and topology, for which likelihood methods are believed to be intractable.
For the nonbinary case, we provide an approximation that works well in practice.
We present an AMNbased method for object segmentation from 3D range data. By
constraining the class of Markov networks to AMNs, our models are learned efﬁ
ciently and, at runtime, can scale up to tens of millions of nodes and edges by using
graphcut based inference [Kolmogorov & Zabih, 2002].
◦ Representation and learning of relational Markov networks
We introduce relational Markov networks (RMNs), which compactly deﬁne tem
plates for Markov networks for domains with relational structure: objects, attributes,
relations. The graphical structure of an RMN is based on the relational structure of
the domain, and can easily model complex interaction patterns over related entities.
We apply this class of models to classiﬁcation of hypertext using hyperlink structure
to deﬁne relations between webpages. We use a compact approximate MAP LP in
these complex Markov networks, in which exact inference is intractable, to derive an
approximate maxmargin formulation.
182 CHAPTER 12. CONCLUSIONS AND FUTURE DIRECTIONS
12.1.3 Broader applications: parsing, matching, clustering
The other large portion of the thesis addresses a range of prediction tasks with very diverse
models: context free grammars for natural language parsing, perfect matchings for disulﬁde
connectivity in protein structure prediction, graph partitions for clustering documents and
segmenting images.
◦ Learning to parse
We exploit dynamic programming decomposition of context free grammars to derive
a compact maxmargin formulation. We build on a recently proposed “unlexicalized”
grammar that allows cubic time parsing and we show how to achieve highaccuracy
parsing (still in cubic time) by exploiting novel kinds of lexical information. We show
experimental evidence of the model’s improved performance over several baseline
models.
◦ Learning to match
We use a combinatorial optimality condition, namely the absence of augmenting al
ternating cycles, to derive an exact, efﬁcient certiﬁcate formulation for learning to
match. We apply our framework to prediction of disulﬁde connectivity in proteins
using perfect matchings. The algorithmwe propose uses kernels, which makes it pos
sible to efﬁciently embed input features in very highdimensional spaces and achieve
stateoftheart accuracy.
◦ Learning to cluster
By expressing the correlation clustering problem as a compact LP and SDP, we use
the minmax formulation to learn a parameterized scoring function for clustering. In
contrast to algorithms that learn a metric independently of the algorithm that will
be used to cluster the data, we describe a formulation that tightly integrates metric
learning with the clustering algorithm, tuning one to the other in a joint optimization.
We formulate the approximate learning problem as a compact convex program. Ex
periments on synthetic and realworld data show the ability of the algorithm to learn
an appropriate clustering metric for a variety of desired clusterings, including email
folder organization and image segmentation.
12.2. EXTENSIONS AND OPEN PROBLEMS 183
12.2 Extensions and open problems
There are several immediate applications, less immediate extensions and open problems for
our estimation framework. We organize these ideas into several sections below, including
further theoretical analysis and new optimization algorithms, novel prediction tasks, and
more general learning settings.
12.2.1 Theoretical analysis and optimization algorithms
◦ Approximation bounds
In several of the intractable models, like multiclass AMNs in Ch. 7 and correlation
clustering in Ch. 11, we used approximate convex programs within the minmax for
mulation. These approximate inference programs have strong relative error bounds.
An open question is to translate these error bounds on inference into error bounds on
the resulting maxmargin formulations.
◦ Generalization bounds with distributional assumptions
In Ch. 5, we presented a bound on the structured error in Markov networks, with
out any assumption about the distribution of P(y [ x), relying only on the samples
(x
(i)
, y
(i)
) being i.i.d. This distributionfree assumption leads to a worst case analy
sis, while some assumptions about the approximate decomposition P(y [ x) may be
warranted. For example, for sequential prediction problems, the Markov assumption
of some ﬁnite order is reasonable (i.e., given the input and previous k labels, the next
label is independent of the labels more than k in the past). In spatial prediction tasks,
a label variable is independent of the rest given a large enough ball of labels around
it. Similar assumptions may be made for some “degree of separation” in relational
domains. More generally, it would be interesting to exploit such conditional indepen
dence assumptions or asymptotic bounds on entropy of P(y [ x) to get generalization
guarantees even from a single structured example (x, y).
◦ Problemspeciﬁc optimization methods
Although our convex formulations are polynomial in the size of the data, scaling
184 CHAPTER 12. CONCLUSIONS AND FUTURE DIRECTIONS
up to larger datasets will require problemspeciﬁc optimization methods. For low
treewidth Markov networks and context free grammars, we have presented the Struc
tured SMO algorithm. Another algorithm useful for such models is Exponentiated
Gradient [Bartlett et al., 2004]. Both algorithms rely on dynamic programming de
compositions. However, models which do not permit such decompositions, such as
graphcuts, matchings, and many others, create a need for new algorithms that can ef
fectively use combinatorial optimization as a subroutine to eliminate the dependence
on generalpurpose convex solvers.
12.2.2 Novel prediction tasks
◦ Bipartite matchings
Maximum weight bipartite matchings are used in a variety of problems to predict
mappings between sets of items. In machine translation, matchings are used to
map words of the two languages in aligned sentences [Matusov et al., 2004]. In 2D
shape matching, points on two shapes are matched based on their local contour fea
tures [Belongie et al., 2002]. Our framework provides an exact, efﬁcient alternative
to the maximum likelihood estimation for learning the matching scoring function.
◦ Sequence alignment
In standard pairwise alignment of biological sequences, a string edit distance is used
to determine which portions of the sequences align to each other [Needleman &
Wunsch, 1970; Durbin et al., 1998]. Finding the best alignment involves a dynamic
program that generalizes the longest common subsequence algorithm. Our frame
work can be applied (just as in context free grammar estimation) to efﬁciently learn
a more complex edit function that depends on the contextual string features, perhaps
using novel string kernels [Haussler, 1999; Leslie et al., 2002; Lodhi et al., 2000].
◦ Continuous prediction problems
We have addressed estimation of models with discrete output spaces, generalizing
classiﬁcation models to multivariate, structured classiﬁcation. Similarly, we can
consider a whole range of problems where the prediction variables are continuous.
12.2. EXTENSIONS AND OPEN PROBLEMS 185
Such problems are a natural generalizations of regression, involving correlated, inter
constrained realvalued outputs. For example, several recent models of metabolic
ﬂux in yeast use linear programming formulations involving quantities of various
enzymes, with stoichiometric constraints [Varma & Palsson, 1994]. It would be
interesting to use observed equilibria data under different conditions to learn what
“objective” the cell is maximizing. In ﬁnancial modeling, convex programs are often
used to model portfolio management; for example, Markowitz portfolio optimization
is formulated as a quadratic program which minimizes risk and maximizes expected
return under budget constraints [Markowitz, 1991; Luenberger, 1997]. In this setting,
one could learn a user’s return projection and risk assessment function from observed
portfolio allocations by the user.
These problems are similar to the discrete structured prediction models we have con
sidered: inference in the model can formulated as a convex optimization problem.
However, there are obstacles to directly applying the minmax or certiﬁcate formu
lations. Details of this are beyond the scope of this thesis, but it sufﬁces to say that
lossaugmented inference using, Hamming distance equivalent, L
1
loss (or L
2
loss),
no longer produces a maximization of a concave objective with convex constraints
since L
1
, L
2
are convex, not concave (it turns out that it is actually possible to use
L
∞
loss). Developing effective loss functions and maxmargin formulations for the
continuous setting could provide a novel set of effective models for structured multi
variate realvalued prediction problems.
12.2.3 More general learning settings
◦ Structure learning
We have focused on the problem of learning parameters of the model (even though
our kernelized models can be considered nonparametric). In the case of Markov
networks, especially in spatial and relational domains, there is a wealth of possible
structures (cliques in the network) one can use to model a problem. It is particularly
interesting to explore the problem of inducing these cliques automatically from data.
The standard method of greedy stepwise selection followed by reestimation is very
186 CHAPTER 12. CONCLUSIONS AND FUTURE DIRECTIONS
expensive in general networks [Della Pietra et al., 1997; Bach & Jordan, 2001].
Recent work on selecting input features in Markov networks (or CRFs) uses several
approximations to learn efﬁciently with millions of candidate features [McCallum,
2003]. However, clique selection is still relatively unexplored. It is possible that
AMNs, by restricting the network to be tractable under any structure, may permit
more efﬁcient clique selection methods.
◦ Semisupervised learning
Throughout the thesis we have assumed completely labeled data. This assumption
often limits us to relatively small training sets where data has been carefully anno
tated, while much of the easily accessible data is not at all or suitably labeled. There
are several more general settings we would like to extend our framework.
The simplest setting is a mix of labeled and unlabeled examples, where a small su
pervised dataset is augmented by a large unsupervised one. There has been much
research in this setting for classiﬁcation [Blum & Mitchell, 1998; Nigam et al., 2000;
Chapelle et al., 2002; Szummer & Jaakkola, 2001; Zhu et al., 2003; Corduneanu &
Jaakkola, 2003]. Although most of this work has been done in a probabilistic set
ting, the principle of regularizing (discouraging) decision boundaries near densely
clustered inputs could be applicable to our structured setting.
A more complex and rich setting involves presence of hidden variables in each ex
ample. For example, in machine translation, word correspondences between pairs of
sentences are usually not manually annotated (at least not on a large scale). These
correspondence variables can be treated as hidden variables. Similarly, in handwrit
ing recognition, we may not have each letter segmented out but instead just get a
word or sentence as a label for the entire image. This setting has been studied mainly
in the probabilistic, generative models often using the EMalgorithm[Dempster et al.,
1977; Cowell et al., 1999]. Discriminative methods have been explored far less. Es
pecially in the case of combinatorial structures, extensions of our framework allow
opportunities for problemspeciﬁc convex approximations to be exploited.
12.3. FUTURE 187
12.3 Future
We have presented a supervised learning framework for a large class of prediction mod
els with rich and interesting structure. Our approach has several theoretical and practical
advantages over standard probabilistic models and estimation methods for structured pre
diction. We hope that continued research in this framework will help tackle evermore
sophisticated prediction problems in the future.
Appendix A
Proofs and derivations
A.1 Proof of Theorem 5.5.1
The proof of Theorem 5.5.1 uses the covering number bounds of Zhang [2002] (in the
DataDependent Structural Risk Minimization framework [ShaweTaylor et al., 1998].)
Zhang provides generalization guarantees for linear binary classiﬁers of the form h
w
(x) =
sgn(w
¯
x). His analysis is based on the upper bounds on the covering number for the class
of linear functions T
L
(w, z) = w
¯
z where the norms of the vectors w and z are bounded.
We reproduce the relevant deﬁnitions and theorems from Zhang [2002] here to highlight
the necessary extensions for structured classiﬁcation.
The covering number is a key quantity in measuring function complexity. Intuitively,
the covering number of an inﬁnite class of functions (e.g. parameterized by a set of weights
w) is the number of vectors necessary to approximate the values of any function in the class
on a sample. Marginbased analysis of generalization error uses the margin achieved by a
classiﬁer on the training set to approximate the original function class of the classiﬁer by
a ﬁnite covering with precision that depends on the margin. Here, we will only deﬁne the
∞norm covering number.
188
A.1. PROOF OF THEOREM 5.5.1 189
A.1.1 Binary classiﬁcation
In binary classiﬁcation, we are given a sample S = ¦x
(i)
, y
(i)
¦
m
i=1
, from distribution D over
A ¸, where A = IR
n
and ¸ is mapped to ±1, so we can fold x and y into z = yx.
Deﬁnition A.1.1 (Covering Number) Let 1 = ¦v
(1)
, . . . , v
(r)
¦, where v
(j)
∈ IR
m
, be a
covering of a function class T(w, S) with precision under the metric ρ, if for all w there
exists a v
(j)
such that for each data sample z
(i)
∈ S:
ρ(v
(j)
i
, T(w, z
(i)
)) ≤ .
The covering number of a sample S is the size of the smallest covering: ^
∞
(T, ρ, , S) =
inf [1[ s.t. 1 is a covering of T(w, S). We also deﬁne the covering number for any sample
of size m: ^
∞
(T, ρ, , m) = sup
S: [S[=m
^
∞
(T, ρ, , S).
When the norms of w and z are bounded, we have the following upper bound on the
covering number of linear functions under the linear metric ρ
L
(v, v
t
) = [v −v
t
[.
Theorem A.1.2 (Theorem 4 from Zhang [2002]) If w
2
≤ a and z
2
≤ b, then ∀
> 0,
log
2
^
∞
(T
L
, ρ
L
, , m) ≤ 36
a
2
b
2
2
log
2
(2 ¸4ab/ + 2 m + 1) .
In order to use the classiﬁer’s margin to bound its expected loss, the bounds below use
a stricter, marginbased loss on the training sample that measures the worst loss achieved
by the approximate covering based on this margin. Let f : IR → [0, 1] be a loss function.
In binary classiﬁcation, we let f(v) = 1I(v ≤ 0) be the step function, so that 01 loss of
sgn(w
¯
x) is f(T
L
(w, z)). The next theorem bounds the expected f loss in terms of the
γmargin loss, f
γ
(v) = sup
ρ(v,v
)<2γ
f(v
t
), on the training sample. For 01 loss and linear
metric ρ
L
, the corresponding γmargin loss is f
γ
(v) = 1I(v ≤ 2γ).
Theorem A.1.3 (Corollary 1 from Zhang [2002]) Let f : IR → [0, 1] be a loss function
and f
γ
(v) = sup
ρ(v,v
)<2γ
f(v
t
) be the γmargin loss for a metric ρ. Let γ
1
> γ
2
> . . . be
190 APPENDIX A. PROOFS AND DERIVATIONS
a decreasing sequence of parameters, and p
i
be a sequence of positive numbers such that
∞
i=1
p
i
= 1, then for all δ > 0, with probability of at least 1 −δ over data:
E
D
[f(T(w, z))] ≤ E
S
[f
γ
(T(w, z))] +
¸
32
m
_
ln 4^
∞
(T, ρ, γ
i
, S) + ln
1
p
i
δ
_
for all w and γ, where for each ﬁxed γ, we use i to denote the smallest index s.t. γ
i
≤ γ.
A.1.2 Structured classiﬁcation
We will extend this framework to bound the average perlabel loss
H
(y)/L for structured
classiﬁcation by deﬁning an appropriate loss f and a function class T (as well as a metric
ρ) such that f(T) computes average perlabel loss and f
γ
(T) provides a suitable γmargin
loss. We will bound the corresponding covering number by building on the bound in The
orem A.1.2.
We can no longer simply fold x and y, since y is a vector, so we let z = (x, y). In
order for our loss function to compute average perlabel loss, it is convenient to make our
function class vectorvalued (instead of scalarvalued as above). We deﬁne a new function
class T
M
(w, z), which is a vector of minimum values of w
¯
∆f
i
(y) for each error level
H
(y) from 1 to L as described below.
Deﬁnition A.1.4 (dtherrorlevel function) The dtherrorlevel function M
d
(w, z) for d ∈
¦1, . . . , L¦ is given by:
M
d
(w, z) = min
y:
H
(y)=d
w
¯
∆f
i
(y).
Deﬁnition A.1.5 (Multierrorlevel function class) The multierrorlevel function class T
M
(w, z)
is given by:
T
M
(w, z) = (M
1
(w, z), . . . , M
d
(w, z), . . . , M
L
(w, z)) .
We can now compute the average perlabel loss from T
M
(w, z) by deﬁning an appropriate
loss function f
M
.
A.1. PROOF OF THEOREM 5.5.1 191
Deﬁnition A.1.6 (Average perlabel loss) The average perlabel loss f
M
: IR
L
→[0, 1] is
given by:
f
M
(v) =
1
L
arg min
d:v
d
≤0
v
d
,
where in case ∀d, v
d
> 0, we deﬁne arg min
d:v
d
≤0
v
d
≡ 0.
With the above deﬁnitions, we have an upper bound on the average perlabel loss
f
M
(T
M
(w, z)) =
1
L
arg min
d:M
d
(w,z)≤0
M
d
(w, z) ≥
1
L
H
_
arg max
y
w
¯
f
i
(y)
_
.
Note that the case ∀d, M
d
(w, z) > 0 corresponds to the classiﬁer making no mistakes:
arg max
y
w
¯
f
i
(y) = y. This upper bound is tight if y = arg max
y
w
¯
f (x, y
t
), Other
wise, it is adversarial: it picks from all y
t
which are better (w
¯
f (y) ≤ w
¯
f (y
t
)), one that
maximizes the Hamming distance from y.
We now need to deﬁne an appropriate metric ρ that in turn deﬁnes γmargin loss for
structured classiﬁcation. Since the margin of the hypothesis grows with the number of
mistakes, our metric can become “looser” with the number of mistakes, as there is more
room for error.
Deﬁnition A.1.7 (Multierrorlevel metric) Let the multierrorlevel metric ρ
M
: IR
L
IR
L
→IR for a vector in IR
L
be given by:
ρ
M
(v, v
t
) = max
d
[v
d
−v
t
d
[
d
.
We now deﬁne the corresponding γmargin loss using the new metric:
Deﬁnition A.1.8 (γmargin average perlabel loss) The γmargin average perlabel loss
f
γ
M
: IR
L
→[0, 1] is given by:
f
γ
M
(v) = sup
ρ
M
(v,v
)≤2γ
f
M
(v
t
).
Combining the two deﬁnitions, we get:
f
γ
M
(T
M
(w, z)) = sup
v:[v
d
−M
d
(w,z)[≤2dγ
1
L
arg min
d:v
d
≤0
v
d
.
192 APPENDIX A. PROOFS AND DERIVATIONS
We also deﬁne the corresponding covering number for our vectorvalued function class:
Deﬁnition A.1.9 (Multierrorlevel covering number) Let 1 = ¦V
(1)
, . . . , V
(r)
¦, where
V
(j)
= (V
(j)
1
, . . . , V
(j)
i
, . . . , V
(j)
m
) and V
(j)
i
∈ IR
L
, be a covering of T
M
(w, S), with 
precision under the metric ρ
M
, if for all w there exists a V
(j)
such that for each data
sample z
(i)
∈ S:
ρ
M
(V
(j)
i
, T
M
(w, z
(i)
)) ≤ .
The covering number of a sample S is the size of the smallest covering: ^
∞
(T
M
, ρ
M
, , S) =
inf [1[ s.t. 1 is a covering of T
M
(w, S). We also deﬁne
^
∞
(T
M
, ρ
M
, , m) = sup
S: [S[=m
^
∞
(T
M
, ρ
M
, , S).
We provide a bound on the covering number of our new function class in terms of a
covering number for the linear function class. Recall that N
c
is the maximum number of
cliques in ((x), V
c
is the maximum number of values in a clique [Y
c
[, q is the maximum
number of cliques that have a variable in common, and R
c
is an upperbound on the 2norm
of clique basis functions. Consider a ﬁrstorder sequence model as an example, with L as
the maximum length, and V the number of values a variable takes. Then N
c
= 2L−1 since
we have L node cliques and L −1 edge cliques; V
c
= V
2
because of the edge cliques; and
q = 3 since nodes in the middle of the sequence participate in 3 cliques: previouscurrent
edge clique, node clique, and currentnext edge clique.
Lemma A.1.10 (Bound on multierrorlevel covering number)
^
∞
(T
M
, ρ
M
, q, m) ≤ ^
∞
(T
L
, ρ
L
, , mN
c
(V
c
−1)).
Proof: We will show that ^
∞
(T
M
, ρ
M
, q, S) ≤ ^
∞
(T
L
, ρ
L
, , S
t
) for any sample S
of size m, where we construct the sample S
t
of size mN
c
(V
c
− 1) in order to cover the
clique potentials as described below. Note that this is sufﬁcient since ^
∞
(T
L
, ρ
L
, , S
t
) ≤
^
∞
(T
L
, ρ
L
, , mN
c
(V
c
−1)), by deﬁnition, so
^
∞
(T
M
, ρ
M
, q, m) = sup
S:[S[=m
^
∞
(T
M
, ρ
M
, q, S) ≤ ^
∞
(T
L
, ρ
L
, , mN
c
(V
c
−1)).
A.1. PROOF OF THEOREM 5.5.1 193
The construction of S
t
below is inspired by the proof technique in Collins [2001],
but the key difference is that our construction is linear in the number of cliques N
c
and
exponential in the number of label variables per clique, while his is exponential in the total
number of label variables per example. This reduction in size comes about because our
covering approximates the values of clique potentials w
¯
∆f
i,c
(y
c
) for each clique c and
clique assignment y
c
as opposed to the values of entire assignments w
¯
∆f
i
(y).
For each sample z ∈ S, we create N
c
(V
c
− 1) samples ∆f
i,c
(y
c
), one for each clique
c and each assignment y
c
,= y
(i)
c
. We construct a set of vectors 1 = ¦v
(1)
, . . . , v
(r)
¦,
where v
(j)
∈ IR
mN
c
(V
c
−1)
. The component of v
(j)
corresponding to the sample z
(i)
and the
assignment y
c
to the labels of the clique c will be denoted by v
(j)
i,c
(y
c
). For convenience,
we deﬁne v
(j)
i,c
(y
(i)
c
) = 0 for correct label assignments, as ∆f
i,c
(y
(i)
c
) = 0. To make 1 an
∞norm covering of T
L
(w, S
t
) under ρ
L
, we require that for any w there exists a v
(j)
∈ 1
such that for each sample z
(i)
:
[v
(j)
i,c
(y
c
) −w
¯
∆f
i,c
(y
c
)[ ≤ ; ∀c ∈ (
(i)
, ∀y
c
. (A.1)
By Deﬁnition A.1.1, the number of vectors in 1 is given by r = ^
∞
(T
L
, ρ
L
, , mN
c
(V
c
−1)).
We can now use 1 to construct a covering 1 = ¦V
(1)
, . . . , V
(r)
¦, where
V
(j)
= (V
(j)
1
, . . . , V
(j)
i
, . . . , V
(j)
m
)
and V
(j)
i
∈ IR
L
, for our multierrorlevel function T
M
. Let v
(j)
i
(y) =
c
v
(j)
i,c
(y
c
), and
M
d
(v
(j)
i
, z
(i)
) = min
y:
H
i
(y)=d
v
(j)
i
(y), then
V
(j)
i
= (M
1
(v
(j)
, z
(i)
), . . . , M
d
(v
(j)
, z
(i)
), . . . , M
L
(v
(j)
, z
(i)
)) . (A.2)
Note that v
(j)
i,c
(y
c
) is zero for all cliques c for which the assignment is correct: y
c
= y
(i)
c
.
Thus for an assignment y with d mistakes, at most dq v
(j)
i,c
(y
c
) will be nonzero, as each
label can appear in at most q cliques. By combining this fact with Eq. (A.1), we obtain:
¸
¸
¸v
(j)
i
(y) −w
¯
∆f
i
(y)
¸
¸
¸ ≤ dq, ∀i, ∀y :
H
i
(y) = d. (A.3)
194 APPENDIX A. PROOFS AND DERIVATIONS
We conclude the proof by showing that 1 is a covering of T
M
under ρ
M
: For each w,
pick V
(j)
∈ 1 such that the corresponding v
(j)
∈ 1 satisﬁes the condition in Eq. (A.1). We
must now bound:
ρ
M
(V
(j)
i
, T
M
(w, z
(i)
)) = max
d
[ min
y:
H
i
(y)=d
v
(j)
i
(y) −min
y:
H
i
(y)=d
w
¯
∆f
i
(y)[
d
.
Fix any i. Let y
v
d
= arg min
y:
H
i
(y)=d
v
(j)
i
(y) and y
w
d
= arg min
y:
H
i
(y)=d
w
¯
∆f
i
(y). Con
sider the case where v
(j)
i
(y
v
d
) ≥ w
¯
∆f
i
(y
w
d
) (the reverse case is analogous), we must
prove that:
v
(j)
i
(y
v
d
) −w
¯
∆f
i
(y
w
d
) ≤ v
(j)
i
(y
w
d
) −w
¯
∆f
i
(y
w
d
) ≤ dq ; (A.4)
where the ﬁrst step follows from deﬁnition of y
v
d
, since v
(j)
i
(y
v
d
) ≤ v
(j)
i
(y
w
d
). The last step
is a direct consequence of Eq. (A.3). Hence ρ
M
(V
(j)
i
, T
M
(w, z
(i)
)) ≤ q.
Lemma A.1.11 (Numeric bound on multierrorlevel covering number)
log
2
^
∞
(T
M
, ρ
M
, , m) ≤ 36
R
2
c
w
2
2
q
2
2
log
2
_
1 + 2
_
4
R
c
w
2
q
+ 2
_
mN
c
(V
c
−1)
_
.
Proof: Substitute Theorem A.1.2 into Lemma A.1.10.
Theorem A.1.12 (Multilabel analog of Theorem A.1.3) Let f
M
and f
γ
M
(v) be as deﬁned
above. Let γ
1
> γ
2
> . . . be a decreasing sequence of parameters, and p
i
be a sequence
of positive numbers such that
∞
i=1
p
i
= 1, then for all δ > 0, with probability of at least
1 −δ over data:
E
z
f
M
(T
M
(w, z)) ≤ E
S
f
γ
M
(T
M
(w, z)) +
¸
32
m
_
ln 4^
∞
(T
M
, ρ
M
, γ
i
, S) + ln
1
p
i
δ
_
for all w and γ, where for each ﬁxed γ, we use i to denote the smallest index s.t. γ
i
≤ γ.
Proof: Similar to the proof of Zhang’s Theorem 2 and Corollary 1 [Zhang, 2002] where
in Step 3 (derandomization) we substitute the vectorvalued T
M
and the metric ρ
M
.
Theorem 5.5.1 follows from above theorem with γ
i
= R
c
w
2
/2
i
and p
i
= 1/2
i
using an
A.2. AMN PROOFS AND DERIVATIONS 195
argument identical to the proof of Theorem 6 in Zhang [2002].
A.2 AMN proofs and derivations
In this appendix, we present proofs of the LP inference properties and derivations of the
factored primal and dual maxmargin formulation from Ch. 7. Recall that the LP relaxation
for ﬁnding the optimal max
y
g(y) is:
max
v∈1
K
k=1
µ
v
(k)g
v
(k) +
c∈(\1
K
k=1
µ
c
(k)g
c
(k) (A.5)
s.t. µ
c
(k) ≥ 0, ∀c ∈ (, k;
K
k=1
µ
v
(k) = 1, ∀v ∈ 1;
µ
c
(k) ≤ µ
v
(k), ∀c ∈ ( ¸ 1, v ∈ c, k.
A.2.1 Binary AMNs
Proof (For Theorem 7.2.1) Consider any fractional, feasible µ. We show that we can con
struct a new feasible assignment µ
t
which increases the objective (or leaves it unchanged)
and furthermore has fewer fractional entries.
Since g
c
(k) ≥ 0, we can assume that µ
c
(k) = min
v∈c
µ
v
(k); otherwise we could in
crease the objective by increasing µ
c
(k). We construct an assignment µ
t
from µ by leaving
integral values unchanged and uniformly shifting fractional values by λ:
µ
t
v
(1) = µ
v
(1) −λ1I(0 < µ
v
(1) < 1), µ
t
v
(2) = µ
v
(2) + λ1I(0 < µ
v
(2) < 1),
µ
t
c
(1) = µ
c
(1) −λ1I(0 < µ
c
(1) < 1), µ
t
c
(2) = µ
c
(2) + λ1I(0 < µ
c
(2) < 1).
Now consider the smallest fractional µ
v
(k), λ(k) = min
v : µ
v
(k)>0
y
v
(k) for k = 1, 2.
Note that if λ = λ(1) or λ = −λ(2), µ
t
will have at least one more integral µ
t
v
(k) than µ.
Thus if we can show that the update results in a feasible and better scoring assignment, we
can apply it repeatedly to get an optimal integer solution. To show that µ
t
is feasible, we
need µ
t
v
(1) + µ
t
v
(2) = 1, µ
t
v
(k) ≥ 0 and µ
t
c
(k) = min
i∈c
µ
t
v
(k).
196 APPENDIX A. PROOFS AND DERIVATIONS
First, we show that µ
t
v
(1) + µ
t
v
(2) = 1.
µ
t
v
(1) + µ
t
v
(2) = µ
v
(1) −λ1I(0 < µ
v
(1) < 1) + µ
v
(2) + λ1I(0 < µ
v
(2) < 1)
= µ
v
(1) + µ
v
(2) = 1.
Above we used the fact that if µ
v
(1) is fractional, so is µ
v
(2), since µ
v
(1) + µ
v
(2) = 1.
To show that µ
t
v
(k) ≥ 0, we prove min
v
µ
t
v
(k) = 0.
min
v
µ
t
v
(k) = min
v
_
µ
v
(k) −( min
i:µ
v
(k)>0
µ
v
(k))1I(0 < µ
v
(k) < 1)
_
= min
_
min
i
µ
v
(k), min
i:µ
v
(k)>0
_
µ
v
(k) − min
i:µ
v
(k)>0
µ
v
(k)
__
= 0.
Lastly, we show µ
t
c
(k) = min
i∈c
µ
t
v
(k).
µ
t
c
(1) = µ
c
(1) −λ1I(0 < µ
c
(1) < 1)
= (min
i∈c
µ
v
(1)) −λ1I(0 < min
i∈c
µ
v
(1) < 1) = min
i∈c
µ
t
v
(1);
µ
t
c
(2) = µ
c
(2) + λ1I(0 < µ
c
(1) < 1)
= (min
i∈c
µ
v
(2)) + λ1I(0 < min
i∈c
µ
v
(2) < 1) = min
i∈c
µ
t
v
(2).
We have established that the new µ
t
are feasible, and it remains to show that we can
improve the objective. We can show that the change in the objective is always λD for some
constant D that depends only on µ and g. This implies that one of the two cases, λ = λ(1)
or λ = −λ(2), will necessarily increase the objective (or leave it unchanged). The change
in the objective is:
v∈1
k=1,2
[µ
t
v
(k) −µ
v
(k)]g
v
(k) +
c∈(\1
k=1,2
[µ
t
c
(k) −µ
c
(k)]g
c
(k)
= λ
_
_
v∈1
[D
v
(1) −D
v
(2)] +
c∈(\1
[D
c
(1) −D
c
(2)]
_
_
= λD
D
v
(k) = g
v
(k)1I(0 < µ
v
(k) < 1), D
c
(k) = g
c
(k)1I(0 < µ
c
(k) < 1).
Hence the new assignment µ
t
is feasible, does not decrease the objective function, and
A.2. AMN PROOFS AND DERIVATIONS 197
has strictly fewer fractional entries.
A.2.2 Multiclass AMNs
For K > 2, we use the randomized rounding procedure of Kleinberg and Tardos [1999]
to produce an integer solution for the linear relaxation, losing at most a factor of m =
max
c∈(
[c[ in the objective function. The basic idea of the rounding procedure is to treat
µ
v
(k) as probabilities and assign labels according to these probabilities in phases. In each
phase, we pick a label k, uniformly at random, and a threshold α ∈ [0, 1] uniformly at
random. For each node i which has not yet been assigned a label, we assign the label k
if µ
v
(k) ≥ α. The procedure terminates when all nodes have been assigned a label. Our
analysis closely follows that of Kleinberg and Tardos [1999].
Lemma A.2.1 The probability that a node i is assigned label k by the randomized proce
dure is µ
v
(k).
Proof The probability that an unassigned node is assigned label k during one phase is
1
K
µ
v
(k), which is proportional to µ
v
(k). By symmetry, the probability that a node is as
signed label k over all phases is exactly µ
v
(k).
Lemma A.2.2 The probability that all nodes in a clique c are assigned label k by the
procedure is at least
1
[c[
µ
c
(k).
Proof For a single phase, the probability that all nodes in a clique c are assigned label k if
none of the nodes were previously assigned is
1
K
min
i∈c
µ
v
(k) =
1
K
µ
c
(k). The probability
that at least one of the nodes will be assigned label k in a phase is
1
K
(max
i∈c
µ
v
(k)). The
probability that none of the nodes in the clique will be assigned any label in one phase is
1 −
1
K
K
k=1
max
i∈c
µ
v
(k).
Nodes in the clique c will be assigned label k by the procedure if they are assigned label
k in one phase. (They can also be assigned label k as a result of several phases, but we can
ignore this possibility for the purposes of the lower bound.) The probability that all the
198 APPENDIX A. PROOFS AND DERIVATIONS
nodes in c will be assigned label k by the procedure in a single phase is:
∞
j=1
1
K
µ
c
(k)
_
1 −
1
K
K
k=1
max
i∈c
µ
v
(k)
_
j−1
=
µ
c
(k)
K
k=1
max
i∈c
µ
v
(k)
≥
µ
c
(k)
K
k=1
i∈c
µ
v
(k)
=
µ
c
(k)
i∈c
K
k=1
µ
v
(k)
=
µ
c
(k)
[c[
.
Above, we ﬁrst used the fact that for d < 1,
∞
i=0
d
i
=
1
1−d
, and then upperbounded
the max of the set of positive µ
v
(k)’s by their sum.
Theorem A.2.3 The expected cost of the assignment found by the randomized procedure
given a solution µ to the linear program in Eq. (A.5) is at least
v∈1
K
k=1
g
v
(k)µ
v
(k) +
c∈(\1
1
[c[
K
k=1
g
c
(k)µ
k
c
.
Proof This is immediate from the previous two lemmas.
The only difference between the expected cost of the rounded solution and the (non
integer) optimal solution is the
1
[c[
factor in the second term. By picking m = max
c∈(
[c[, we
have that the rounded solution is at most m times worse than the optimal solution produced
by the LP of Eq. (A.5).
We can also derandomize this procedure to get a deterministic algorithm with the same
guarantees, using the method of conditional probabilities, similar in spirit to the approach
of Kleinberg and Tardos [1999].
Note that the approximation factor of m applies, in fact, only to the clique poten
tials. Thus, if we compare the logprobability of the optimal MAP solution and the log
probability of the assignment produced by this randomized rounding procedure, the terms
corresponding to the logpartitionfunction and the node potentials are identical. We obtain
an additive error (in logprobability space) only for the clique potentials. As node poten
tials are often larger in magnitude than clique potentials, the fact that we incur no loss
proportional to node potentials is likely to lead to smaller errors in practice. Along similar
lines, we note that the constant factor approximation is smaller for smaller cliques; again,
we observe, the potentials associated with large cliques are typically smaller in magnitude,
reducing further the actual error in practice.
A.2. AMN PROOFS AND DERIVATIONS 199
A.2.3 Derivation of the factored primal and dual maxmargin QP
Using Assumptions 7.4.1 and 7.4.4, we have the dual of the LP used to represent the
interior max subproblem max
y
w
¯
f
i
(y) +
i
(y) in Eq. (3.2):
min
v∈1
ξ
i,v
(A.6)
s.t. −w
¯
f
i,v
(k) −
c⊃v
m
i,c,v
(k) ≥
i,v
(k) −ξ
i,v
, ∀i, v ∈ 1
(i)
, k;
−¨ w
¯
¨
f
i,c
(k) +
v∈c
m
i,c,v
(k) ≥
i,c
(k), ∀i, c ∈ (
(i)
¸ 1
(i)
, k;
m
i,c,v
(k) ≥ 0, ∀i, c ∈ (
(i)
¸ 1
(i)
, v ∈ c, k;
where f
i,c
(k) = f
i,c
(k, . . . , k) and
i,c
(k) =
i,c
(k, . . . , k). In the dual, we have a variable
ξ
i,v
for each normalization constraint in Eq. (7.1) and variables m
i,c,v
(k) for each of the
inequality constraints.
Substituting this dual into Eq. (5.1), we obtain:
min
1
2
[[w[[
2
+ C
i
ξ
i
(A.7)
s.t. w
¯
f
i
(y
(i)
) + ξ
i
≥
v∈1
(i)
ξ
i,v
, ∀i;
−w
¯
f
i,v
(k) −
c⊃v
m
i,c,v
(k) ≥
i,v
(k) −ξ
i,v
, ∀i, v ∈ 1
(i)
, k;
−¨ w
¯
¨
f
i,c
(k) +
v∈c
m
i,c,v
(k) ≥
i,c
(k), ∀i, c ∈ (
(i)
¸ 1
(i)
, k;
m
i,c,v
(k) ≥ 0, ∀i, c ∈ (
(i)
¸ 1
(i)
, v ∈ c, k;
¨ w ≥ 0.
Now let ξ
i,v
= ξ
t
i,v
+ w
¯
f
i,v
(y
(i)
v
) +
c⊃v
¨ w
¯
¨
f
i,c
(y
(i)
c
)/[c[ and m
i,c,v
(k) = m
t
i,c,v
(k) +
¨ w
¯
¨
f
i,c
(y
(i)
c
)/[c[. Reexpressing the above QP in terms of these new variables, we get:
200 APPENDIX A. PROOFS AND DERIVATIONS
min
1
2
[[w[[
2
+ C
i
ξ
i
(A.8)
s.t. ξ
i
≥
v∈1
(i)
ξ
t
i,v
, ∀i;
w
¯
∆f
i,v
(k) −
c⊃v
m
t
i,c,v
(k) ≥
i,v
(k) −ξ
t
i,v
, ∀i, v ∈ 1
(i)
, k;
¨ w
¯
∆
¨
f
i,c
(k) +
v∈c
m
t
i,c,v
(k) ≥
i,c
(k), ∀i, c ∈ (
(i)
¸ 1
(i)
, k;
m
t
i,c,v
(k) ≥ −¨ w
¯
¨
f
i,c
(y
(i)
c
)/[c[, ∀i, c ∈ (
(i)
¸ 1
(i)
, v ∈ c, k;
¨ w ≥ 0.
Since ξ
i
=
i,v∈1
(i)
ξ
t
i,v
at the optimum, we can eliminate ξ
i
and the corresponding set
of constraints to get the formulation in Eq. (7.4), repeated here for reference:
min
1
2
[[w[[
2
+ C
i,v∈1
(i)
ξ
i,v
(A.9)
s.t. w
¯
∆f
i,v
(k) −
c⊃v
m
i,c,v
(k) ≥
i,v
(k) −ξ
i,v
, ∀i, v ∈ 1
(i)
, k;
¨ w
¯
∆
¨
f
i,c
(k) +
v∈c
m
i,c,v
(k) ≥
i,c
(k), ∀i, c ∈ (
(i)
¸ 1
(i)
, k;
m
i,c,v
(k) ≥ −¨ w
¯
¨
f
i,c
(y
(i)
c
)/[c[, ∀i, c ∈ (
(i)
¸ 1
(i)
, v ∈ c, k;
¨ w ≥ 0.
A.2. AMN PROOFS AND DERIVATIONS 201
Now the dual of Eq. (A.9) is given by:
max
i,c∈(
(i)
, k
µ
i,c
(k)
i,c
(k) −
1
2
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,v∈1
(i)
, k
µ
i,v
(k)∆
˙
f
i,v
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
(A.10)
−
1
2
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¨ τ +
i,c∈(
(i)
\1
(i)
,v∈c, k
λ
i,c,v
(k)
¨
f
i,c
(y
(i)
c
)/[c[ +
i,c∈(
(i)
, k
µ
i,c
(k)∆
¨
f
i,c
(k)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
s.t. µ
i,c
(k) ≥ 0, ∀i, ∀c ∈ (
(i)
, k;
K
k=1
µ
i,v
(k) = C, ∀i, ∀v ∈ 1
(i)
;
µ
i,c
(k) −µ
i,v
(k) = λ
i,c,v
(k), ∀i, ∀c ∈ (
(i)
¸ 1
(i)
, v ∈ c, k;
λ
i,c,v
(k) ≥ 0 ∀i, ∀c ∈ (
(i)
¸ 1
(i)
, v ∈ c, k,
¨ τ ≥ 0.
In this dual, µ correspond to the ﬁrst two sets of constraints, while λ and ¨ τ correspond
to third and fourth set of constraints. Using the substitution
¨ ν = ¨ τ +
i,c∈(
(i)
\1
(i)
,v∈c, k
λ
i,c,v
(k)
¨
f
i,c
(y
(i)
c
)/[c[
and the fact that λ
i,c,v
(k) ≥ 0 and
¨
f
i,c
(y
(i)
c
) ≥ 0, we can eliminate λ and ¨ τ, as well as divide
µ’s by C, and reexpress the above QP as:
max
i,c∈(
(i)
, k
µ
i,c
(k)
i,c
(k) −
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
i,v∈1
(i)
, k
µ
i,v
(k)∆
˙
f
i,v
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
−
1
2
C
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¨ ν +
i,c∈(
(i)
, k
µ
i,c
(k)∆
¨
f
i,c
(k)
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
¸
2
s.t. µ
i,c
(k) ≥ 0, ∀i, ∀c ∈ (
(i)
, k;
K
k=1
µ
i,v
(k) = 1, ∀i, ∀v ∈ 1
(i)
;
µ
i,c
(k) ≤ µ
i,v
(k), ∀i, ∀c ∈ (
(i)
¸ 1
(i)
, v ∈ c, k; ¨ ν ≥ 0.
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c Copyright by Ben Taskar 2005 All Rights Reserved
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I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy.
Daphne Koller
Computer Science Department Stanford University
(Principal Advisor)
I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy.
Andrew Y. Ng
Computer Science Department Stanford University
I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy.
Fernando Pereira
Computer Science Department University of Pennsylvania
Approved for the University Committee on Graduate Studies:
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Mark and Tsilya. and my love.To my parents. . Anat.
.
likelihoodbased estimation methods by concentrating directly on the robustness of the decision boundary of a model. parse tree.Abstract Most questions require more than just truefalse or multiplechoice answers. coherent analysis of a sentence. recursive language models such as context free grammars. reconstruct 3D shapes from stereo and video. Our framework deﬁnes a suite of efﬁcient learning algorithms that rely on the expressive power of convex optimization to compactly capture inference or vii . we analyze genetic sequences to predict 3D structure of proteins. grammatical. In computational biology. chemical. The acquired expertise must now be used to address tasks that demand answers as complex as the questions. or translation into another language. has placed the heaviest emphasis on complex questions with simple answers. spatial constraints and correlations. we often need to construct a global. Intuitively. combinatorial optimization problems such as weighted matchings and graphcuts. ﬁnd global alignment of related DNA strings. such as its corresponding partofspeech sequence. like standardized testing. Yet supervised learning. and recognize functional portions of a genome. and track motion of articulated bodies. Such complex answers may consist of multiple interrelated decisions that must be weighed against each other to arrive at a globally satisfactory and consistent solution to the question. We typically handle the exponential explosion of possible answers by building models that compactly capture the structural properties of the problem: sequential. This thesis presents a discriminative estimation framework for structured models based on the large margin principle underlying support vector machines. In natural language processing. In computer vision. the largemargin criterion provides an alternative to probabilistic. Such structured models include graphical models such as Markov networks (Markov random ﬁelds). we segment complex objects in cluttered scenes. temporal.
We use combinatorial properties of weighted matchings to develop an exact.solution optimality in structured models. We use graph decomposition to derive an exact. we derive a maxmargin formulation for learning the scoring metric for clustering from clustered training data. we solve very large estimation problems. accurate prediction in realworld tasks. which compactly deﬁne templates for Markov networks for domains with relational structure: objects. our framework applies to a wide range of other models: We exploit context free grammar structure to derive a compact maxmargin formulation that allows highaccuracy parsing in cubic time by using novel kinds of lexical information. associative Markov networks (AMNs). convex formulation for largemargin estimation of Markov networks with sequence and other lowtreewidth structure. our framework allows exact estimation of such networks of arbitrary connectivity and topology. including handwriting recognition. Finally. In addition to graphical models. tuning one to the other in a joint optimization. compact. viii . We describe experimental applications to a diverse range of tasks. While likelihoodbased methods are believed to be intractable for AMNs over binary variables. hypertext categorization. For some of these models. disulﬁde connectivity prediction in proteins. which captures positive correlations between variables and permits exact inference which scales up to tens of millions of nodes and edges. We also introduce relational Markov networks (RMNs). email organization and image segmentation. which are undirected probabilistic graphical models widely used to efﬁciently represent and reason about joint multivariate distributions. These empirical evaluations show signiﬁcant improvements over stateoftheart methods and promise wide practical use for our framework. Using an efﬁcient onlinestyle algorithm that exploits inference in the model and analytic updates. 3D terrain classiﬁcation. alternative estimation methods are intractable. natural language parsing. We analyze the theoretical generalization properties of maxmargin estimation in Markov networks and derive a novel type of bound on structured error. Seamless integration of kernels with graphical models allows efﬁcient. The largest portion of the thesis is devoted to Markov networks. which tightly integrates metric learning with the clustering algorithm. efﬁcient formulation for learning to match and apply it to prediction of disulﬁde connectivity in proteins. relations. attributes. We deﬁne an important subclass of Markov networks.
Lise Getoor. Eran Segal.Acknowledgements I am profoundly grateful to my advisor. I ix . Alexis Battle. I am very lucky to have been a part of it and shared the company. Christian Shelton. Carlos Guestrin. the questions and the expertise of Pieter Abbeel. Dirk Ormoneit. for their excellent suggestions and thoughtprovoking questions. Uri Nodelman. writing and presenting results in an engaging manner. advising. Luke Biewald. I have learned a great deal from their work and their inﬂuence on this thesis is immense. Sebastian introduced me to the fascinating problems in 3D vision and robotics. Her tireless pursuit of excellence in research. Uri Lerner. Stephen Boyd and Sebastian Thrun. David Vickrey. Andrew Ng and Fernando Pereira. His thoughtful guidance and quick wit were a great welcome and inspiration to continue my studies. Andrew’s research on clustering and classiﬁcation has informed many of the practical problems addressed in the thesis. JeanClaude Latombe was my ﬁrst research advisor when I was still an undergraduate at Stanford. teaching. I would like to thank my thesis committee. When I started my research in machine learning with Daphne. Simon Tong. Daphne Koller. the ideas. as well as my defense committee members. In particular. Xavier Boyen. Fernando’s work on Markov networks has inspired my focus on this subject. Gal Chechik. Haidong Wang and Ming Fai Wong. Daphne’s research group is an institution in itself. Stephen’s book on convex optimization is the primary source of many of the insights and derivations in this thesis. pushing ideas to their full development. Vassil Chatalbashev. Finally. I am indebted to Daphne for priceless and copious advice about selecting interesting problems. Ron Parr. and every other aspect of her academic work is truly inspirational. making progress on difﬁcult ones. Drago Anguelov.
David McAllester. Peter Bartlett. tennis court. who is always willing to share with me everything from research problems to music and backpacking treks to Russian books and Belgian beer. David’s wideranging research on probability and logic. They have taught me to remain steadfast when elegant theories meet the ragged edge of real problems. Geremy Heitz. Merci beaucoup to Pieter Abbeel. over cheap Thai food. I could not wish for more caring advice and encouragement than she has given me all these years. Michael Collins. enlightened much of my work. Daphne Koller. my personal climbing instructor. Vasco Chatalbashev. biking to EV. for numerous enlightening discussions that we have had anytime. I would like to express my appreciation and gratitude to all my collaborators for their excellent ideas. Carlos Guestrin. Ogromnoye spasibo to my ofﬁcemate. Blagodarya vi mnogo for another great Bulgarian I have the good luck to know. Luke Biewald. and better yet. sportsmate. my sounding board for many ideas in convex optimization and learning.had the privilege and pleasure to work with Nir Friedman. Michael Littman and David McAllester all in one place. avid grillmaster x . Muchas gracias to Carlos Guestrin. languages and generalization bounds. Eran Segal. Nir Friedman. Chris Manning. David Vickrey and Ming Fai Wong. Lise has been a great friend and my other big sister throughout my graduate life. Vassil Chatalbashev. I am very glad I had the chance to work with him on the maxmargin parsing project. I was lucky to meet Michael Collins. (Almost) everything I know about natural language processing I learned from Chris Manning and Dan Klein. Drago Anguelov. Dan Klein. everready to checkmate. explaining why other ideas do not work. to mention a few. for his company and ideas. while I was a summer intern at AT&T. good cheer and the great knack for always coming through. always late. Chris’ healthy scepticism and emphasis on the practical has kept me from going down many deadend paths. Michael Littman. Drago Anguelov. fellow photography fanatic. Lise Getoor and Eran Segal. Collins’ work on learning largemargin tagging and parsing models motivated me to look at such methods for other structured models. hard work and dedication: Pieter Abbeel. has been a constant source of encouragement and inspiration. lightness and depth. Lise Getoor. Audrey Gasch. with his endearing combination of humor and warmth. Dan has an incredible gift of making ideas work. anywhere: gym.
kind heart and excellent work. Mark and Tsilya. for his sense of humor. thank you for making me happy next to you. Talia. To my sister. My parents. I will not list all of you here. I am grateful for bringing me so much joy and love. Anat Caspi. my brotherinlaw.and exploiterofstructure extraordinaire. tears and laughter. but worked hard to keep my relative sanity throughout. xi . I thank them for all the sacriﬁces they have made to ensure that their children would have freedom and opportunities they never had in Soviet Union. Mhgoisaai to Ming Fai Wong. Anna. and my sweet niece. Many thanks to my friends who have had nothing to do with work in this thesis. but my gratitude to you is immense. hardship and love. To my tireless partner in work and play. Ilya. have given me unbending support and constant encouragement. for opening his ear and heart to me when it matters most.
xii .
. . .1 1. . . . . . . . . . . . . . . . . . . . . . . vii ix 1 2 4 6 8 Thesis outline . . 22 24 3 Structured models 3. .3 2. . . . . . . . . . . . . . . . . . . . . . . . . . . Complex prediction problems . 25 xiii . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4 1. . . . . . . . . . . . . . . . . . . . . . 21 SVM dual and kernels . . . . . . . . . . . 21 Support vector machines .1 2. . . . . . . . . . Contributions . . . . . . . . . . 13 I Models and methods 2 Supervised learning 2. . . . . . . . . . . . . . .5 15 16 Classiﬁcation with generalized linear models . . 11 Previously published work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Structured models . . . . . .1 Probabilistic models: generative and conditional . . . . . . . . . . .2 1. . . .3 1. . . . . . .Contents Abstract Acknowledgements 1 Introduction 1. . . . . . . . . . . . . .6 Supervised learning . .2 2. .4 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Logistic regression . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Logistic dual and maximum entropy . . . . . . . . . . . . . . . . . . .5 1. . . . . . . .
3. . 31 Linear programming MAP inference . . . . . .7 Maximum likelihood estimation . . . . . . . . . . . . . . . .1 4.3. . . . . . . . . . . . . . . . . . . . . . . . . .1 4. . . . . . . 34 3. . . . .3. . . . . . . . . . . . . . 65 Untriangulated models . . . . . . . . . . . . . . 74 75 6 M3 N algorithms and experiments 6. . . . . . .3 Representation . . . . . . . . . . . . . . . . . . .3. . . . . . . . . . . . . . . . . . 53 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . 69 Generalization bound . . .1 6. . . . . 48 Constraint generation . . . . . . . . . . .1. . . . . . . . . . . 37 Combinatorial problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2 5. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3 Prediction models: normalized and unnormalized . 27 3. . . 59 Maximum margin estimation . . . 70 Related work . . 43 Minmax formulation . . . . . . . . 61 M3 N dual and kernels . . . . . . . . . . . . . . . . . . . . . . . . . .3 4. . . . . . . . . . . . . . . . . . . . . .5 Context free grammars . . . . . .1 3. . . . .5 5. . .1. . . . . . . . . . . . . . . . . . . . . . . . . . 50 Related work . . . . . . . . . . . . .2 3.2 4. . . . . . . . . . . . . . . . . . . . . . . . . . . 50 Constraint strengthening . . . . . . . . . . . . 78 xiv . . . . . . .1 4. . . . . . . . . . . . . . . . . . 43 Certiﬁcate formulation . . . .4 3. . . . . . . . . . . . . . . .6 5. . . . . . 27 Markov networks . .1 5. . . . . . . . . . . . . . . . . . . . 55 II Markov networks 57 58 5 Markov networks 5. . . .2 3.2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3 5. . . . . . . . . . . . . . . . . . 40 42 4 Structured maximum margin estimation 4. . . . . . . 52 Approximations: upper and lower bounds . . . . . . . .2 4. . . . . . . . . . . . . 28 Inference . . . . . . . . . . . . .4 Maxmargin estimation .4 5. . . . . .1. . . . . . . . . . . . . .1 Solving the M3 N QP . . . .2. . . . . . . . 73 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 SMO . . . . . . . . . . . . . . . . .2 4. . . .
. . . . . . . . .7 Maxmargin estimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 8. . . . . . . 118 8. . . . . . . . . . . . . . clustering 9 Context free grammars 9. . .3 8. . . . . . . . . . . . . . . . . . . . . .4 Selecting SMO pairs . . . . . . 95 7. . . . . . . . . . . . . . . . . . 121 8. .1. . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 Related work . . . .3. . . . . . . . . . . . . . . . . . . . . . . . 93 Multiclass case . . . . . . . . . . . . . . . . . . .3 Associative networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 Structured SMO . .3 Flat models . . . . . . . . . . .2 6. . . 124 III Broader applications: parsing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4 7. .4. . . . . . . . . . . . . . 97 Experiments . 87 Conclusion . . . . . . . .5 8. . . . . . . . . . . . . . . .4. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 Cocite model . . . . . . . . . . . . . . . . . . . . . . . . . .1. . . . . . . .4 Relational classiﬁcation . . . . . . . . .1 7. . 90 LP Inference . . . . . . . . . 110 Relational Markov networks . . 81 Experiments . . . . . .2 8. . 119 Link model . . . 113 Approximate inference and learning . . . . . . . . . . . . . . . . . . . .6 7. . . . . . . . . . . . . . . . . . . . .6. . . .3. . . .2 8. . . . . . . . . . . . . . . . . 104 Conclusion . . . . matching. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2 7. . . . . . .2 Graph construction . . . . . . . 116 Experiments . .1 8. . . . . . . 123 Conclusion . . . . . . . . . . . . . . . . . . . . . . .2 6. 91 Mincut inference . . . . . . . 104 109 8 Relational Markov networks 8. . . . .6 Related work . . . . . . . 93 7. .4. . . . . . . . . . . . . . . . . . . . . . . . .5 7. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128 xv . . .3 6. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 89 7 Associative Markov networks 7.3 6. . . . . . . . . . . . . . . . . . . .1 127 128 Context free grammar model . .1 7. .
. 135 9. . . . .1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4. . . . 143 144 10 Matchings 10. . . . . . . . . . . . . . . . . . . . . 168 11.3 Image segmentation . . . . . . . . . . . . . . . . . 157 10. . . . . . . . . . . . .1 Linear programming relaxation . . . . . .4. . . . . . . . . . . . . . . . . . .5 9. . .4 9. . . . .2 Learning formulation . . . . . .2 Semideﬁnite programming relaxation . . . . . . . . . . . . . . . . . 148 10. . . 153 10. . . . .3 Minmax formulation .1 9. . . . . . . . . . . . . . . . . . . . . . . 163 11. . . . . . . .3. . . . . . . . . . . . . . . . . . .2 9. . . . . . . . . 172 11. . . . . . . . . . . . . . . . . . . . . . . . . . . . 159 11 Correlation clustering 160 11. . . . .1 Irrelevant features . . .2 Maximum likelihood estimation . . . . . . .1. . . . . . . . . . . .8 Conclusion . . . . . . . . 161 11. . . . . . . . . . . . . . . . . . . . . . . . . .3 Dual formulation and kernels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168 11. . . . .2 Email clustering . . . 154 10. . . . . . . . . . . . . . . . . . . .6 9. . . . . . . . . 150 10. . . . . . . . . 145 10. .1 Clustering formulation . . . . . . . 133 9. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146 10. . . . . . . .9. . . . . . .4 Certiﬁcate formulation . . . . . . 170 11. . . . . . . . . . . . . . . . . . . . . . 173 xvi .4 Experiments . .3. . . . . . . . .7 Structured SMO for CFGs . . . . .6 Conclusion . . .2 Learning to match . . . . . . . . .3 Context free parsing . . . . . . . . . 138 Related work . . . . . . . . . . . . . . . . . . . . . . . . .5 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5 Kernels . . . . . . . . . . . . . . . . . . . . . . . . . . . 168 11. . . . . . . . . . . . . . . . . 134 Maximum margin estimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6 Experiments . 164 11. . . . . . . . . . . . . . . . . 162 11.4. . . . . . . 132 Discriminative parsing models . . . . . . . . . . . . . . 138 Experiments . . .1 Disulﬁde connectivity prediction .7 Related work . . . . . . . . . . . 142 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 11. . .
. . . . . .IV Conclusions and future directions 12 Conclusions and future directions 175 176 12. . .2. . . . . . . .2. .1. . . . . . . 190 A. . . . . . . . . . relational . . . . . . 185 12. . .1. . .1 Binary classiﬁcation . . .3 Broader applications: parsing. . . .1. . . . . . . 188 A. . . . . . . . . . . . . . . . . . . .5. . . . . . . . . . . . . . . . . . . . .1. . . . . . . . . 176 12. . . . . 195 A. . 183 12. . . . . . . . . . .2 Structured classiﬁcation . . . . . . .2 Multiclass AMNs . . . . . . . . . . . . 177 12. . . .2. . . . . . . . . . .1 . . . . . . . . . . . .2 AMN proofs and derivations . . . . 197 A. . . . . . . . . . . . . . . . . . . . . . . . . . .1 Structured maximum margin estimation . . .2. . . clustering . . . . . . . . .1 Proof of Theorem 5. . . . . 187 A Proofs and derivations 188 A. . 189 A. . . 199 Bibliography 202 xvii . .2. . . . . . . associative. . . . .1 Theoretical analysis and optimization algorithms . . . 180 12. . . . . . . . . .2 Extensions and open problems . . . . . . . . . . . . . . . .3 More general learning settings . . . matching. . . . . 182 12. . . . .2 Novel prediction tasks . .1 Summary of contributions . . . . . .1 Binary AMNs . . . . . .2 Markov networks: maxmargin. . . . . . . . . . . . . .2. . . . . . . .1. . . . 184 12. . . 183 12. . . . . . . . . . . . . . .3 Derivation of the factored primal and dual maxmargin QP . . . . . . . . . .3 Future . . . . . 195 A. . . . . .
. . . . . . . . . . . . . 140 10. . .2 Parsing results on development set . . . . . . . . . . 156 xviii . . . . . . . . . . . . .1 Bond connectivity prediction results . 140 Parsing results on test set . . . . . . . . .List of Tables 9. . . . . . . . .1 9. . . . . . . . . . . . . . . .
6 Supervised learning setting . . .5 3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 5. . . .3 6. . . 52 Chain M3 N example . . . . 29 Diamond Markov network . 51 A constraint generation algorithm. . . . . . . . . . . . . . . . . . . . 19 Classiﬁcation loss and upper bounds . . . . . . . . . . . . . . . . . . . . .6 4. . . . . . . . . . . . . . . . . . . . . . . . . . 25 Chain Markov network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Example parse tree . . . . . . . . . .3 3. . . . 79 SMO pair selection . . . . . . . . . . . 86 xix .2 6. . . . . . . . . . . . 85 OCR results . . . .1 4. . 77 SMO subproblem . . . . . . . . . .4 3. . . .2 2. . . . . . . . . . . . . . . 34 Marginal agreement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4 6. . . . . . . 80 Structured SMO diagram . . . . . . . . . . . . . . 3 4 Handwritten character recognition . . . . . . . . . . . . . .1 6. .2 6. . . . 37 Exact and approximate constraints for maxmargin estimation . . . . . . . . . . . . . . . . . . . . . . . . . 64 Diamond Markov network . . . . . . 32 Diamond network junction tree . . . . . . . . . . . . . . 82 Structured SMO pair selection . . . . . 69 Blockcoordinate ascent . . . . . . . . . 20 Handwritten word recognition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2 5. . . . . Examples of complex prediction problems . . . . . . . . .2 3. . . . . . . . . . . . . . . .1 1. . . . . . . . . . . . . . . . . .2 3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 3. . . . . .5 6. .1 2. . . . . . . . . . . . . . .List of Figures 1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
113 WebKB results: ﬂat models . . . . . . . . .7. . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 11. . . . . . . . . . .1 7. . . . . . . . . . . . . . . . . 171 11. . . .3 Two segmentations by different users . . . . . . . . . . . . .4 7. .4 Two segmentations by different models . . . . . . . . . . . . . . . 170 11. . . . . . . . . 120 WebKB results: link model . . . 96 Segbot: roving robot equipped with SICK2 laser sensors. . . 147 10. 150 10. 130 10. . . . . . . . . . . .2 7. . . . . . . . . . . . number of bonds . . .2 8. . . . . . . . . . . . 94 αexpansion algorithm . . . . . . . . . . . .4 9. . . 101 Comparison of terrain classiﬁcation models (detail) . . .1 PDB protein 1ANS . . . 172 xx . .8 7. . . . . . . . . . . . . . . . . . . . . . . . . . . 100 3D laser scan range map of the Stanford Quad. . . . . . . . . . .9 8. . . . . . . . . . . . . . . . . . . . . .1 8. . . . . . 106 Labeled portion of the test terrain dataset (Ground truth and SVM predictions)107 Labeled portion of the test terrain dataset (VotedSVM and AMN predictions)108 Link model for document classiﬁcation . . . . . . .2 Number of constraints vs. . . . . . . . . . . . . . . . . . . . . . . 169 11. . . . . 122 Two representations of a binary parse tree . . .7 7. . . . .5 7. . . . . . . . . . . . . . . . . . . . . . . . 102 Mincut inference running times .2 Learning to organize email . . . . . . . . . . . . . .1 Mincut graph construction . . . . 121 WebKB results: cocite model . . . . . .3 Learning curve for bond connectivity prediction . . . . . . . . . . . . . . . . . . . . . . .1 Learning to cluster with irrelevant features . . . . . . . . . . . . . .3 8. . . . . . . . . . . . . . . .3 7. . . . . . . . . . . 103 Comparison of terrain classiﬁcation models (zoomedout) .6 7. . . . . . . . .
say. the list of things we would like a computer to learn to do is much. for example. One of its primary goals 1 . are primarily concerned with achieving acceptable speed and accuracy of recognition rather than modeling this complicated process with any biological verity.Chapter 1 Introduction The breadth of tasks addressed by machine learning is rapidly expanding. Of course. image analysis. The reconstruction of an entire sentence from the photons hitting the retina off of each tiny patch of an image undoubtedly requires an elaborate interplay of recognition and representation of the penstrokes. Computational models for handwriting recognition aim to capture the salient properties of the problem: typical shapes of the letters. etc. DNA sequence analysis. scientiﬁc discovery. likely letter combinations that make up words. Machine learning offers an alternative to encoding all the intricate details of such a model from scratch. Some tasks. common ways to combine words into phrases. game playing. the individual letters. Computer scientists. As we work our way down that list. Major applications include medical diagnosis. fraud detection. neuroscientists. as opposed to. are performed almost effortlessly by a person. but remain difﬁcult and errorprone for computers. we encounter the need for very sophisticated decision making from our programs. whole words and constituent phrases. The complex synthesis of many levels of signal processing a person executes when confronted by a line of handwritten text is daunting. speech and handwriting recognition. ﬁnancial analysis. handwriting recognition. much longer. robot locomotion and many more. frequent grammatical constructions of the phrases.
2
CHAPTER 1. INTRODUCTION
is to devise efﬁcient algorithms for training computers to automatically acquire effective and accurate models from experience. In this thesis, we present a discriminative learning framework and a novel family of efﬁcient models and algorithms for complex recognition tasks in several disciplines, including natural language processing, computer vision and computational biology. We develop theoretical foundations for our approach and show a wide range of experimental applications, including handwriting recognition, 3dimensional terrain classiﬁcation, disulﬁde connectivity in protein structure prediction, hypertext categorization, natural language parsing, email organization and image segmentation.
1.1 Supervised learning
The most basic supervised learning task is classiﬁcation. Suppose we wish to learn to recognize a handwritten character from a scanned image. This is a classiﬁcation task, because we must assigns a class (an English letter from ‘a’ through ‘z’) to an observation of an object (an image). Essentially, a classiﬁer is a function that maps an input (an image) to an output (a letter). In the supervised learning setting, we construct a classiﬁer by observing labeled training examples, in our case, sample images paired with appropriate letters. The main problem addressed by supervised learning is generalization. The learning program is allowed to observe only a small sample of labeled images to produce an accurate classiﬁer on unseen images of letters. More formally, let x denote an input. For example, a blackandwhite image x can be represented as a vector of pixel intensities. We use X to denote the space of all possible inputs. Let y denote the output, and Y be the discrete space of possible outcomes (e.g., 26 letters ‘a’‘z’). A classiﬁer (or hypothesis) h is a function from X to Y, h : X → Y. We denote the set of all classiﬁers that our learning program can produce as H (hypothesis class). Then given a set of labeled examples {x(i) , y (i) }, i = 1, . . . , m, a learning program seeks to produce a classiﬁer h ∈ H that will work well on unseen examples x, usually by ﬁnding h that accurately classiﬁes training data. The diagram in Fig. 1.1 summarizes the supervised learning setting.
1.1. SUPERVISED LEARNING
3
Hypotheses
Labeled data
Learning Prediction New data
Figure 1.1: Supervised learning setting
The problem of classiﬁcation has a long history and highly developed theory and practice (see for example, Mitchell [1997]; Vapnik [1995]; Duda et al. [2000]; Hastie et al. [2001]). The two most important dimensions of variation of classiﬁcation algorithms is the hypothesis class H and the criterion for selection of a hypothesis h from H given the training data. In this thesis, we build upon the generalized linear model family, which underlies standard classiﬁers such as logistic regression and support vector machines. Through the use of kernels to implicitly deﬁne highdimensional and even inﬁnitedimensional input representations, generalized linear models can approximate arbitrarily complex decision boundaries. The task of selecting a hypothesis h reduces to estimating model parameters. Broadly speaking, probabilistic estimation methods associate a joint distribution p(x, y) or conditional distribution p(y  x) with h and select a model based on the likelihood of the data [Hastie et al., 2001]. Joint distribution models are often called generative, while conditional models are called discriminative. Large margin methods, by contrast, select a model based on a more direct measure of conﬁdence of its predictions on the training data called the margin [Vapnik, 1995]. The difference between these two methods is one of the key
4
CHAPTER 1. INTRODUCTION
The screen was a sea of red
RSCCPCYWGGCPW GQNCYPEGCSGPKV
brace
(a)
(b)
(c)
(d)
Figure 1.2: Examples of complex prediction problems (inputstop, outputsbottom):
(a) handwriting recognition [image → word]; (b) natural language parsing [sentence → parse tree]; (c) disulﬁde bond prediction in proteins [aminoacid sequence → bond structure (shown in yellow)]; (d) terrain segmentation [3D image → segmented objects (trees, bushes, buildings, ground)]
themes in this thesis. Most of the research has focused on the analysis and classiﬁcation algorithms for the case of binary outcomes Y = 2, or a small number of classes. In this work, we focus on prediction tasks that involve not a single decision with a small set of outcomes, but a complex, interrelated collection of decisions.
1.2 Complex prediction problems
Consider once more the problem of character recognition. In fact, a more natural and useful task is recognizing words and entire sentences. Fig. 1.2(a) shows an example handwritten word “brace.” Distinguishing between the second letter and fourth letter (‘r’ and ‘c’) in isolation is actually far from trivial, but in the context of the surrounding letters that together form a word, this task is much less errorprone for humans and should be for computers as well. It is also more complicated, as different decisions must be weighed against each other to arrive at the globally satisfactory prediction. The space of all possible outcomes
1.2. COMPLEX PREDICTION PROBLEMS
5
Y is immense, usually exponential in the number of individual decisions, for example, the number of 5 letter sequences (265 ). However, most of these outcomes are unlikely given the observed input. By capturing the most salient structure of the problem, for example the strong local correlations between consecutive letters, we will construct compact models that efﬁciently deal with this complexity. Below we list several examples from different ﬁelds. • Natural language processing Vast amounts of electronically available text have spurred a tremendous amount of research into automatic analysis and processing of natural language. We mention some of the lowerlevel tasks that have received a lot of recent attention [Charniak, 1993; Manning & Sch¨ tze, 1999]. Partofspeech tagging involves assigning each u word in a sentence a partofspeech tag, such as noun, verb, pronoun, etc. As with handwriting recognition, capturing sequential structure of correlations between consecutive tags is key. In parsing, the goal is to recognize the recursive phrase structure of a sentence, such as verbal, noun and prepositional phrases and their nesting in relation to each other. Fig. 1.2(b) shows a parse tree corresponding to the sentence: “The screen was a sea of red” (more on this in Ch. 9). Many other problems, such as namedentity and relation extraction, text summarization, translation, involve complex global decision making. • Computational biology The last two decades have yielded a wealth of highthroughput experimental data, including complete sequencing of many genomes, precise measurements of protein 3D structure, genomewide assays of mRNA levels and proteinprotein interactions. Major research has been devoted to geneﬁnding, alignment of sequences, protein structure prediction, molecular pathway discovery [Gusﬁeld, 1997; Durbin et al., 1998]. Fig. 1.2(c) shows disulﬁde bond structure (shown in yellow) we would like to predict from the aminoacid sequence of the protein (more on this in Ch. 10). • Computer vision As digital cameras and optical scanners become commonplace accessories, medical imaging technology produces detailed physiological measurements, laser scanners
bushes. and relational interactions in prediction problems arising in many ﬁelds. Inference in these models refers to computing the highest scoring output given the input and usually involves dynamic programming or combinatorial optimization. motion tracking. typically through a compact. Such models are encoded by a graph. 2002]. a model assigns a score (or likelihood in probabilistic models) to each possible input/output pair (x. INTRODUCTION capture 3D environments. and much more [Forsyth & Ponce. spatial. Fig. Markov random ﬁelds) are extensively used to model complex sequential. The graphical structure of the network (more precisely. ground.3 Structured models This wide range of problems have been tackled using various models and methods. Abstractly. We focus on the models that compactly capture correlation and constraint structure inherent to many tasks. which we formally deﬁne in Ch. Markov networks compactly represent complex joint distributions of the label variables by modeling their local interactions. 1. parameterized scoring function. satellites and telescopes bring pictures of Earth and distant stars. buildings. and whose edges represent and quantify direct dependencies between them.2(d) shows a 3D laser range data image of the Stanford campus collected by a roving robot which we would like to segment into objects such as trees. These problems involve labeling a set of related objects that exhibit local consistency. The graphical structure of the models encodes the qualitative aspects of the distribution: direct dependencies as well as conditional independencies. 7). (more on this in Ch. • Context free grammars . etc. 1. the treewidth of the graph.k. 3D reconstruction from stereo and video. y). Example tasks include object detection and segmentation. we are ﬂooded with images we would like our computer to analyze. whose nodes represent the different object labels. The quantitative aspect of the model is deﬁned by the potentials that are associated with nodes and cliques of the graph.a.6 CHAPTER 1. • Markov networks Markov networks (a. 3) is critical to efﬁcient inference and learning in the model.
the nonterminal symbols (labels of internal nodes) correspond to syntactic categories such as noun phrase (NP). determiners (DT) and prepositions (IN). both joint and conditional. Although the term ‘model’ is often reserved for probabilistic models. A CFG consists of recursive productions (e. graphcut. probabilistic CFGs construct a distribution over parse trees and sentences. verbs (VBD). the disulﬁde connectivity prediction in Fig. For example. where the weights deﬁne potential bond strength based on the local aminoacid sequence properties. By compactly deﬁning a probability distribution over individual productions. and spanning trees.2(c) can be modeled by maximum weight perfect matchings. STRUCTURED MODELS 7 Contextfree grammars are one of the primary formalisms for capturing the recursive structure of syntactic constructions [Manning & Sch¨ tze. verbal phrase (VP) or prepositional phrase (PP) and partofspeech tags like nouns (NN). The terminal symbols (leaves) are the words of the sentence. 2001]. we use the term model very broadly. 1. spanning tree. The context free restriction allows efﬁcient inference and learning in such models. However. 1976. u in Fig. 1. Papadimitriou & Steiglitz. The other combinatorial structures we consider and apply in this thesis include graph cuts and partitions. edgecover. The productions deﬁne the set of syntactically allowed phrase structures (derivations). 1999]. • Combinatorial structures Many important computational tasks are formulated as combinatorial optimization problems such as the maximum weight bipartite and perfect matching. V P → V P P P . 1982. and many others [Lawler. to include any scheme that assigns scores to the output space Y and has a procedure for ﬁnding the optimal scoring y..2. maximum likelihood estimation of scoring function parameters for combinatorial structures is often intractable because of the problem of deﬁning a normalized distribution over an exponential set of combinatorial structures. and the prediction task reduces to ﬁnding the most likely tree given the sentence.g.1.3. For example. The standard methods of estimation for Markov networks and context free grammars are based on maximum likelihood. Cormen et al. . DT → The) that can be applied to derive a sentence of the language. bipartite matchings.
The seamless integration of kernels with graphical models allows us to create . representational extensions. taking advantage of prediction task structure. convex learning formulation for Markov networks with sequence and other lowtreewidth structure. We develop general conditions under which exact large margin estimation is tractable and present two formulations for structured maxmargin estimation that deﬁne compact convex optimization problems. ◦ Learning framework for structured models We propose a general framework for efﬁcient estimation of models for structured prediction. or can be efﬁciently approximated.4 Contributions This thesis addresses the problem of efﬁcient learning of highaccuracy models for complex prediction problems. from Markov networks to context free grammars to combinatorial graph structures such as matchings and cuts. We focus on those models where exact inference is tractable. These two formulations form the foundation which the rest of the thesis develops. compact. Lowtreewidth Markov networks We use graph decomposition to derive an exact. combinatorial optimization) predicts the correct answers on the training data with maximum conﬁdence. generalization analysis and experimental validation for Markov networks. ◦ Markov networks The largest portion of the thesis is devoted to novel estimation algorithms.8 CHAPTER 1. An alternative to likelihoodbased methods. The ﬁrst formulation relies on the ability to express inference in the model as a compact convex optimization problem. vision and biology. INTRODUCTION 1. Intuitively. We consider a very large class of structured models. The second one only requires compactly expressing optimality of a given assignment according to the model and applies to a broader range of combinatorial problems. a model class of choice in many structured prediction tasks in language. we ﬁnd parameters such that inference in the model (dynamic programming. this framework builds upon the large margin estimation principle.
our framework allows exact estimation of networks of arbitrary connectivity and topology. We show that for AMNs over binary variables. Scalable online algorithm We present an efﬁcient algorithm for solving the estimation problem called Structured SMO. proportion of mislabeled pixels in an image) and uses a proof that exploits the graphical model structure. for which likelihood methods are believed to be intractable. For the nonbinary case. We present an AMNbased method for object segmentation from 3D range data. By constraining the class of Markov networks to AMNs. which compactly deﬁne templates for Markov networks for domains with relational structure objects. scale up to tens of millions of nodes and edges. Generalization analysis We analyze the theoretical generalization properties of maxmargin estimation in Markov networks and derive a novel marginbased bound for structured prediction. at runtime. Learning associative Markov networks (AMNs) We deﬁne an important subclass of Markov networks that captures positive correlations present in many domains. we provide an approximation that works well in practice.1. We also use approximate graph decomposition to derive a compact approximate formulation for Markov networks in which inference is intractable. our models are learned efﬁciently and. Representation and learning of relational Markov networks We introduce relational Markov networks (RMNs). accurate prediction in realworld tasks. Our onlinestyle algorithm uses inference in the model and analytic updates to solve extremely large estimation problems.g. This bound is the ﬁrst to address structured error (e. .4. CONTRIBUTIONS 9 very rich models that leverage the immense amount of research in kernel design and graphical model decompositions for efﬁcient.
INTRODUCTION attributes. Learning to parse We exploit context free grammar structure to derive a compact maxmargin formulation and show highaccuracy parsing in cubic time by exploiting novel kinds of lexical information. relations. and can easily model complex interaction patterns over related entities. The algorithm we propose uses kernels. clustering The other large portion the thesis addresses a range of prediction tasks with very diverse models: context free grammars for natural language parsing. We apply our framework to prediction of disulﬁde connectivity in proteins using perfect nonbipartite matchings. Experiments on synthetic and realworld data show the ability of the algorithm to learn an appropriate . we describe a formulation that tightly integrates metric learning with the clustering algorithm. which makes it possible to efﬁciently embed the features in very highdimensional spaces and achieve stateoftheart accuracy. We show experimental evidence of the model’s improved performance over several baseline models. to derive an approximate learning formulation. We use approximate inference in these complex models. We apply this class of models to classiﬁcation of hypertext using hyperlink structure to deﬁne relations between webpages. perfect matchings for disulﬁde connectivity in protein structure prediction. ◦ Broader applications: parsing. matching. The graphical structure of an RMN is based on the relational structure of the domain. tuning one to the other in a joint optimization. efﬁcient algorithm for learning to match. In contrast to algorithms that learn a metric independently of the algorithm that will be used to cluster the data.10 CHAPTER 1. in which exact inference is intractable. Learning to cluster We derive a maxmargin formulation for learning the afﬁnity metric for clustering from clustered training data. Learning to match We use combinatorial properties of weighted matchings to develop an exact. graph partitions for clustering documents and segmenting images.
5. including dynamic and linear programming inference. we deﬁne the abstract class of structured prediction problems and models addressed by the thesis. including logistic regression and support vector machines. We describe representation and inference for Markov networks.5 Thesis outline Below is a summary of the rest of the chapters in the thesis: Chapter 2. risk. Markov networks: We review maximum conditional likelihood estimation and present maximum margin estimation for Markov networks. including email folder organization and image segmentation. Supervised learning: We review basic deﬁnitions and statistical framework for classiﬁcation. We also discuss approximations. conditional likelihood and margin. We use graphical model decomposition to derive a convex. THESIS OUTLINE 11 clustering metric for a variety of desired clusterings. We address the exponential blowup of the naive problem formulation by deriving two general equivalent convex formulation. We also brieﬂy describe context free grammars and combinatorial structures as models. We analyze the theoretical generalization . We compare probabilistic models. Structured models: In this chapter. loss functions. minmax and certiﬁcate. for solving intractable or very large problems. We describe the relationship between the dual estimation problems and kernels. and review estimation methods based on maximizing likelihood. Structured maximum margin estimation: This chapter outlines the main principles of maximum margin estimation for structured models. allow us to exploit decomposition and combinatorial structure of the prediction task. They lead to polynomial size programs for estimation of models where the prediction problem is tractable. Chapter 3. These formulations. We consider generalized linear models. Chapter 5. compact formulation that seamlessly integrates kernels with graphical models. Chapter 4. generative and discriminative and unnormalized models.1. 1. We deﬁne hypothesis classes. in particular using upper and lower bounds.
discriminative graphical model avoids the difﬁculties of deﬁning a coherent generative model for graph structures in directed models and allows us tremendous ﬂexibility in representing complex patterns. We show that for associative Markov networks of over binary variables. As we show. For the nonbinary case. attributes and relations. associative Markov networks (AMNs). called Structured SMO. We provide experimental results on a webpage classiﬁcation task. we provide an approximation that works well in practice. which compactly deﬁnes templates for Markov networks in domains with rich structure modeled by objects. maxmargin estimation allows exact training of networks of arbitrary connectivity and topology. Chapter 6.12 CHAPTER 1. Associative Markov networks: We deﬁne an important subclass of Markov networks. M3 N algorithms and experiments: We present an efﬁcient algorithm for solving the estimation problem in graphical models. Chapter 9. Relational Markov networks: We introduce the framework of relational Markov networks (RMNs). Chapter 8. for which maximum likelihood methods are believed to be intractable. We present an AMNbased method for object segmentation from 3D range data that scales to very large prediction tasks involving tens of millions of points. the use of an undirected. INTRODUCTION properties of maxmargin estimation and derive a novel marginbased bound for structured classiﬁcation. Context free grammars: We present maxmargin estimation for natural language parsing on the decomposition properties of context free grammars. where our models signiﬁcantly outperform other approaches by effectively capturing correlation between adjacent letters and incorporating highdimensional input representation via kernels. We show . Our onlinestyle algorithm uses inference in the model and analytic updates to solve extremely large quadratic problems. that captures positive interactions present in many domains. Chapter 7. and can easily model complex patterns over related entities. We present experiments with handwriting recognition. The graphical structure of an RMN is based on the relational structure of the domain. showing that accuracy can be signiﬁcantly improved by modeling relational dependencies.
Chapter 10. We formulate the approximate learning problem as a compact convex program with quadratic objective and linear or positivesemideﬁnite constraints. which makes it possible to efﬁciently embed the features in very highdimensional spaces and achieve stateoftheart accuracy. Perfect matchings: We apply our framework to learning to predict disulﬁde connectivity in proteins using perfect matchings. Chapter 12. 2004a]. We discuss extensions and future research directions not addressed in the thesis. 1. Experiments on synthetic and realworld data show the ability of the algorithm to learn an appropriate clustering metric for a variety of desired clusterings. Conclusions and future directions: We review the main contributions of the thesis and summarize their signiﬁcance. The algorithm we propose uses kernels.6 Previously published work Some of the work described in this thesis has been published in conference proceedings. using a dual decomposition technique [Taskar et al. 2003a]. A paper . Chapter 11. we derive a maxmargin formulation for learning afﬁnity scores for correlation clustering from clustered training data. Correlation clustering: In this chapter. PREVIOUSLY PUBLISHED WORK 13 that this framework allows highaccuracy parsing in cubic time by exploiting novel kinds of lexical information. 5 was published for a less general case.. The polynomial formulation of maximum margin Markov networks presented in Ch. although they underly several papers mentioned below. 7) was published with experiments on hypertext and newswire classiﬁcation [Taskar et al. 4.6.1.. The minmax and certiﬁcate formulations for structured maxmargin estimation have not been published in their general form outlined in Ch. including email folder organization and image segmentation. We use combinatorial properties of weighted matchings to develop an exact. efﬁcient algorithm for learning the parameters of the model. Work on associative Markov networks (Ch. We show experimental evidence of the model’s improved performance over several baseline models. applicability and limitations.
using maximum (conditional) likelihood estimation. Natural language parsing in Ch. Vassil Chatalbashev. Disulﬁde connectivity prediction using perfect matchings in Ch. . INTRODUCTION on 3D object segmentation using AMNs. [2003b] deﬁned and applied the Relational Markov networks (Ch. done jointly with Pieter Abbeel and Andrew Ng. 8). 9 was published in Taskar et al. [2002] and Taskar et al. Taskar et al. Dinkar Gupta. Daphne Koller and Andrew Ng). 10 (joint work with Vassil Chatalbashev and Daphne Koller) is currently under review. is currently under review (joint work with Drago Anguelov. 11. has not been published. work on correlation clustering in Ch. Geremy Heitz. Finally.14 CHAPTER 1. which presents a experiments on terrain classiﬁcation and other tasks. [2004b].
Part I Models and methods 15 .
The input to an algorithm is training data. [2001]. for indepth discussion of these and many other models). y) ∼ D. .Chapter 2 Supervised learning In supervised learning. A supervised learning problem with discrete outputs. Hastie et al.1). Learning algorithms can be distinguished among several dimensions. we seek a function h : X → Y that maps inputs x ∈ X to outputs y ∈ Y.d. Numerous classes of functions have been well studied. We arrive at such a criterion by quantifying what it means for h(x) to approximate 16 . [2000]. for several reasons we discuss below. efﬁciency. including accuracy. where k is the number of classes. In handwritten character recognition. neural networks. for example.i. The second crucial dimension of a learning algorithm is the criterion for selection of h from H. while the output space Y we consider in this chapter discrete. yk }. chief among them is the hypothesis class H of functions h the algorithm outputs. X is the set of images of letters and Y is the alphabet (see Fig. Bishop [1995]. . a set of m i. (independent and identically distributed) samples S = {(x(i) . The goal of a learning algorithm is to output a hypothesis h such that h(x) will approximate y on new samples from the distribution (x. y (i) )}m drawn from a ﬁxed but unknown distribution D i=1 over X × Y. Duda et al. is called classiﬁcation. We will concentrate on the last two classes. nearestneighbors. . 2. . Y = {y1 . and extensibility to more complex structured prediction tasks will consider in the next chapter. generalized loglinear models and kernel methods (see Quinlan [2001]. including decision trees. The input space X is an arbitrary set (often X = IRn ).
simply selecting a hypothesis with lowest risk h∗ = arg min RS [h]. For a vast majority of supervised learning algorithms.2) where we abbreviate (x(i) .. computed on the training sample S: 1 RS [h] = m m i=1 1 (x . ˆ ˆ A common loss function for classiﬁcation is 0/1 loss 0/1 (x. Since we do not generally know the distribution D. . h∈H is generally not a good idea. H. that is. y ) = 0 if y = y . that is. i = (1. y). This polynomial is very likely to overﬁt the training data. The risk functional RD [(h)] measures the expected error of the approximation: RD [h] = E(x. the degree of the polynomial) with the error on the training data as measured by empirical risk RS . The key to selecting a good hypothesis is to tradeoff complexity of class H (e. y (i) . Y = IR and H includes all polynomials of degree m − 1. m) assuming that all the x(i) are unique.y)∼D [ (x. y (i) ). h(x )) = m (i) (i) (i) (i) i (h(x )). it will have zero empirical risk. 1 I(·) I(true) = 1 and 1 I(false) = 0. For example. y. but high actual risk..g. However. h(x)) ≡ 1 = h(x)). y . we assume that (x. y. y. if X = IR. RS [h] is often called the training If our set of hypotheses. this fundamental balance is .1) : X × Y × Y → IR+ measures the penalty for predicting h(x) on the sample (x.17 y. m i (h(x i=1 (i) )). we will be able to ﬁnd h that has zero or very small empirical risk. h(x))]. h(x(i) )) = error or training loss. is large enough. In general.. I(y where 1 denotes the indicator function. we can always ﬁnd a polynomial h that passes through all the sample points (x(i) . where the loss function (2. RS [h] is simply the proportion of training examples that h misclassiﬁes. (2. For 0/1 loss. we estimate the risk of h using its empirical risk RS .
The term D[h] is often called regularization. x. we consider hypothesis classes of the following parametric form: hw (x) = arg max f (w. h∈H (2.3) where D[h] measures the inherent dimension or complexity of h. the search for the optimal h∗ in (2. but simply adopt the standard measures as needed and refer the reader to Vapnik [1995]. For many classes.4) of the hypothesis class in terms of an optimization procedure will become crucial to extending supervised learning techniques to cases where the output space Y is more complex. the learning algorithms we consider are completely characterized by the hypothesis class H. and C ≥ 0 is a tradeoff parameter. and we must resort to approximate. In general.18 CHAPTER 2. We assume that ties in the arg max are broken using some arbitrary but ﬁxed rule. for example decision trees and multilayer neural networks. x. [2001] for details. it is intractable [Bishop. usually with W ⊆ IRn .4) where f (w. We will not go into derivation of various complexity measures D[h] here. SUPERVISED LEARNING achieved by minimizing the weighted combination of the two criteria: h∗ = arg min D[h] + CRS [h] . 1 . As we discuss below. Hastie et al. minimizing the objective with the usual 0/1 training error is generally a very difﬁcult problem with multiple maxima for most realistic H. 2001]. 1995. Depending on the complexity of the class H. this class of hypotheses is very rich and includes many standard models. y∈Y (2. [1996]. Hence. Below however. See discussion in the next section about approaches to dealing with 0/1 loss. and the regularization D[h]. For these intractable classes. the loss function . the search procedure used by the learning algorithm is crucial.3) may be a daunting task1 . we will concentrate on models where the optimal h∗ can be found efﬁciently using convex optimization in polynomial time. For classiﬁcation. Devroye et al. y). The formulation in (2. greedy optimization methods. Quinlan. where w ∈ W is a set of parameters. y) is a function f : W × X × Y → IR.
z}. h(x)) ≥ (x. The most common loss for classiﬁcation is 0/1 loss. (In addition to computational advantages of this approach. there are statistical beneﬁts of minimizing a convex upper bound [Bartlett et al. 2. this very simple model captures enough information to perform reasonably well. Minimizing the 0/1 risk is generally a very difﬁcult problem with multiple maxima for any large class H. Two of the primary classiﬁcation methods we consider. . 2003]). y) and hence is simpler than a hw with a large weight wj .col denotes the value of pixel (row. col). The regularization D[hw ] for the linear family is typically the norm of the parameters wp for p = 1. We might have a basis function fj (x.1 Classiﬁcation with generalized linear models For classiﬁcation. or small weight wj implies that the hypothesis hw does not depend on the value of fj (x. . . a zero. a hypothesis hw ∈ H is deﬁned by a set of n coefﬁcients wj ∈ IR such that: n hw (x) = arg max y∈Y i=1 wj fj (x.1. y.1. h(x)). Given n realvalued basis functions fj : X × Y → IR. Since different letters tend to have different pixels turned on.1: Handwritten character recognition: sample letters from Kassel [1995] data set. CLASSIFICATION WITH GENERALIZED LINEAR MODELS 19 a b c d e Figure 2. we consider the generalized linear family of hypotheses H. 2. y∈Y (2. The standard solution is minimizing an upper bound on the 0/1 loss.2. y). differ primarily in their choice of the upper bound on the training 0/1 loss. . col) and char ∈ Y. y) = arg max w f (x. I(x where xrow. Intuitively. y. (x. y) = 1 row. Our input x is a vector of pixel values of the image and y is the alphabet {a. 2.5) Consider the character recognition example in Fig.col = on ∧ y = char) for each possible (row. .. logistic regression and support vector machines.
5 2 Figure 2.7) where C is a userspeciﬁed constant the determines the tradeoff between regularization and likelihood of the data. we use 2norm below: min 1 w2 + C 2 log Zw (x(i) ) − w f (x(i) . where y is the correct label for x. y) − maxy =y w f (x.5 2 1. Zw (x) (2. This approach is called the (regularized) maximum likelihood estimation. y)}.5 log−loss hinge−loss 0/1−loss 3 2.2).5 0 −2 −1. y) is an upper bound (up to a constant) on the 0/1 loss 0/1 (see Fig.2 Logistic regression In logistic regression. Common choices for regularization are 1 or 2norm regularization on the weights.6) y∈Y exp{w f (x. The logloss is shown up to an additive constant for illustration purposes.5 0 0. 2.5 −1 −0. y ).5 1 0. SUPERVISED LEARNING 3. Horizontal axis shows w f (x. . The logloss log Zw (x) − w f (x.2: 0/1loss upper bounded by logloss and hingeloss. 2.20 CHAPTER 2. y (i) ). i (2. while the vertical axis show the value of the associated loss. y)}. The optimal weights are selected by maximiz ing the conditional likelihood of the data (minimizing the logloss) with some regularization. we assign a probabilistic interpretation to the hypothesis hw as deﬁning a conditional distribution: Pw (y  x) = where Zw (x) = 1 exp{w f (x.5 1 1.
3. − i.3 Logistic dual and maximum entropy The objective function is convex in the parameters w. so we have an unconstrained (differentiable) convex optimization problem. 2.2. y (i) ) − f (x(i) . y) = min w ∆fi (y).w [∆fi (y)]. LOGISTIC DUAL AND MAXIMUM ENTROPY 21 2.w [∆fi (y)] = 0. It can be shown [Cover & Thomas. ∀i.y Pw (y  x(i) ) log Pw (y  x(i) ) (2.w [f (y)] = y f (y)Pw (y  x(i) ) is the expectation under the conditional distribu tion Pw (y  x(i) ) and ∆fi (y) = f (x(i) . 2001]. y). We can interpret logistic regression as trying to match the empirical basis function expectations while maintaining a high entropy conditional distribution Pw (y  x). y)] − fi (x(i) . 1995] select the weights based on the “margin” of conﬁdence of hw .w [fi (x(i) . y (i) ) = w − C i Ei. Ignoring the regularization term. Crammer & Singer. y (i) ) − w f (x(i) . The gradient with respect to w is given by: w+C i Ei.4 Support vector machines Support vector machines [Vapnik.t. the gradient is zero when the basis function expectations are equal to the basis functions evaluated on the labels y (i) .8) Ei. 1991] that the dual of the maximum likelihood problem (without regularization) is the maximum entropy problem: max s. the margin on example i quantiﬁes by how much the true label “wins” over the wrong ones: γi = 1 1 min w f (x(i) . 1998. In the multiclass SVM formulation [Weston & Watkins. w y=y(i) w y=y(i) . where Ei.
We can also express ξi as maxy 0/1 i (y) − w ∆fi (y). (y) − ξi . Maximizing the smallest such margin (and allowing for negative margins) is equivalent to solving the following quadratic program: min s.10) The hingeloss maxy [ (see Fig. . (2. max i. SUPERVISED LEARNING where ∆fi (y) = f (x(i) . 1 w2 + C 2 w ∆fi (y) ≥ ξi i 0/1 (2.2). (2. y (i) ) − f (x(i) . ∀y ∈ Y. 0/1 i (y) − w ∆fi (y)] is also an upper bound on the 0/1 loss 0/1 2. the αi (y) variables correspond to the w ∆fi (y) ≥ ∗ (y)−ξi constraints in the primal Eq. y). 2. αi (y) ≥ 0. The solution to the dual α gives the solution to the primal as a weighted combination of basis functions of examples: w∗ = i.y (2. (2.y αi (y) 0/1 i (y) 1 − 2 2 αi (y)∆fi (y) i.5 SVM dual and kernels The form of the dual of Eq.22 CHAPTER 2.t. y.y ∗ αi (y)∆fi (y).9) ∀i. Note that the slack variable ξi is constrained to be positive in the above program since w ∆fi (y (i) ) = 0 and 0/1 (y (i) ) = 0. (2.7): min 1 w2 + C 2 max[ i y 0/1 i (y) − w ∆fi (y)].t. y αi (y) = C. and the optimization problem Eq.9) is crucial to efﬁcient solution of SVM and the ability to use a high or even inﬁnite dimensional set of basis functions via kernels.11) s.9) in a form similar to Eq. 0/1 In the dual. ∀i.9). (2. ∀i.
Zhu & Hastie. cold ) and char ∈ Y. SVM DUAL AND KERNELS 23 ∗ The pairings of examples and incorrect labels.y = i. we can x ¯ solve Eq. y (i) ) f (x. y ) = ¯ i. while solutions to the corresponding kernelized logloss problem are generally nonsparse (all examples are support vectors) and require approximations for even relatively small datasets [Wahba et al. 1993. . we might have basis functions that are polynomial of degree d in terms of image pixels.cold = on ∧ y = char) for each I(x possible (row1 . col1 ) .¯ y αi (y)αj (¯)∆fi (y) ∆fj (¯).y αi (y)[f (x(i). y )]. fj (x. y) f (x. . y ) can be computed efﬁciently.col1 = on ∧ . 2001]. In fact. are called support vectors. (i. Note that at classiﬁcation time. logistic regression can also be kernelized. However. y) = 1 row1 . y )−f (x(i).. we have: 2 αi (y)∆fi (y) i. that have nonzero αi (y). y y Hence. (2.y j. y) f (¯ . ∧ xrowd . Expanding the quadratic term. . ¯ ¯ For example.11) independently of the actual dimension of f . y). 1995].y αi (y)∆fi (y) f (x. the hinge loss formulation usually produces sparse solutions in terms of the number of support vectors. (rowd . .2. even though the number of basis functions grows exponentially with d [Vapnik. An important feature of the dual formulation is that the basis functions f appear only as dot products. y ) = ¯ i.5. Computing this polynomial kernel can be done independently of the dimension d. . as long as the dot product f (x. we also do not need to worry about the dimension of f since: w f (x.
. . Y ⊂ Y1 ×. respecting the constraints and exploiting the correlations in the output space. In this chapter. The output space Y ⊆ Y1 × . We call problems with discrete output spaces structured classiﬁcation or structured prediction. In word recognition. consecutive letters in a word. In fact. 3. In word recognition. but a set of values y = (y1 . . we might restrict that the letter ‘q’ never follows by ‘z’ in English. This joint output space is often a proper subset of the product of singleton output spaces. yL ). we consider prediction problems in which the output is not a single discrete value y. For concreteness. The range of prediction problems these broad deﬁnitions encompass is immense. machine vision. e. a more natural and useful task is recognizing words and entire sentences. Structured models we consider in this chapter (and thesis) predict the outputs jointly. let the number of variables L be ﬁxed. . but in the context of the surrounding letters that together form a word. In addition to “hard” constraints. . for example an entire sequence of L characters. while Y is the dictionary. the output variables are often highly correlated.g.Chapter 3 Structured models Consider once more the problem of character recognition.” Distinguishing between the second letter and fourth letter (‘r’ and ‘c’) in isolation is far from trivial. arising in ﬁelds as diverse as natural language analysis. We refer to joint spaces with constraints and correlations as structured. each Yj is the alphabet.×YL .1 shows an example handwritten word “brace. . this task is much less errorprone for humans and should be for computers as well. and computational 24 . Fig. . . × YL we consider is a subset of product of output spaces of single variables.
y∈Y x∈X p(x. y).1 Probabilistic models: generative and conditional The term model is often reserved for probabilistic models. to name a few. which can be subdivided into generative and conditional with respect to the prediction task. y) to the input and output space X × Y with p(x. except that y has been replaced by y: hw (x) = arg max w f (x. The output space Y = {y : g(x.1: Handwritten word recognition: sample from Kassel [1995] data set. combinatorial optimization problems like mincut and matching. 8) and correlation clustering (Ch. convex optimization such as linear. . The class of structured models H we consider is essentially of the same form as in previous chapter. This formulation is very general.1. Clearly. 11). we will restrict our attention to models where this optimization problem can be solved in polynomial time.1) where as before f (x. y) ≥ 0. A generative model assigns a normalized joint density p(x.y)≤0 (3. y) is a vector of functions f : X × Y → IRn . for example. In other cases. 3. y : g(x. For the most part. like intractable Markov networks (Ch. This includes. PROBABILISTIC MODELS: GENERATIVE AND CONDITIONAL 25 b r a c e Figure 3. y) ≤ 0} is deﬁned using a vector of functions g(x. biology.3. y) that deﬁne the constraints. we use an approximate polynomial time optimization procedure. probabilistic models like Markov networks (in certain cases) and contextfree grammars. y) = 1. for many f . g pairs. where g : X × Y → IRk . quadratic and semideﬁnite programming. ﬁnding the optimal y is intractable.
In a regime with very few training samples (relative to the number of parameters w). however. Because of this. A generative model must make simplifying assumptions (more precisely. y) will not necessarily do so. generative models may actually outperform conditional models [Ng & Jordan. generative models actually need fewer samples to converge to a good estimate of the joint distribution than conditional models need to accurately represent the conditional distribution. independence assumptions) about the entire p(x. y). by optimizing the model to ﬁt the joint distribution p(x.26 CHAPTER 3. 2001].. y∈Y p(y  x) = 1 ∀x ∈ X . y). 1970. 2001]. Probabilistic interpretation of the model offers wellunderstood semantics and an immense toolbox of methods for inference and learning. the conditional model will learn the best approximation to p(y  x) possible using w. Given sufﬁcient data. while the generative model p(x. STRUCTURED MODELS A conditional model assigns a normalized density p(y  x) only over the output space Y with p(y  x) ≥ 0. y)] [DeGroot. Any model is an approximation to the true distribution underlying the data. . y)}. It also provides an intuitive measure of conﬁdence in the predictions of a model in terms of conditional probabilities. generative models are typically structured to allow very efﬁcient maximum likelihood learning. while a conditional model makes many fewer assumption by focusing on p(y  y). Typically. the maximum likelihood parameters w with respect to the joint distribution can be computed in closed form using the empirical basis function expectations ES [f (x. y) ∝ exp{w f (x. which we use to make the predictions. this efﬁciency comes at a price. A very common class of generative models is the exponential family: p(x. Of course. For exponential families. we may be tuning the approximation away from optimal conditional distribution p(y  x). Hastie et al. In addition.
This fact makes standard maximum likelihood estimation infeasible. PREDICTION MODELS: NORMALIZED AND UNNORMALIZED 27 3. normalizing the model (summing over the entire Y) is intractable.3. 3. As we discussed in the previous chapter. support vector machines. we can often achieve higher accuracy models when we do not learn a normalized distribution over the outputs.3 Markov networks Markov networks provide a framework for a rich family of models for both discrete and continuous prediction [Pearl. 1988.2 Prediction models: normalized and unnormalized Probabilistic semantics are certainly not necessary for a good predictive model if we are simply interested in the optimal prediction (the arg max in Eq. to include any scheme that assigns scores to the output space Y and has a procedure for ﬁnding the optimal scoring y. The learning methods we advocate in this thesis circumvent this problem by requiring only the maximization problem to be tractable. 2000]. the difference between the optimal y and the rest. Cristianini & ShaweTaylor. 1995. we use the term model very broadly.2. 1999]. (3. which do not represent a conditional distribution. We also brieﬂy touch upon examples of contextfree grammars and combinatorial problems that will be explained in greater detail in Part III to illustrate the range of prediction problems we address. while the optimal y can be found in polynomial time. in many cases we discuss below. typically perform as well or better than logistic regression [Vapnik.. The models treat the inputs and outputs as random variables X with domain X and Y with domain Y and compactly deﬁne a conditional density p(Y  X) or distribution P (Y  X) (we concentrate here on the . but largely dispense with the probabilistic interpretation when needed. we review basic concepts in probabilistic graphical models called Markov networks or Markov random ﬁelds. Cowell et al. but concentrate on the margin or decision boundary. We still heavily rely on the representation and inference tools familiar from probabilistic models for the construction of and prediction in unnormalized models. In this chapter. In general. Even more importantly. Essentially.1)).
. We denote the set of variables in a clique c as Yc . . 2001]). Ya . 3. {Y4 . For the purposes of ﬁnding the most likely y. it sufﬁces to separately ﬁnd the optimal subsequence from 1 to j ending with yj . No assumption is . an assignment of variables in the clique as yc and the space of all assignments to the clique as Yc .2.2. . . Before a formal deﬁnition. {Y5 }. and we consider each node a singleton clique. E). For example.. Yj+1 . . x).28 CHAPTER 3. . and the optimal subsequence starting with yj from j to L. but the ﬁrstorder model is making the assertion (which is certainly an approximation) that once the value of a letter Yj is known. we use a model where P (Yb  Yj . . Yb . Y2 }. but many of the same representation and inference concepts translate to continuous domains. A clique is a set of nodes c ⊆ V that form a fully connected subgraph (every two nodes are connected by an edge). {Y1 . In the chain network in Fig. the nodes are associated with output variables Yi and the edges correspond to direct dependencies or correlations. this conditional independence property means that the optimization problem is decomposable: given that Yj = yj . adjacent letters in a word are highly correlated. YL }. the cliques are simply the nodes and the edges: C(G) = {{Y1 }. 3.3. where the nodes are associated with variables V = {Y1 . x). We do not explicitly represent the inputs X in the ﬁgure. x) = P (Yb  Yj . STRUCTURED MODELS conditional Markov networks or CRFs [Lafferty et al. P (Ya  Yj . In Fig. the model encodes that Yj is conditionally independent of the rest of the variables given Yj−1 . . The advantage of a graphical framework is that it can exploit sparseness in the correlations between outputs Y . The graphical structure of the models encodes the qualitative aspects of the distribution: direct dependencies as well as conditional independencies. x) = P (Ya  Yj . Note that each subclique of a clique is also a clique. Y5 }}.1 Representation The structure of a Markov network is deﬁned by an undirected graph G = (V. More precisely. b < j < a. Intuitively. We focus on discrete output spaces Y below. . The quantitative aspect of the model is deﬁned by the potentials that are associated with nodes and cliques of the graph. the correlation between a letter Yb before j and a letter Ya after j is negligible. 3. consider a ﬁrstorder Markov chain a model for the word recognition task. . . .
The Markov network (G. 3. YL }. . E) and a set of potentials Φ = {φc }. appropriate node potentials in our network should give high scores to the correct letters (‘b’.‘r’. Conditioned on the image input. φi. which speciﬁes a nonnegative value for each assignment yc to variables in Yc and any input x.1 A Markov network is deﬁned by an undirected graph G = (V. the node potentials quantify the correlation between the input x and the value of the node.2: Firstorder Markov chain: φi (Yi ) are node potentials. Intuitively. . assume that the edge potentials would not depend .i+1 (Yi . Yi+1 ) are edge potentials (dependence on x is not shown). while the edge potentials quantify the correlation between the pair of adjacent output variables as well as the input x. In our example Fig.2. Each clique c ∈ C(G) is associated with a potential φc (x.‘a’. yc ). Deﬁnition 3.‘c’.‘e’). The nodes are associated with variables V = {Y1 . .3. though perhaps there would be some ambiguity with the second and fourth letter.3. made about X . Potentials do not have a local probabilistic interpretation. . yc ).3. Φ) deﬁnes a conditional distribution: P (y  x) = 1 Z(x) φc (x. we have node and edge potentials. but can be thought of as deﬁning an unnormalized score for each assignment in the clique. For simplicity. c∈C(G) where C(G) is the set of all the cliques of the graph and Z(x) is the partition function given by Z(x) = y∈Y c∈C(G) φc (x. yc ) with φc : X × Yc → IR+ . MARKOV NETWORKS 29 Figure 3.
j+1.30 CHAPTER 3. Multiplied together.k (x. For the sequence model. all single node potentials would share the same weights and basis functions (albeit the relevant portion of the input xc is different) and similarly for the pairwise cliques. col) in xj .k (x.row. yc ) are deﬁned to evaluate to zero. we are likely to “tie” or “share” the parameters of the model wc across cliques.k (x. In this problem (as well as many others). yc : nc φc (xc . these scores should favor the correct output “brace”. but simply should give high scores to pairs of letters that tend to appear often consecutively.1 With slight abuse of notation. yj+1 ) = 1 j = char1 ∧yj+1 = I(y char2 ) for each char1 ∈ Yj and char2 ∈ Yj+1 . In case of node potentials for word recognition. yc ) = exp wc fc (x. Usually.k fc. we stack all basis functions into one vector f . when c is an edge. Hence the log of the conditional probability is given by: log P (y  x) = c∈C(G) wc fc (x. yj . In general. we could use the same basis functions as for individual character recognition: fj.col = on ∧ yj = char) for each I(x possible (row. f has node functions and edge functions. we condition a clique only on a portion of the input x. which can be accomplished by adding more basis functions that condition on the position of the clique. yc ) could be represented (in logspace) as a sum of basis functions over x. In fact. 1 . since the potentials φc (xc . yc ) = exp k=1 wc. no matter in what position they appear in the sequence. the window of the image that corresponds to letter j and each char ∈ Yj (we assume the input has been segmented into images xj that correspond to letters). yc ) − log Zw (x). so when c is a node. STRUCTURED MODELS on the images. the edge functions in f (xc . For the edge potentials. yj ) = 1 j. Similarly. which we denote as xc . yc ) where nc is the number of basis functions for the clique c. the node Sometimes we might actually want some dependence on the position in the sequence. a Markov network is a generalized loglinear model. we can deﬁne basis functions for each combination of letters (assume for simplicity no dependence on x) : fj.
y∈Y y∈Y in the same form as Eq. ∀yk ∈ Yk . We stack the weights in the corresponding manner. 1 φ∗ (yk ) = k yk−1 ∈Yk−1 ∀y1 ∈ Y1 . MARKOV NETWORKS 31 functions in f (xc .k−1 φj (x. yk−1 . y) = c∈C(G) f (xc . Let the highest score of any subsequence from 1 to k > 1 ending with value yk be deﬁned as φ∗ (yk ) = max k y1. but most relevant to our discussion. The task of ﬁnding the most likely assignment.1). yc ) are also deﬁned to evaluate to zero. max φ∗ (yk−1 )φj (x.3. 3. yk )φj (x. is just one of such questions. say according to some lexicographic order of the symbols.. . 1 < k ≤ L.2 Inference There are several important questions that can be answered by probabilistic models. y1 ). yj ). yj )φj (x. (3.3. Now we can write: f (x. j The algorithm computes the highest scores recursively: φ∗ (y1 ) = φ1 (x. The Viterbi dynamic programming algorithm solves this problem for chain networks in O(L) time. yj−1 . Using the arg max’s of the max’s in L the computation of φ∗ . y). yc ). we can backtrace the highest scoring sequence itself.3. known as maximum aposteriori (MAP) or most likely explanation (MPE). We assume that score ties are broken in a predetermined way. so the most likely assignment according to the model is given by: arg max log Pw (y  x) = arg max w f (x. yk ). k−1 The highest scoring sequence has score maxyL φ∗ (yL ).
v1 . To triangulate it. The treewidth of an untriangulated graph G is the minimum treewidth of all triangulations of G. vl ). Y4 ). The inference procedure creates a tree of cliques using the graph augmented by triangulation. Recall that a cycle of length l in an undirected graph G is a sequence of nodes (v0 .3. . we can add the edge (Y1 . there are many possible sets of edges that can be added to triangulate a graph. A chord of this cycle is an edge (vi . In general Markov networks.. Y3 ) or (Y2 . 3. The simplest untriangulated network is the diamond in Fig. . In general. 1999]. However. there are several important subclasses of networks that allow polynomial time inference.3. like chains and trees. STRUCTURED MODELS Figure 3. .3. vj ) ∈ G between nonconsecutive nodes. distinct except that v0 = vl . Singlyconnected graphs. We need the concept of triangulation (or chordality) to formally deﬁne treewidth.32 CHAPTER 3.3: Diamond Markov network (added triangulation edge is dashed). . The most important of these is the class of networks with low treewidth. Deﬁnition 3. The critical property of a triangulation for the inference procedure is the size of the largest clique. Deﬁnition 3. MAP inference is NPhard [Cowell et al.2 (Triangulated graph) An undirected graph G is triangulated if every one of its cycles of length ≥ 4 possesses a chord.3 (Treewidth of a graph) The treewidth of a triangulated graph G is the size of its largest clique minus 1. are triangulated since they contain no cycles. which are connected by edges (vi . . vi+1 ) ∈ G.
∀yc ∈ Yc . . Y2 )φ23 (Y2 . The junction tree is an alternative representation of the same distribution that allows simple dynamic programming inference similar to the Viterbi algorithm for chains. Y4 )φ34 (Y3 . Y4 } and {Y1 . Y4 ). MARKOV NETWORKS 33 The treewidth of a chain or a tree is 1 and the treewidth of Fig.4 shows a junction tree for the diamond network. V ⊆ C(G) and the edges E satisfy the running intersection property: for any two cliques c and c . Deﬁnition 3. Y4 ) = φ1 (Y1 )φ4 (Y4 )φ14 (Y1 .3. yl ). the variables in the intersection c ∩ c are contained in the clique of every node of the tree on the (unique) path between c and c . l φ∗ (yc ) = φc (x. Fig. Y3 ). ∀yl ∈ Yl . the potentials for the {Y1 . Algorithms for constructing junction trees from triangulated graphs are described in detail in Cowell et al. Y2 .3. Y3 . Finding the minimum treewidth triangulation of a general graph is NPhard. Y4 } nodes are the product of the associated clique potentials: φ134 (Y1 . Each of the original clique potentials must associated with exactly one node in the junction tree. 3. φ123 (Y1 . The inference procedure is based on a data structure called junction tree that can be constructed for a triangulated graph. E) for a triangulated graph G is a tree in which the nodes are a subset of the cliques of the graph.3..3 is 2. 3. Y3 . 1999]. Y3 ) = φ2 (Y2 )φ3 (Y3 )φ12 (Y1 . c ∀c ∈ V(T ) \ Lv(T ). yc ∼yc max φ∗ (yc ). but good heuristic algorithms exist [Cowell et al. The Viterbi algorithm for junction trees picks an arbitrary root r for the tree T and proceeds recursively from the leaves to compute the highest scoring subtree at a node by combining the subtrees with highest score from its children. [1999]. For example. yc ) c c ∈Chr (c) ∀l ∈ Lv(T ). Y3 .4 (Junction tree) A junction tree T = (V. We denote the leaves of the tree as Lv(T ) and the children of node c (relative to the root r) as Chr (c): φ∗ (yl ) = φl (x.
Each of the original potentials is associated with a node in the tree. 3.3.yc µc (yc ) log φc (x. Although solving the MAP inference using a general LP solver is less efﬁcient than the dynamic programming algorithms above. where yc ∼ yc denotes whether the partial assignment yc is consistent with the partial assignment yc on the variables in the intersection of c and c . Let us begin with a linear integer program to compute the optimal assignment y. We represent an assignment as a set binary variables µc (yc ). we present an alternative inference method based on linear programming. yc ). .4: Diamond network junction tree. yc ) = c. we can backr trace the highest scoring assignment itself.. The highest score is given by maxyr φ∗ (yr ).3 Linear programming MAP inference In this section. that denotes whether the assignment has that value. such that: log c φc (x. Note that this algorithm is exponential in the treewidth. 1999]. one for each clique c and each value of the clique yc . the size of the largest clique. STRUCTURED MODELS Figure 3. this formulation is crucial in viewing Markov networks in a uniﬁed framework of the structured models we consider and to our development of common estimation methods in later chapters. Similar type of computations using the junction tree can be used to compute the partition function Zw (x) (by simply replacing max by ) as well as marginal probabilities P (yc x) for the cliques of the graph [Cowell et al.34 CHAPTER 3. Using the arg max’s of the max’s in the computation of φ∗ .
5. ∀c ∈ C. ∀yc .t. We can also show that converse is true: any I(y valid setting of µc (yc ) corresponds to a valid assignment y. we can deﬁne µc (yc ) variables that satisfy the above constraints by setting µc (yc ) = 1 c = yc ). we will have node and edge marginals that sum to 1 and agree with each other as in Fig. these constraints deﬁne a linear integer program: max c. For example. ∀c ∈ C. µs (ys ). ∀ys . 3. µc (yc ). For any clique c ∈ C and a subclique s ⊂ c. s.2) µc (yc ) ∈ {0. the marginals for cliques that share variables are consistent. We call these variables marginals. 1}.yc µc (yc ) log φc (x. There are several elementary constraints that such marginals satisfy. Second.3. yc ) µc (yc ) = 1.5: Example of marginal agreement: row sums of µ12 (y1 . In fact.3. Clearly. s ⊂ c. c ∈ C. column sums agree with µ2 (y2 ). they must sum to one for each clique. MARKOV NETWORKS 35 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 Figure 3. µs (ys ) = yc ∼ys µc (yc ). y2 ) agree with µ1 (y1 ). First. . the assignment of the subclique. Together. for any assignment y . yc (3. must be consistent with the assignment of the clique. in case the network is a chain or a tree. ∀s. as they correspond to the marginals of a distribution that has all of its mass centered on the MAP instantiation (assuming it is unique).
0) = µ12 (0. µ34 (0. µ34 (1.5. with the following edge marginals that are consistent with the constraints: µ12 (0. for example.5.5. but the edge marginal for (1. (2. the diamond network in Fig. 7. Hence this set of marginals disallows all assignments.5. we discuss another subclass of networks where MAP inference using LPs is tractable for any network topology. the value of the LP is the same as the value of the integer program. 1) = 0. µ23 (0. (3. A proof of this lemma appears in Wainwright et al. Consider. the constraints force the marginals µc (yc ) to correspond to some valid joint distribution over the assignments. 0) = µ12 (1. µ12 (1. If we triangulate the graph and add the cliques {Y1 . but with a restricted type of potentials. µ23 (1. 1) = 0. Y3 } and {Y1 . 0) = µ34 (0. 0) = µ34 (1.5 For a triangulated network with unique MAP assignment. Y2 . 3). exact inference is intractable. Y3 . The optimal distribution with the respect to the objective puts all its mass on the MAP assignment. and any linear combination of the MAP assignments maximizes the LP. the integrality constraint in the integer program in Eq. 2). .2) can be relaxed and the resulting LP is guaranteed to have integer solutions. If the MAP assignment is not unique. Intuitively. 0) = µ23 (1. In graphs where triangulation produces very large cliques. [2002].3 with binary variables. 4) disallow any assignment other than 0000 or 1111. Y4 } with their corresponding constraints. 0) = µ34 (1. 1) = 0. 1) = 0. 1) = 0. µ14 (0. 1) = 0. 1) = 0.36 CHAPTER 3.3. In case the network is not triangulated. STRUCTURED MODELS Lemma 3. The corresponding node marginals must all be set to 0. 0) = µ14 (0. 4) disallows any assignment that has Y1 = Y4 . 0) = µ23 (0. the set of marginals is not guaranteed to represent a valid distribution. In Ch. 1) = 0. We can resort to the above LP without triangulation as an approximate inference procedure (augmented with some procedure for rounding possibly fractional solutions). µ14 (1. Note that the edge marginals for (1. (3.5. 3. the above marginals will be disallowed.
verbs (VBD).1 (CFG) A CFG G consists of: ◦ A set of nonterminal symbols. verbal phrase (VP) or prepositional phrase (PP) and partofspeech tags like nouns (NN). 1999]. Deﬁnition 3. where A.3. where all rules in the grammar are of the form: A → B C and A → D. and D is a terminal symbol. For clarity of presentation.4. 1993]. This tree is from the Penn Treebank [Marcus et al. determiners (DT) and prepositions (IN).6: Example parse tree from Penn Treebank [Marcus et al.4 Context free grammars Contextfree grammars are one of the primary formalisms for capturing the recursive structure of syntactic constructions [Manning & Sch¨ tze. 3. . CONTEXT FREE GRAMMARS 37 Figure 3.. N ◦ A designated set of start symbols. 3.6 shows u a parse tree for the sentence The screen was a sea of red. we restrict our grammars to be in Chomsky normal form2 (CNF). a primary linguistic resource for expertannotated English text.4. B and C are nonterminal symbols. Fig. The terminal symbols (leaves) are the words of the sentence. The nonterminal symbols (labels of internal nodes) correspond to syntactic categories such as noun phrase (NP). 1993]. NS ⊆ N 2 Any CFG can be represented by another CFG in CNF that generates the same set of sentences. For example..
IN → from} A grammar generates a sentence by starting with a symbol in NS and applying the productions in P to rewrite nonterminal symbols. ◦ PU = {DT → The. NN → tree. but now with DT → the and NN → dog. NP. For example. we can generate The cat saw the dog by starting with S → NP VP. saw the dog. PU }. from} ◦ PB = {S → NP VP. The likely analysis of the sentence is that the cat. then rewriting the VP as VP → VBD NP with VBD → saw. T ◦ A set of productions. saw. sitting in the tree. there are exponentially many parse trees that produce a sentence of length l. NP → DT NN. VP → VBD NP. DT. PP. 3.38 CHAPTER 3. VBD → saw. The simple grammar above can generate sentences of arbitrary length. D ∈ T }. We can represent such derivations using trees like in Fig. C ∈ N } and Unary productions. rewriting the NP as NP → DT NN with DT → The and NN → cat. NN → dog. NN → cat. P = {PB .6 or (more compactly) using bracketed expressions like the one below: [[TheDT catNN ]NP [sawVBD [theDT dogNN ]NP ]VP ]S . An unlikely but possible alternative is that the cat . B. since it has several recursive productions. NN. tree. NP → NP PP. again using NP → DT NN. divided into Binary productions. VBD. VP → VP PP. PU = {A → D : A ∈ N . cat. Consider a very simple grammar: ◦ N = {S. IN} ◦ NS = {S} ◦ T = {The. dog. PP → IN NP}. PB = {A → B C : A. DT → the. the. In general. Consider the sentence The cat saw the dog from the tree. STRUCTURED MODELS ◦ A set of terminal symbols. It can also generate the same sentence several ways. VP.
∀A ∈ N . we can cast PCFG as a structured linear model (in log space). y) is deﬁned by assigning a probability to each production and making sure that the sum of probabilities of all productions starting with a each symbol is 1: P (A → B C) = 1. The probability of a tree is simply the product of probabilities of the productions used in the tree (times the probability of the starting symbol). . 9. called prepositional attachment.1) as hw (x) = arg max w f (x.y)≤0 and describe the associated algorithm to compute the highest scoring parse tree y given a sentence x. (3. The distribution P (x. A standard approach to resolving ambiguity is to use a PCFG to deﬁne a joint probability distribution over the space of parse trees Y and sentences X . with the difference being in the analysis of the toplevel VP: [sawVBD [theDT dogNN ]NP ]VP [[fromIN [theDT treeNN ]NP ]PP . is very common in many realistic grammars. Hence the logprobability of a tree is a sum of the logprobabilities of its productions. y : g(x. This kind of ambiguity. sawVBD [[theDT dogNN ]NP [fromIN [theDT treeNN ]NP ]PP ]NP . B. We also need to assign a probability to the different starting symbols P (A) ∈ NS such that A∈NS P (A) = 1. y) as the most likely parse tree for a sentence x. CONTEXT FREE GRAMMARS 39 actually saw the dog who lived near the tree or was tied to it in the past.4. Our grammar allows both interpretations. In Ch. Standard PCFG parsers use a Viterbistyle algorithm to compute arg maxy P (x.3. y) consist of the counts of the productions and w be their logprobabilities. y). we will show how to represent a parse tree as an assignment of variables Y with appropriate constraints to express PCFGS (and more generally weighted CFGs) in the form of Eq.C:A→B C∈PB D:A→D∈PU P (A → D ) = 1. By letting our basis functions f (x.
5 Combinatorial problems Many important computational tasks are formulated as combinatorial optimization problems such as the maximum weight bipartite and perfect matching. graphcut. We represent a matching with a set of binary variables yjk that take the value 1 if reviewer j is assigned to paper k. but in many others. s. such as matchings or graphcuts or trees). together with a scoring scheme that assigns weights to candidate outputs is a kind of a model. job assignment. Cormen et al. we have an a weight qjk indicating the qualiﬁcation level of reviewer j for evaluating paper k. 1982. consider modeling the task of assigning reviewers to papers as a maximum weight bipartite matching problem. As a particularly simple and relevant example. The bipartite matching problem can be solved using a combinatorial algorithm or the following linear program: max j. 1999].t. A simple scheme could measure the “expertise” as the percent of word . a combinatorial space of structures. constructing the weights is an important and laborintensive design task. More speciﬁcally. The quality of the solution found depends critically on the choice of weights that deﬁne the objective. Treated abstractly.40 CHAPTER 3. network design and many more. routing. suppose we would like to have R reviewers per paper. This LP is guaranteed to produce integer solutions (as long as P and R are integers) for any weights q(y) [Nemhauser & Wolsey. STRUCTURED MODELS 3. These problems arise in applications such as resource allocation. the weights of the objective function in the optimization problem are simple and natural to deﬁne (for example.3) µjk ≤ P. and 0 otherwise. Our objective is to ﬁnd an assignment for reviewers to papers that maximizes the total weight. 0 ≤ µjk ≤ 1. 2001]. and that each reviewer be assigned at most P papers. 1976. For each paper and reviewer. and many others [Lawler. Euclidian distance or temporal latency). scheduling. edgecover. Papadimitriou & Steiglitz. spanning tree.k µjk qjk µjk = R.. where the weights represent the “expertise” of each reviewer for each paper. j k (3. binpacking. In some domains.
Constructing and tuning the weights for a problem is a difﬁcult and timeconsuming process. As usual. Then the d words. a weighted combination of overlapping the web page of a reviewer and the abstract of the paper that were matched in y. However. the web page of a reviewer j and the abstract of the paper k. COMBINATORIAL PROBLEMS 41 overlap in the reviewer’s home page and the paper’s abstract. This fact makes a probabilistic interpretation of the model as a distribution over matchings intractable to compute. even simply counting the number of matchings is #Pcomplete [Valiant. 1979. The space of bipartite matchings illustrates an important property of many structured spaces: the maximization problem arg maxy∈Y w f (x. Note that counting is easier than normalization. y) is easier than the normalization problem y∈Y exp{w f (x. y)}. In the next chapter we will show how to learn the parameters w in much the same way we learn the parameters w of a Markov network. just as it is for Markov networks for handwriting recognition. Let xjk denote the intersection of the set of words occurring in webpage(j)∩abstract(k). 1979].5. Similarly. y) = score qjk is simply qjk = jk yjk 1 I(wordd ∈ xjk ). the number of times word d was in both wd 1 I(wordd ∈ xjk ). y). We can deﬁne fd (x. we would want to weight certain words much more (words that are relevant to the subject and infrequent). The maximum weight bipartite matching can be found in polynomial (cubic) time in the number of nodes in the graph using a combinatorial algorithm. However. since it requires computing the normalization.3. . Garey & Johnson. which is essentially weighted counting. we will represent the objective q(y) as a weighted combination of a set of basis functions w f (x. exact maximum likelihood estimation is intractable.
we can use standard optimization software to solve the problem. we develop methods for ﬁnding parameters w i=1 such that: arg max w f (x(i) . y) can be solved or approximated by a compact convex optimization problem for some convex subset of parameters w ∈ W.1) where we assume that the optimization problem maxy : g(x. y∈Y (i) where Y (i) = {y : g(x(i) . y : g(x. ∀i. Given a sample S = {(x(i) .y)≤0 w f (x. First and foremost.y)≤0 (4. y) ≈ y(i) . There are several reasons to derive compact convex formulations. y). y) ≤ 0}. we described several important types of structured models of the form: hw (x) = arg max w f (x. Although specialpurpose algorithms that exploit the structure of a particular problem are often much faster 42 . we can ﬁnd globally optimal parameters (with ﬁxed precision) in polynomial time. y(i) )}m . In this chapter. we describe at an abstract level two general approaches to structured estimation that we apply in the rest of the thesis.Chapter 4 Structured maximum margin estimation In the previous chapter. Second. A compact problem formulation is polynomial in the description length of the objective and the constraints. Both of these approaches deﬁne a convex optimization problem for ﬁnding such parameters w.
4. the availability of offtheshelf software is very important for quick development and testing of such models. MAXMARGIN ESTIMATION 43 (see Ch.1 Maxmargin estimation As in the univariate prediction. 4. In structured problems. 7 and Ch. we can analyze the generalization performance of the framework without worrying about the actual algorithms used to carry out the optimization and the associated woes of intractable optimization problems: local minima. the loss is often not just the simple 01 loss or squared error. etc. where we are jointly predicting multiple variables. we measure the error of approximation using a loss function .1. 6). 10). but also to a wide range of “unconventional” predictive models. where maximum likelihood estimation is intractable. For structured classiﬁcation. y∈Y (i) . In prediction problems where the maximization in Eq. (4. we consider convex programs that provide only an upper or lower bound on the true solution.4. we will adopt the hinge upper bound i (h(x(i) )) on the loss function for structured classiﬁcation inspired by maxmargin criterion: i (h(x (i) )) = max [w fi (y) + i (y)] − w fi (y(i) ) ≥ i (h(x(i) )). We will explore these and more general loss functions in the following chapters. Our framework applies not only to the standard models typically estimated by probabilistic methods.1) is intractable. We provide exact maximum margin solutions for several of these problems (Ch. a natural loss function is a kind of Hamming distance between y(i) and h(x(i) ): the number of variables predicted incorrectly.1 Minmax formulation Throughout. such as Markov networks and contextfree grammars.1. Such models include graph cuts and weighted matchings. We discuss how to use these approximate solutions for approximate learning of parameters. Third. greedy and heuristic methods.
3) is a standard QP with linear constraints.t. y(i) . but its exponential .9) and Eq. which is generally exponential in Li . STRUCTURED MAXIMUM MARGIN ESTIMATION where as before. most often IRn ). Another way to express this problem is using i Y (i)  linear constraints. i (h(x(i) )) = (x(i) . the number of variables in yi . and show a strong connection between the lossscaled margin and expected risk of the learned model. 1 w2 + C 2 (i) ξi i y∈Y (i) (4. since maxy∈Y (i) [w fi (y) + i (y)] is convex in w (maximum of afﬁne functions is a convex function). ∀i. 5 we analyze the effect of nonuniform loss function (Hamming distance type loss) on generalization. y(i) . but assume this throughout this chapter.2) w fi (y ) + ξi ≥ max [w fi (y) + i (y)]. For brevity. (4. The problem with Eq.10): min s. so minimizing w maximizes the smallest such margin. The formulation in Eq. then the constraints make costly mistakes (those with high i (y)) less likely. y). (2. We can interpret 1 w w [fi (y(i) ) − fi (y)] as the margin of y(i) over another y ∈ Y (i) . the minmax formulation for structured classiﬁcation problem is analogous to multiclass SVM formulation in Eq. (2.44 CHAPTER 4. min s. and fi (y) = f (x(i) .t. scaled by the loss i (y). This form reveals the “maximum margin” nature of the formulation. ∀i. ∀y ∈ Y (i) . In Ch.2) is that the constraints have a very unwieldy form. we did not explicitly include the constraint that the parameters are in some legal convex set (w ∈ W. h(x(i) )). h(x(i) )). The slack variables ξi allow for violations of the constraints at a cost Cξi . If the loss function is not uniform over all the mistakes y = y(i) . With this upper bound. (4. i (h(x(i) )) = (x(i) . The above formulation is a convex quadratic program in w. 1 w2 + C 2 (i) ξi i (4. Assuming ξi are all zero (say because C is very large). the constraints enforce w fi (y(i) ) − w fi (y) ≥ i (y).3) w fi (y ) + ξi ≥ w fi (y) + i (y).
In the next section. (4. since Eq. MAXMARGIN ESTIMATION 45 size is in general prohibitive. The key to solving Eq. the number of variables in y(i) . (4. (4. with a concave (in µi ) objective fi (w. µi ) must be convex in w.2) and transform it to a a more manageable problem. Let yjk indicate whether reviewer j is matched to the paper k.4) is. Assume that we ﬁnd such a formulation in terms of a set of variables µi . compact convex problem for estimating the parameters w.5) y∈Y (i) µi :gi (µi )≤0 We call such formulation compact if the number of variables µi and constraints gi (µi ) is polynomial in Li . We now return to Eq.4. Let xjk denote the intersection of the set of words occurring in the web page of a reviewer j and the abstract of the paper k.1. To make the symbols concrete.4) y∈Y (i) Even if maxy∈Y (i) w fi (y) can be solved in polynomial time using convex optimization. µi ). Each training sample i consists of a matching of Np papers and Nr reviewers from some previous year.2) efﬁciently is the lossaugmented inference max [w fi (y) + i (y)]. Even within the range of tractable losses. we can assume that it is feasible and bounded if Eq. The range of tractable losses will depend strongly on the problem itself (f and Y). A large part of the development of structured estimation methods in the following chapters is identifying appropriate loss functions for the application and designing convex formulations for the lossaugmented inference. (4. Likewise. some are more efﬁciently computable than others.4) is. µi ) and subject to convex constraints gi (µi ): max [w fi (y) + i (y)] = max fi (w. (4. which indicates whether the word d is (i) (i) . the form of the loss term i (y) is crucial for the lossaugmented inference to remain tractable. We can deﬁne a basis function fd (xjk . we develop a maxmargin formulation that uses Lagrangian duality (see [Boyd & Vandenberghe. yjk ) = yjk 1 I(wordd ∈ xjk ). 2004] for an excellent review) to deﬁne a joint. consider the example of the reviewerassignment problem we discussed in the previous chapter: we would like a bipartite matching with R reviewers per paper and at most P papers per reviewer. Note that maxµi :gi (µi )≤0 fi (w. (4.
µi ) = RNp + and gi (µi ) ≤ 0 ⇔ j i. when we can express maxy∈Y (i) w f (x(i) . (4. (3.jk = R. STRUCTURED MAXIMUM MARGIN ESTIMATION in both the web page of a reviewer and the abstract of the paper that are matched in y. In general. Ai . hence RNp − (i) (i) jk yjk yjk represents exactly the number of edges that (i) are different between y and y(i) . Ai µi ≤ bi . Fi . k µi. For example.jk (yjk )] (i) = RNp + jk yjk [w fjk − yjk ]. 0 ≤ µi. We abbreviate the vector of all the basis functions for each edge jk as yjk fjk = f (xjk . we have w f (x(i) .3) (without the constant term RNp ): max jk (i) µi.t. y(i) . yjk ) + 0/1 i.46 CHAPTER 4. Note that the dependence on w is linear and only in the objective of the LP.jk ≤ 1.jk = R. (4. (i) In terms of Eq. 0 ≤ µi. y) as an LP and we use a loss function this is linear in the number of mistakes. ci . µi.t.jk ≤ P. Combining the two pieces.j µi. we have a linear program of this form for the lossaugmented inference: di + max (Fi w + ci ) µi s. fi and gi are afﬁne in µi : fi (w. yjk ).jk (yjk ) = jk (i) 1 jk = yjk ) = RNp − I(y jk (i) yjk yjk . We assume that the loss function decomposes over the variables yij . y) and g(x.5). y) = jk [w f (xjk . f (x.jk [w fjk −yjk ] µi.jk [w fjk − yjk ] µi. µi ≥ 0. y). If this LP is compact (the number of variables and constraints is polynomial in the number of .6) for appropriately deﬁned di .jk ≤ P. the Hamming loss simply counts the number of different edges in the matchings y and y(i) : H i (y) (i) (i) = jk 0/1 i. (i) The last equality follows from the fact that any valid matching for example i has R reviewers for Np papers.jk ≤ 1. j k (i) (i) s. which depend only on x(i) . (i) The lossaugmented inference problem can be then written as an LP in µi similar to Eq. bi .
(We folded λi ≥ 0 into qi (w.w (µi . (4. we can write the Lagrangian dual minλi ≥0 maxµi Li. ξ}. then we can use it to solve the maxmargin estimation problem efﬁciently by using convex duality. λi ) and qi (w. λi ) for brevity.1.t.) Since the original problem had polynomial size. (4. λi ≥0 µi µi :gi (µi )≤0 For many forms of f and g. λi ) ≤ 0.9) where hi (w. w fi (y(i) ) + ξi ≥ Moreover. λi ). (4. ∀i. we get min s.4. λi ≥ 0. we have strong duality: max fi (w. one for each constraint function in gi (µi ). µi ) = min max Li. (4. λi ) ≤ 0 is {Fi w + ci − Ai λi ≤ 0. λi ) = fi (w. MAXMARGIN ESTIMATION 47 label variables).t. hi (w.7) where λi ≥ 0 is a vector of Lagrange multipliers.8) where hi (w.w (µi .λi )≤0 (4.t. µi ) − λi gi (µi ). Plugging Eq. Ai λi ≥ Fi w + ci . The Lagrangian associated with Eq. we can combine the minimization over λ with minimization over {w.8) into Eq. λi ) explicitly as: min s. The . the dual of the LP in Eq. λi ) qi (w. λi ) = di + bi λi and qi (w. (4. the dual is polynomial size as well. λi ) are convex in both w and λi .4) is given by Li.w (µi . µi ) is concave in µi and bounded on the nonempty set µi : gi (µi ) ≤ 0. −λi ≤ 0}. Since we assume that fi (w. 1 w2 + C 2 ξi i qi (w.6) is di + min bi λi s. (4. λi ). (4.2).10) min hi (w. For example.
but no polynomial formulation is known [Bertsimas & Tsitsiklis. can be solved in polynomial time using combinatorial algorithms. leading to a suboptimal solution w. ∀i. 1 w2 + C 2 ξi i (4. we have a QP with linear constraints: min s. ∀i.t. Optimizing jointly over λ as well will produce a solution to {w.2 Certiﬁcate formulation In the previous section. λi ). Intuitively.11) w fi (y(i) ) + ξi ≥ hi (w. though. . ξ} that is optimal. Hence we have a joint and compact convex optimization program for estimating w. we assumed a compact convex formulation of the lossaugmented max in Eq. 1997. maximum weight perfect (nonbipartite) matching and spanning tree problems can be expressed as linear programs with exponentially many constraints. ∀i.1. qi (w. In some cases. we can ﬁnd a compact certiﬁcate of optimality that guarantees that y(i) = arg maxy [w fi (y) + i (y)] without expressing lossaugmented inference as a compact convex program. Ai λi ≥ Fi w + ci . λi ) ≤ 0. just verifying that a given assignment is optimal is sometimes easier than actually ﬁnding it. ∀i.12) ∀i. For our LPbased example.t. STRUCTURED MAXIMUM MARGIN ESTIMATION reason for this is that if the right hand side is not at the minimum. Both of these problems. 1 w2 + C 2 ξi i (4. 4. There are several important combinatorial problems which allow polynomial time solution yet do not have a compact convex optimization formulation. 2003]. w fi (y(i) ) + ξi ≥ di + bi λi .4). For example. Schrijver. however.48 CHAPTER 4. min s. (4. λi ≥ 0. the constraint is tighter than necessary. The exact form of this program depends strongly on f and g.
Vk [jk])..t. In the spanning tree problem. k) is larger than (or equal to) the weight of any other edge (j . RS [hw ] = 0. where V (i)  is the number of nodes in the graph for example i. this formulation requires that the upper bound on the empirical risk be zero.j k + i. (i) Then the optimality conditions are: (i) . MAXMARGIN ESTIMATION 49 Consider the maximum weight spanning tree problem.13) ∀i. with loss for each wrong edge given by w fi.j k i. qi (w. then Eq. the weight of (j. where j ∈ Vj [jk] and k ∈ Vk [jk]. Note that this formulation does not allow for violations of the margin constraints (it has no slack variables ξi ). Then the following joint convex program in w and ν computes the maxmargin parameters: min s. νi ). ∀jk.t. Essentially. If the basis functions are not sufﬁciently rich to ensure that each y(i) is optimal. For a full graph. Suppose that we can ﬁnd a compact convex formulation of these conditions via a polynomial (in Li ) set of functions qi (w. such as in perfect matching optimality in Ch.2) may be infeasible. we have V (i) 3 ) constraints for each example i. yjk ). A spanning tree is optimal with respect to a set of edge weights if and only if for every edge (j. Expressing the spanning tree optimality does not require additional variables νi . 2001]. A basic property of a spanning tree is that cutting any edge (j. j ∈ Vj [jk]. k) is in the tree and the score of the edge is given by w fi. but in other problems. such auxiliary variables are needed.4.1. 10. 10. νi ) ≤ 0 ⇔ w fi (y(i) ) ≥ w fi (y) + i (y). jointly convex in w and auxiliary variables νi : ∃νi s.jk ≥ w fi. (4. k) in the tree creates two disconnected sets of nodes (Vj [jk]. k ∈ Vk [jk]. yjk = 1. We also assume that the loss function decomposes into a sum of losses over the edges. ∀y ∈ Y (i) . 1 w2 2 qi (w. suppose yjk encodes whether edge (j.t. k ) in the graph with j ∈ Vj [jk]. and minimizes the complexity .1. k ∈ Vk [jk] [Cormen et al. (4. νi ) ≤ 0.jk . j k s. k) in the tree connecting Vj [jk] and Vk [jk].jk for some basis functions f (xjk . We discuss the conditions for optimality of perfect matchings in Ch.
and therefore are less justiﬁed. not more than the number of parameters n plus the number of examples m can be active in general.3). but the maximization problem can be solved or approximated by a combinatorial algorithm. where we have an exponential number of linear constraints. but can only upper or lower bound it. STRUCTURED MAXIMUM MARGIN ESTIMATION of the hypothesis hw as measured by the norm of the weights. If we continue adding constraints until there are no more violated ones.50 CHAPTER 4. The nature of these lower and upper bounds depends on the problem. 4. the resulting solution is optimal. If the problem is infeasible. Consider Eq. the designer could add more basis functions f (x. these slack variables would not represent upper bounds on the loss as they are in the minmax formulation. one for each i and y ∈ Y (i) . Only a subset of those constraints will be active at the optimal solution w. identifying these constraints is in general as difﬁcult as solving the problem.1 Constraint generation When neither compact maximization or optimality formulation is possible. since that is the number of variables. One could also add slack variables for each example and each constraint that would allow violations of optimality conditions with some penalty. Of course. but a greedy approach of adding the most violated constraints often achieves good approximate solutions after adding a small (polynomial) number of constraints. 4. However. we can resort to constraint generation or cutting plane methods. Fig. If we can identify a small number of constraints that are critical to the solution. 4. y) that take into account additional information about x. (4. In fact.2. but we consider two general cases below.2 Approximations: upper and lower bounds There are structured prediction tasks for which we might not be able to solve the estimation problem exactly. We assume that we have an algorithm that produces y = arg maxy∈Y (i) [w fi (y) + . we do not have to include all of them. we cannot compute maxy∈Y (i) [w fi (y) + i (y)] exactly or explicitly.1 shows schematically how approximating of the max subproblem reduces or extends the feasible space of w and ξ and leads to approximate solutions. Often.
We maintain. i (y)]. The algorithm is described in Fig. and be more stringent or relaxed in others.14) ∀i. The solid red line represents the constraints imposed by the assignments y ∈ Y(i) .4. The algorithm terminates when no constraints are violated. a small but growing set of assignments Y (i) ⊂ Y (i) . whereas the dashed and dotted lines represent approximate constraints. terminating when the desired precision is reached. we set Y = Y (i) ∪ y. ‘x’ and ‘o’ mark the different optima. The approximate constraints may coincide with the exact constraints in some cases. the lowerbound on the constraints provided by Y (i) ∪ y keeps tightening with each iteration.2. w fi (y(i) ) + ξi ≥ w fi (y) + i (y). ∀y ∈ Y (i) . In Fig. 4. for each example i. APPROXIMATIONS: UPPER AND LOWER BOUNDS 51 Upperbound Exact Lowerbound + × Figure 4. we solve the problem with a subset of constraints: min s.t. (4.1. The parabolic contours represent the value of the objective function and ‘+’. 1 w2 + C 2 ξi i (4.2. We note that if the algorithm that produces y = arg maxy∈Y (i) [w fi (y)+ i (y)] is . (4. where (i) is a user deﬁned precision parameter. The only difference between Eq. is violated. If it is violated.14) is that Y (i) has been replaced by Y (i) .1: Exact and approximate constraints on the maxmargin quadratic program. At each iteration. 4. We then compute y = arg maxy∈Y (i) [w fi (y) + i (y)] for each i and check whether the constraint w fi (y(i) ) + ξi + ≥ w fi (y) + i (y).3) and Eq.
QPs or SDPs often provide excellent approximation algorithms [Hochbaum. ∀i. The relaxation usually deﬁnes a larger feasible space Y (i) ⊃ Y (i) over . ∀y ∈ Y (i) . 1997. Nemhauser & Wolsey. Figure 4. STRUCTURED MAXIMUM MARGIN ESTIMATION Input: precision parameter . ∀ i. 11.2. if w fi (y(i) ) + ξi + ≤ w fi (y) + i (y). graphpartitioning in Ch. the maximization problem we are interested in may be very expensive or intractable. Initialize: Y (i) = {}. 4. 8. the approximation error of the solution we achieve might be much greater than . while the maximization algorithm is comparatively fast. 2. See [Bertsimas & Tsitsiklis. 2004] for a more indepth discussion of cutting planes methods. if violation = 1 goto 2. Relaxations of such integer programs into LPs. 1999]. The number of constraints that must be added before the algorithm terminates depends on the precision and problem speciﬁc characteristics.52 CHAPTER 4.2 Constraint strengthening In many problems. For each i. Boyd & Vandenberghe. but very large. 3. multiway cut in Ch. This approach may also be computationally faster in providing a very good approximation in practice if the explicit convex programming formulation is polynomial in size.t. For example. Many such problems can be written as integer programs. 1. suboptimal. Compute y = arg maxy∈Y (i) [w fi (y) + i (y)]. we consider MAP inference in large treewidth Markov networks in Ch. 1997. 1 w2 + C 2 (i) ξi i w fi (y ) + ξi ≥ w fi (y) + i (y). then set Y (i) = Y (i) ∪ y and violation = 1 4.2: A constraint generation algorithm. Set violation = 0 and solve for w and ξ by optimizing min s. Return w. 7.
As the objective includes a penalty for the slack variable. which make the . By contrast. where y ∈ Y (i) may correspond to a “fractional” assignment. Ahuja & Orlin. the approximation is an overestimate of the constraints: max [w fi (y) + i (y)] ≥ max [w fi (y) + i (y)].1 shows how the overestimate reduces the feasible space of w and ξ. Fig. the approximate MAP solution has higher value than any integer solution. In such a case. intuitively. 2004]. An inverse optimization problem is deﬁned by an instance of an optimization problem maxy∈Y w f (y). and a target solution yt . In practice. the approximate constraints are tightened because of the additional invalid assignments. Note that for every setting of the weights w that produces fractional solutions for the relaxation. minimizing the objective tends to drive the weights w away from the regions where the solutions to the approximation are fractional. a solution to the MAP LP in Eq. a set of nominal weights w0 .3 Related work Our maxmargin formulation is related to a body of work called inverse combinatorial and convex optimization [Burton & Toint. 4. the estimation algorithm is ﬁnding weights that are not necessarily optimal for an exact maximization algorithm. we will show experimentally that such approximations often work very well. thereby driving up the corresponding slack ξi . 2001. In this case. The goal is to ﬁnd the weights w closest to the nominal w0 in some norm. Zhang & Ma. (3. Heuberger. but (close to) optimal for the particular approximate maximization algorithm used.4. y∈Y (i) y∈Y (i) Hence the constraint set is tightened with such invalid assignments. 4. for weights w for which the MAP approximation is integervalued. the margin has the standard interpretation as the difference between the score of y(i) and the MAP y (according to w). 1992. For example. including the true assignment y(i) . In essence. 1996.2) for an untriangulated network may not correspond to any valid assignment.3. RELATED WORK 53 which the maximization is done.
A rational agent executes a policy (essentially. which generally depends on the on the current and the next state and the action taken. Most of the attention has been on L1 and L∞ norms. we do not assume as given a nominal set of weights. The environment is modeled as a system that can be in one of a set of discrete states. but L2 norm is also used. note that a policy roughly corresponds to the labels . which is not appropriate in the learning setting. 2004] is much closer to our setting.54 CHAPTER 4. 2000. Moreover. Although there is a strong connection between inverse optimization problems and our formulations. but we brieﬂy describe the Markov decision process (MDP) model commonly used for sequential decision making problems where an agent interacts with its environment. The inverse reinforcement learning problem [Ng & Russell. At every time step. The study of inverse problems began with geophysical scientists (see [Tarantola. the goals are very different than ours. ∀y ∈ Y. the agent chooses an action from a discrete set of actions and the system transitions to a next state with a probability that depends on the current state and the action taken. In our framework. 1987] for indepth discussion of a wide range of applications). a state to action mapping) that maximizes its expected reward. To map this problem (approximately) to our setting. w − w0 p w f (yt ) ≥ w f (y).t. A full description of the problem is beyond our scope. The solution w depends critically on the choice of nominal weights. The agent collects a reward at each step. then w = 0 is trivially the optimal solution. the inverse optimization problem attempts to match the behavior while not perturbing the “guesstimate” too much. The goal is to learn a reward function that will cause a rational agent to act similar to the observed behavior of an expert. Note that if we set w0 = 0. Provided educated guesses for the parameters w0 and the behavior of the system as a target. we are learning a parameterized objective function that depends on the input x and will generalize well in prediction on new instances. Modeling a complex physical system often involves a large number of parameters which scientists ﬁnd hard or impossible to set correctly. STRUCTURED MAXIMUM MARGIN ESTIMATION target solution optimal: min s. Abbeel & Ng.
maximum margin estimation can be tractable when maximum likelihood is not. Our framework applies to a wide range of prediction problems that we explore in the rest of the thesis. Because our approach only relies using the maximum in the model for prediction. CONCLUSION 55 y.4. only requires expressing optimality of a given assignment according to the model. By contrast. context free grammars. and many combinatorial structures such as matchings and graphcuts. In models that are tractable for both maximum likelihood and maximum margin. we presented two formulations of structured maxmargin estimation that deﬁne a compact convex optimization problem. Similar results hold for nonbipartite matchings and mincuts. The ﬁrst formulation. and does not require a normalized distribution P (y  x) over all outputs. the state sequence correspond to the input x and the reward for a state/action sequence is assumed to be w f (x. minmax. y). (such as lowtreewidth Markov networks. The goal is to learn w from a set of state/action sequences (x(i) . certiﬁcate. to learn a probabilistic model P (y  x) over bipartite matchings using maximum likelihood requires computing the normalizing partition function. 1979. Garey & Johnson. maximum margin estimation can be formulated as a compact QP with linear constraints. we resort to approximations that only provide upper/lower bounds on the predictions. The second one. y) for some basis functions w f (x. which is #Pcomplete [Valiant. y(i) ) of the expert such that the maximizing the expected reward according to the system model makes the agent imitate the expert. When the prediction problem is intractable or very expensive to solve exactly. 4. many other problems in which . including Markov networks. This and related problems are formulated as a convex program in Ng and Russell [2000] and Abbeel and Ng [2004]. The estimation problem is tractable and exact whenever the prediction problem can be formulated as a compact convex optimization problem or a polynomial time combinatorial algorithm with compact convex optimality conditions. relies on the ability to express inference in the model as a compact convex optimization problem. context free grammars.4.4 Conclusion In this chapter. 1979]. For example. The estimated parameters are then approximate. but produce accurate approximate prediction models in practice.
2004. Because of the hingeloss.56 CHAPTER 4. The forthcoming formulations in the thesis follow the principles laid out in this chapter.. Maximum likelihood estimation with kernels results in models that are generally nonsparse and require pruning or greedy support vector selection methods [Lafferty et al. from Markov networks and contextfree grammars to graph cuts and perfect matchings. The range of applications of these principles is very broad and leads to estimation problems with very interesting structure in each particular problem. which makes the use of kernels much more efﬁcient. .. our approach has an additional advantage. 2004]. STRUCTURED MAXIMUM MARGIN ESTIMATION inference is solvable by dynamic programming). Altun et al. the solutions to the estimation are relatively sparse in the dual space (as in SVMs).
Part II Markov networks 57 .
a Markov network for the hypertext domain would include a node for each webpage. Sequential prediction problems arise in natural language processing (partofspeech tagging. 1998. 2002]. encoding its label.g. neighboring pixels exhibit spatial label coherence in denoising.Chapter 5 Markov networks Markov networks are extensively used to model complex sequential. because one links to the other). In hypertext or bibliographic classiﬁcation. and many other ﬁelds. 1986. and whose edges represent and quantify direct dependencies between them.. 1999a]. location and function of proteins that interact are often highly correlated [Vazquez et al.. labels of linked and cocited documents tend to be similar [Chakrabarti et al. and relational interactions in prediction problems arising in many ﬁelds. 1999]). segmentation and stereo correspondence [Besag.. and an edge between any pair of webpages whose labels are directly correlated (e... In image processing. These problems involve labeling a set of related objects that exhibit local consistency. In sequential labeling problems (such as handwriting recognition). Taskar et al. compuu tational biology (gene ﬁnding. information extraction [Manning & Sch¨ tze. 2003].. speech recognition. In proteomic analysis. Such models are encoded by a graph. protein structure prediction. whose nodes represent the different object labels. sequence alignment [Durbin et al. spatial. We address the problem of maxmargin estimation the parameters of Markov networks 58 . Markov networks compactly represent complex joint distributions of the label variables by modeling their local interactions. the labels (letters) of adjacent inputs (images) are highly correlated. For example. 1998]). Boykov et al.
We assume the structure of the network is given: we have a mapping from an input x to the corresponding Markov network graph G(x) = {V. y) − log Zw (x).2. usually the squarednorm of the weights w [Lafferty et al. 2001]). y): log Pw (y  x) = w f (x. We show a compact convex formulation that seamlessly integrates kernels with graphical models. 5. we review the standard maximum likelihood method. We focus on conditional Markov networks (or CRFs [Lafferty et al. drawn from a ﬁxed disi=1 tribution D over X × Y. for example.3. Before we present the maximum margin estimation. this mapping depends on the segmentation algorithm that determines how many letters the sample image contains and splits the image into individual images for each letter. ﬁrstorder Markov chain or a higherorder models. 2. The objective is to minimize the training logloss with an additional regularization term. y)} and w ∈ IRn . We are given a labeled training sample S = {(x(i) . Note that the topology and size of the graph G (i) . i i .1. 3.1 Maximum likelihood estimation The regularized maximum likelihood approach of learning the weights w of a Markov network is similar to logistic regression we described in Sec.1 is deﬁned via a vector of n basis functions f (x. We abbreviate G(x(i) ) as G (i) below. where Zw (x) = y exp{w f (x. the training sequences might have different lengths.5. y). For instance.. 2001]: 1 w2 − C 2 1 log Pw (y(i)  x(i) ) = w2 + C 2 log Zw (x(i) ) − w fi (y(i) ). E} where the nodes V map to the variables in y. The loglinear representation we have described in Sec. MAXIMUM LIKELIHOOD ESTIMATION 59 for such structured classiﬁcation problems.. In handwriting recognition. y(i) )}m . We analyze the theoretical generalization properties of maxmargin estimation and derive a novel marginbased bound for structured classiﬁcation. It also depends on the basis functions we use to model the dependencies of the problem. which represent P (y  x) instead of generative models P (x. might be different for each example i.
3. Since the basis functions decompose over the cliques of the network.w [fi (y)]. such as Newton’s method. 1999. but uses only the gradient information [Nocedal & Wright. MARKOV NETWORKS where fi (y) = f (x(i) . Pw (yc∪c  xi ) as well as covariances of all basis functions.. Pinto et al.w [fi (y)] = (i) c∈C (i) yc ∈Yc fi. the expectation decomposes as well: Ei. A standard approach is to use an approximate second order method that does not need to compute the Hessian. To compute the expectations. y). Conjugate Gradients or LBFGS methods have been shown to work very well on large estimation problems [Sha & Pereira. This objective function is convex in the parameters w.w [∆fi (y)]. where I is a n × n identity matrix. as before.w δfi (y)δfi (y) . y). where Ei. Boyd & Vandenberghe. so we have an unconstrained convex optimization problem. The gradient with respect to w is given by: w+C i Ei.60 CHAPTER 5. since we need to calculate joint marginals of every pair of cliques c and c . require the second derivatives as well as the gradient.3. y(i) ) − f (x(i) . 2003].w [fi (y)] =  x(i) ) is the expectation under the conditional dis tribution Pw (y  x(i) ) and ∆fi (y) = f (x(i) . 2003. even with millions of parameters w. Second order methods for solving unconstrained convex optimization problems. Let δfi (y) = fi (y) − Ei. The Hessian of the objective depends on the covariances of the basis functions: I +C i Ei. Computing the Hessian is more expensive than the gradient.w [fi (y)] − fi (y(i) ) = w − C i y∈Y fi (y)Pw (y Ei.c (yc )Pw (yc  x(i) ).2. which is quadratic in the number of cliques and the number of functions. we can use inference in the Markov network to calculate marginals Pw (yc  x(i) ) for each clique c in the network Sec. 2004]. .
3. y(i) . where we are predicting multiple labels.1) s. s. 3. The simplest loss is the 0/1 loss i (y) ≡ 1 (i) = y).t.3 how to express maxy w fi (y) as an LP. ∀c ∈ C (i) .c (yc )] (5. [2003]. 3.c (yc )[w fi. ∀i. the loss is often not just the simple 0/1 loss. in structured problems. In fact I(y this loss for sequence models was used by Collins [2001] and Altun et al.c (yc ). but may depend on the number of labels and type of labels predicted incorrectly or perhaps the number of cliques of labels predicted incorrectly. We will focus on decomposable loss functions below. w fi (y(i) ) + ξi ≥ max [w fi (y) + i (y)]. like the basis functions. yc ) = c c∈C(G (i) ) i.t. y) = v∈V (i) 1 v = yv ). we assume that the loss. s ⊂ c. Assumption 5. ∀s.c (yc ) = 1.5. we can express this inference problem for a triangulated graph as a linear program for each example i as in Sec.c (yc ) + i. 4.1: min 1 w2 + C 2 ξi i y (5. decomposes over the cliques of labels.2 Maximum margin estimation For maximummargin estimation.3: max c. µi.3.2. . but the important difference is the loss function i . In general. yc µi. However.2) µi.c (yc ). ∀i.1 The loss function i (y) is decomposable: i (y) = c∈C(G (i) ) (i) (x(i) . MAXIMUM MARGIN ESTIMATION 61 5. ∀c ∈ C (i) . yc . c ∈ C (i) .yc µi. ∀ys . ∀yc .s (ys ) = yc ∼ys µi. A natural choice that we use in our experiments is the Hamming distance: H (x(i) .c (yc ) ≥ 0. We know from Sec. we begin with the minmax formulation from Sec.2. I(y (i) With this assumption.
c + ∀c ∈ C (i) .c. ys ∼yc In this dual.2) is given by: min c λi. 1 w2 + C 2 ξi i (5. (If the arg max is not unique. ∀yc .1) for each example i and maximizing jointly over all the variables (w.4) λi.c to ξi.3) mi. (5. ∀c ∈ C (i) .c mi.s.c (yc ) = s⊂c.c (yc ) + ξi.c variables correspond to the normalization constraints.s. (5. any convex combination of the assignments is a valid solution). ∀c ∈ C (i) . s⊂c.c.c w fi (y(i) ) + ξi ≥ λi.c . For readability.c (yc ) + i. s⊂c.t. ∀yc . i.c (yc ) − s⊃c (5.s (yc ) variables correspond to the agreement constraints in the primal in Eq.c.c (yc ) + i. ∀yc .c (yc ). then the distribution that maximizes the objective puts all its weight on that assignment. As we showed before. If the most likely assignment is unique. ys ∼yc In order to gain some intuition about this formulation. ∀c ∈ C (i) .s. λi.2). s.c = w fi.t.c . . we make a change of variables from λi. the constraints ensure that the µi ’s form a proper distribution. we also introduce variables that capture the effect of all the agreement variables m: Mi. MARKOV NETWORKS where C (i) = C(G (i) ) are the cliques of the Markov network for example i.62 CHAPTER 5. Plugging the dual into Eq.c + s⊃c mi. ξ.c.s (ys ) − s⊃c mi. The reason for naming the new variables using the letter ξ will be clear in the following.c (yc ). (5.c (yc ).c (yc ) − mi. we have: min s.s (ys ) ≥ w fi. while mi. The dual of Eq.c : (i) λi. λ and m). ∀i. ∀i. the λi. ys ∼yc mi.s (ys ) ≥ w fi. ∀i.
ys ∼yc mi. ∀yc . Hence we can simply eliminate c ξi. 1 w2 + C 2 ξi ≥ c (i) w fi. we can write this in a form that resembles our original formulation Eq.c (yc ) + i.c . ∀i. ∀yc . ∀c ∈ C (i) .t. (i) w fi. or a margin requirement. ∀c ∈ C (i) .c (yc ) = s⊂c. .s (ys ) − s⊃c mi. (i) w fi. ∀i.c (yc ) = s⊂c.s variables.t. 1 w2 + C 2 ξi.s (ys ) − s⊃c mi.c (yc ). but deﬁned at a local level. (5.c at the optimum. ∀yc . ∀i.7) + Mi.c (yc )].s.2.c (yc ). ∀c ∈ C (i) .1).5. we essentially treat each clique as an independent classiﬁcation problem: for each clique we have a hinge upperbound on the local loss. ys ∼yc mi.c.s. Finally. we have: min s.s (ys ) variables correspond to a certain kind of messages between cliques that distribute “credit” to cliques to fulﬁll this margin requirement from other cliques which have sufﬁcient margin. Mi.c this set of variables: min s.c.c ≥ max [w fi.c i.6) + Mi.c (yc ). ∀c ∈ C (i) .c and mi.5) ξi.c (yc ) + Mi. since the slack variable ξi only appears only in the and the objective minimizes Cξi .s (ys ) − s⊃c mi.c (yc ). ∀i.c (yc ) = s⊂c.c.c i. The mi. for each clique: min s.c i. ∀i. + Mi.c (yc ) + ξi.c (yc ) + ξi. Note that ξi = constraint ξi ≥ c ξi.c.c yc i.c (yc ) (5. Note that without Mi. ys ∼yc mi.c ≥ w fi. ∀yc .c (yc ).s. ∀c ∈ C (i) .c ≥ w fi. ∀i.c (yc ) + ξi.c (yc ) (5. 1 w2 + C 2 ξi.c (yc ) + Mi. ∀i. MAXIMUM MARGIN ESTIMATION 63 With these new variables.t.c (yc ) ξi i (5. ∀c ∈ C (i) .c. ∀yc .
12 (y1 ). ∀y1 .34 (y4 ) − m4. The ﬁgure shows the local slack variables ξ and messages m between cliques for this sample. As an example. ∀y3 .23 (y2 ).45 (y4 ). consider the ﬁrstorder Markov chain in Fig. which decomposes into local terms = 1 j = yj ) for each node and is I(y (∗) zero for the edges. 5. we drop the dependence on the sample index i in the indexing of the variables (we also used yj loss H (∗) instead of yj below). The set of cliques consists of the ﬁve nodes and the four edges. I(y w f4 (y4 ) + ξ4 ≥ w f4 (y4 ) + 1 4 = y4 ) − m4. below we use the Hamming j (yj ) (i) . The constraints associated with the node cliques in this sequence are: w f1 (y1 ) + ξ1 ≥ w f1 (y1 ) + 1 1 = y1 ) − m1. Also shown are the corresponding local slack variables ξ for each clique and messages m between cliques.45 (y5 ). ∀y4 . I(y (∗) (∗) (∗) (∗) (∗) (∗) (∗) (∗) (∗) (∗) .12 (y2 ) − m2.64 CHAPTER 5.1. I(y w f3 (y3 ) + ξ3 ≥ w f3 (y3 ) + 1 3 = y3 ) − m3. Suppose for the sake of this example that our training data consists of only one training sample. MARKOV NETWORKS Figure 5.1: Firstorder chain shown as a set of cliques (nodes and edges).34 (y3 ). I(y w f5 (y5 ) + ξ5 ≥ w f5 (y5 ) + 1 5 = y5 ) − m5. For concreteness. ∀y5 . I(y w f2 (y2 ) + ξ2 ≥ w f2 (y2 ) + 1 2 = y2 ) − m2. ∀y2 .23 (y3 ) − m3. For brevity of notion in this example.
∀i.12 (y2 ). The dual is given by: max i. ∀y4 . y4 ) + m3. ∀i. we develop an alternative dual derivation that provides a very interesting interpretation of the problem and is a departure for specialpurpose algorithms we develop. In the dual.8) w ∆fi (y) ≥ i (y) − ξi . y3 ) + ξ23 ≥ w f23 (y2 . ∀y2 . y4 ) + ξ34 ≥ w f34 (y3 .3 M3N dual and kernels In the previous section. so that they sum . y(i) ) − f (x(i) .9) s. y2 ) + m1.23 (y3 ). We begin with the formulation as in Eq. w f23 (y2 . where ∆fi (y) ≡ f (x(i) .t.34 (y3 ) + m4. y2 ) + ξ12 ≥ w f12 (y1 . y3 ) + m2.t. 2 αi (y)∆fi (y) i. y5 ) + m4. y4 . y5 . y). 1 w2 + C 2 ξi i (5. y3 . (4. In this section. y αi (y) ≥ 0.45 (y5 ). y. ∀y3 . the exponential number of αi (y) variables correspond to the exponential number of constraints in the primal.y 1 αi (y) i (y) − 2 αi (y) = C.y (5.12 (y1 ) + m2. ∀y1 .3. M3 N DUAL AND KERNELS 65 The edge constraints are: w f12 (y1 .5. y2 . we showed a derivation of a compact formulation based on LP inference. y. w f45 (y4 .34 (y4 ). w f34 (y3 . y5 ) + ξ45 ≥ w f45 (y4 . ∀i.23 (y2 ) + m3.3): min s. (∗) (∗) (∗) (∗) (∗) (∗) (∗) (∗) 5.45 (y4 ) + m5. We make two small transformations to the dual that do not change the problem: we normalize α’s by C (by letting αi (y) = Cαi (y)).
2 αi (y)∆fi (y) i. The resulting dual is given by: max i.yc i. As in multiclass SVMs. ∀yc .10) in terms of these marginal dual variables. ∀i.y (5. This dual distribution does not represent the probability that the model assigns to an instantiation. (5.yc µi. we only need clique marginals of the distribution αi (y) to compute their expectations. y αi (y) ≥ 0.c (yc ) i.66 CHAPTER 5. since they lie in the simplex αi (y) = 1. Note that the number of µi. y αi (y) ≥ 0. for example. Since i (y) = c i.y ∗ αi (y)∆fi (y). Our main insight is that the variables αi (y) in the dual formulation Eq. ∀c ∈ C (i) . The dual objective is a function of expectations of i (y) and ∆fi (y) with respect to αi (y). Consider.c (yc ) variables is small (polynomial) compared to the number of αi (y) variables (exponential) if the size of the largest clique is constant with respect to the size of the network. Now we can reformulate our entire QP (5. y. MARKOV NETWORKS to 1 and divide the objective by C. ∀i. ∀y.c (yc ) y ∼yc αi (y ) = c.c (yc ) decompose over the cliques of the Markov network.c (yc ) and ∆fi (y) = c ∆fi. the ﬁrst term in the objective function (ﬁxing a particular i): αi (y) i (y) = y y αi (y) c i.11) where y ∼ yc denotes whether the partial assignment yc is consistent with the full assignment y . ∀i.10) can be interpreted as a kind of distribution over y. but the importance of the constraint associated with the instantiation to the solution. (5.10) s. We deﬁne the marginal dual variables as follows: µi.c (yc ) = c.y 1 αi (y) i (y) − C 2 αi (y) = 1. .c (yc ) = y ∼yc αi (y ).c (yc ). the solution to the dual α gives the solution to the primal as a weighted combination: w∗ = C i.t.
In general.c.10): max i. Therefore. D[M]. Q(α) = Q (M(α)).12) s.yc µ∗ (yc )∆fi. that is. ∀i.c. (5. the set of legal marginals? Characterizing this set (also known as marginal polytope) compactly will allow us to work in the space of µ’s: max Q(α) ⇔ max Q (µ). is the product of simplices for all the m examples.c (yc ) i.c (yc ) = 1. ∀c ∈ C (i) . ∀s. yc µi. µ∈R[M] α∈D[M] Hence we must ensure that µi corresponds to some distribution αi . the following structured dual QP has the same primal solution (w∗ ) as the original exponential dual QP in Eq.t. The solution to the structured dual µ∗ gives us the primal solution: w∗ = C i.11) .yc µi. M3 N DUAL AND KERNELS 67 The decomposition of the second term in the objective is analogous. when all G (i) are triangulated.5. where M denotes the marginalization operator deﬁned by Eq. but there is a continuum of distributions consistent with a set of marginals. which is exactly what the constraints in the LP for MAP inference enforce (see discussion of Lemma 3. we only enforce that there exists an αi consistent with µi . the α distribution is not unique.c (yc ) ≥ 0. Let us denote the the objective of Eq.3. ∀yc . c ∈ C (i) .yc (5. ∀ys .c (yc ) − C 2 2 µi. (5. Note that it only depends on αi (y) through its marginals µi. (5.c (yc ).c In this structured dual.s (ys ) = yc ∼ys µi.c (yc ) y ∼yc αi (y ) = c. µi. but do not make a commitment about what it is. s ⊂ c.yc 1 µi. ∀c ∈ C (i) . The objective of .c (yc ).c (yc ) i.c (yc ). What is its range.c (yc ).5).10) as Q(α). R[M].c (yc )∆fi.yc ∆fi. i. αi (y)∆fi (y) = y c.3.c (yc )∆fi. µi. ∀i. ∀i. The domain of this operator.c.
.g. Speciﬁcally. (5. since it only depends on their marginals.c (yc ) ∆fj. the solutions to the maxmargin QP are typically sparse in the µ variables. We denote the set of separators as S (i) . other deﬁnitions are possible and may be useful when the assignments in each clique yc have interesting structure. c ) in the tree T (i) is a set of variables called the separator s = c ∩ c . 1999]. yc ) ≡ 1 c = yc )k(xc . Now we can deﬁne the maximumentropy distribution αi (y) as follows: αi (y) = Again. MARKOV NETWORKS the QP Eq.13) Kernels Note that the solution is a weighted combination of local basis functions and the objective of Eq. c∈T (i) µi. xc ).¯(yc ) = [f (x(i) . since it is a subclique of a larger clique. we use a ¯ polynomial kernel on the pixel values for the node cliques.68 CHAPTER 5. We usually extend the kernel over the input space to the joint input and output space by simply deﬁning f (xc . Note that each separator s and complement of a separator c \ s is also a clique of the original graph.2 we experiment with several kernels for the handwriting example. yc ) f (xc .10) does not distinguish between these distributions. each logpotential in the network “remembers” only a small proportion of the relevant training data inputs. I(y ¯ ¯ ¯ ¯ Of course. (i) (j) . In our handwriting example.c (yc ) . In Sec. (5. is unique for a triangulated model and can be computed using the junction tree T (i) for the network [Cowell et al. by convention 0/0 ≡ 0. yc )]. yc )] [f (xc . s∈S (i) µi. (5. Kernels are typically deﬁned on the input. yc ) − f (x(i) . however. As in SVMs. Hence. c ¯ ¯ ¯ ¯ ¯ c c (j) (j) (j) Hence.s (ys ) (5. we can locally kernelize our models and solve Eq. The maximumentropy distribution αi consistent with a set of marginals µi . e.12) efﬁciently. 6. associated with each edge (c. yc ) − f (xc .12) can be expressed in terms of dot products between local basis functions (i) ∆fi. xc ). k(xc .
y3 ) = µ12 (y1 . y1 µ134 (y1 . y4 ) = µ13 (y1 .5. y3 . . y3 . µ123 (y1 . y3 The new marginal variables appear only in the constraints. For example. we must address the problem by triangulating the graph. y2 . we can triangulate the graph by adding an arc Y1 —Y3 .2. y4 . y3 ). y3 . they do not add any new basis functions nor change the objective function. y4 ). 5. ∀y3 . y2 . y3 . y1 ∀y2 . y2 . y3 .4 Untriangulated models If the underlying Markov net is not chordal. Y4 and the corresponding marginals. y4 ). if our graph is a 4cycle Y1 —Y2 —Y3 —Y4 —Y1 as in Fig. 5.4. Y3 . ∀y1 . y3 ) and µ134 (y1 . y3 ). We can then use this new graph to produce the constraints on the marginals: µ123 (y1 .2: Diamond Markov network (added triangulation edge is dashed and threenode marginals are in dashed rectangles). This will introduce new cliques Y1 . y3 µ134 (y1 . that is. ∀y1 . Y2 . y3 ) = µ23 (y2 . µ123 (y1 . y2 ). adding ﬁllin edges to ensure triangulation. y2 . y4 ) = µ34 (y3 . Y3 and Y1 . UNTRIANGULATED MODELS 69 Figure 5.
70 CHAPTER 5. they are often much more expensive. Although this and other more complex relaxations are a very interesting area of future development.12) deﬁned by an untriangulated graph. But do we really need these optimal parameters if we cannot perform exact inference? A more useful goal is to make sure that training error is minimized using the approximate inference procedure via the untriangulated LP. For C in intermediate range. We conjecture that the parameters learned by the approximate QP in fact do that to some degree. we can add positive semideﬁnite constraints on the marginals µ used by Wainwright and Jordan [2003]. 8 demonstrate. the number of constraints introduced is exponential in the number of variables in the new cliques — the treewidth of the graph. (5. we can still solve the QP in the structured primal Eq. 5. we show a generalization bound for the task of structured classiﬁcation that allows us to relate the error rate on the training set to the generalization error. the formulation trades off fractionality of the untriangulated LP solutions with complexity of the weights w2 .5 Generalization bound In this section. MARKOV NETWORKS In general. for example 2D grids often used in image analysis. where 100% accuracy is achievable on the training data by some parameter setting w such that approximate inference (using the untriangulated LP) produces integral solutions. consider the separable case.6) or the structured dual Eq. which enforces only local consistency of marginals. the learned parameters produce very accurate approximate models in practice. (5. which tend to improve the approximation of the marginal polytope. Note that we could also strengthen the untriangulated relaxation without introducing an exponential number of constraints. For instance. Solving the problem as C → ∞ will ﬁnd this solution even though it may not be optimal (in terms of the norm of the w) using exact inference. However. Such a formulation. To the best . Unfortunately. optimizes our objective only over a relaxation of the marginal polytope. even sparsely connected networks. For example. as experiments in Ch. The approximate QP does not guarantee that the learned model using exact inference minimizes the true objective: (upperbound on) empirical risk plus regularization. have large treewidth. However.
Our analysis of Hamming loss allows to prove a signiﬁcantly stronger result than previous bounds for the 0/1 loss. this bound is the ﬁrst to deal with structured error. As in other generalization bounds for marginbased classiﬁers. Let Nc be the maximum number of cliques in G(x). y ). Consider an upper bound on the above loss: L(w.5. x. y where L is the number of label variables in y. y ).To state the bound. as we detail below. We can now deﬁne a γmargin perlabel loss: L(w. it picks from all y which are better when helped by γ H (y. or the Hamming distance between y and h(x). x. one that maximizes the Hamming distance from y. y )). y) ≤ L(w.5. arg max w f (x. y) = max 1 f (y ) L H y : w f (y)≤w (y. This upper bound is even more adversarial: it is tight if y = arg maxy [w f (x. one that maximizes the Hamming distance from y. q be the maximum number of cliques that have a variable in common. Our goal in structured classiﬁcation is often to minimize the number of misclassiﬁed labels. x. x. such as the Hamming distance. and Rc be an upperbound on the 2norm of clique basis functions. An appropriate error function is the average perlabel loss L(w. y ). Otherwise. y ) + H (y. This upper bound is tight if y = arg maxy w f (x. it is adversarial: it picks from all y which are better (w f (y) ≤ w f (y )). y )]. Vc be the maximum number of values in a clique Yc . otherwise. Consider a ﬁrstorder sequence . we relate the generalization error to the margin of the classiﬁer. GENERALIZATION BOUND 71 of our knowledge. x. y) ≤ Lγ (w. y) ≤ L(w.y ) L H y : w f (y)≤w f (y )+γ (y. y ). y) = 1 L H (y. y) = max 1 H (y. x. We can now prove that the generalization accuracy of any hypothesis w is bounded by its empirical γmargin perlabel loss. we need to deﬁne several other factors it depends upon. Note that the loss we minimize in the maxmargin formulation is very closely related (although not identical to) this upper bound. plus a term that grows inversely with the margin.
This new type of cover is polynomial in the number of cliques. 2001]. and depends on the joint 2norm of all of the basis functions for an example (which is ∼ Nc Rc ). However we propose a novel method for covering the space of structured prediction models by using a cover of the individual clique basis function differences ∆fi. Vc = V 2 because of the edge cliques.72 CHAPTER 5. x. and any δ > 0. our bound has a logarithmic dependence on the number of cliques (ln Nc ) and depends only on the 2norm of the basis functions perclique (Rc ). This is a signiﬁcant gain over the previous result of Collins [2001] for 0/1 loss. y)] + 2 K Rc w2 q 2 1 [ln m + ln Nc + ln Vc ] + ln m γ2 δ . y)] at high margin γ quantiﬁes the conﬁdence of the prediction model. The proof uses a covering number argument analogous to previous results in SVMs [Zhang. an open problem for marginbased sequence classiﬁcation [Collins.1 for the proof details and the exact value of the constant K. and m > 1 samples. and V the number of values a variable takes. x. Then Nc = 2L − 1 since we have L node cliques and L − 1 edge cliques. 2002]. for sequences. then our bound is independent . Proof: See Appendix A. The ﬁrst term upper bounds the training error of w. which has linear dependence (inside the square root) on the number of nodes (L). Thus. if the number of instances is at least a constant times the length of a word). yielding signiﬁcant improvements in the bound. which corresponds to the complexity of the classiﬁer (normalized by the margin level).1 For the family of hypotheses parameterized by w. Low loss ES [Lγ (w. L m = O(1) (for example. Such a result was. the result provides a bound to the generalization error that trades off the effective complexity of the hypothesis space with the training error. with probability at least 1 − δ. and q = 3 since nodes in the middle of the sequence participate in 3 cliques: previouscurrent edge clique. until now. x. MARKOV NETWORKS model as an example. y)] ≤ ES [Lγ (w. in OCR. The second term depends on w/γ.c (yc ). node clique. Theorem 5. and currentnext edge clique.5. with L as the maximum length. the expected perlabel loss is bounded by: ED [L(w. Speciﬁcally. there exists a constant K such that for any γ > 0 perlabel margin. note that if of the number of labels L. Finally.
has linear dependence (inside the square root) on the number of nodes (L). He provides generalization guarantees (for 0/1 loss) that hold for separable case and depend on the number of mistakes the perceptron makes before convergence. 1998]. the corresponding problem needs to be resolved (or at least approximately resolved) after each additional constraint is added. [2003] presents LP decompositions based on graphical model structure for the value function approximation problem in factored MDPs (Markov decision processes with structure). In a followup paper. Describing the exact setting is beyond our scope. although undoubtedly the number of mistakes does. Tsochantaridis et al. However. Remarkably. computational biology. His generalization bound (for 0/1 loss) based on the SVMlike margin. the number of constraints in many important cases is several orders higher (in L) than in the the approach we present. The work of Guestrin et al.5. we achieve a much tighter analysis. By considering the more natural Hamming loss. [2004] show that only a polynomial number of constraints are needed to be generated to guarantee a ﬁxed level of precision of the solution. It also depends on the joint 2norm of all of the basis functions for an example (which is ∼ Nc Rc ). In addition.2. 4. [2001] has inspired many applications in natural language. The work of Lafferty et al. computer vision and relational modeling [Sha . Altun et al. but it sufﬁces to say that our original decomposition of the maxmargin QP was inspired by the proposed technique to transform an exponential set of constraints into a polynomial one using a triangulated graph. which is prohibitively expensive for large number of examples and label variables. however. Collins [2004] also suggested an SVMlike formulation (with exponentially many constraints) and a constraint generation method for solving it.6. There has been a recent explosion of work in maximum conditional likelihood estimation of Markov networks.1 to problems natural language processing. [2003] have applied the exponentialsize formulation with constraint generation we described in Sec. RELATED WORK 73 5.6 Related work The application of marginbased estimation methods to parsing and sequence modeling was pioneered by Collins [2001] using the VotedPerceptron algorithm [Freund & Schapire. the bound does not explicitly depend on the length of the sequence.
maximum conditional likelihood estimation for Markov networks can also be kernelized [Altun et al. 2003b]. 2003. We also use approximate graph decomposition to derive a compact approximate formulation for Markov networks in which inference is intractable. 2003. 5. However. Lafferty et al.. compact. 2004. Sutton et al. The seamless integration of kernels with graphical models allows us to create very rich models that leverage the immense amount of research in kernel design and graphical model decompositions. 2003. Pinto et al.7 Conclusion We use graph decomposition to derive an exact. Taskar et al.... convex maxmargin formulation for Markov networks with sequence and other lowtreewidth structure. 2004]. . we present an efﬁcient algorithm that exploits graphical model inference and show experiments on a large handwriting recognition task that utilize the powerful representational capability of kernels. Our generalization bound signiﬁcantly tightens previous results of Collins [Collins. 2001] and suggests possibilities for analyzing perlabel generalization properties of graphical models. MARKOV NETWORKS & Pereira. Our formulation avoids the exponential blowup in the number of constraints in the maxmargin QP that plagued previous approaches. We provide theoretical guarantees on the average perlabel generalization error of our models in terms of the training set margin.. In the next chapter. Taskar et al.74 CHAPTER 5. Kumar & Hebert. 2002. 2004. As in the case of logistic regression.. the solutions are nonsparse and the proposed algorithms are forced to use greedy selection of support vectors or heuristic pruning methods.
y.12) is polynomial in the size of the data. 1999.t. these conditions have certain locality with respect to each example i. ∀i. for standard QP solvers.y s. w ∆fi (y) ≥ (y) − ξi . we use a coordinate dual ascent method analogous to the sequential minimal optimization (SMO) used for SVMs [Platt. y. unfortunately. s.Chapter 6 M3N algorithms and experiments Although the number of variables and constraints in the structured dual in Eq. 6. 1999]. the problem is often too large even for small training sets. Instead. Boyd & Vandenberghe. αi (y)∆fi (y) i.y 1 αi (y) i (y) − C 2 αi (y) = 1. ∀i. y αi (y) ≥ 0. The KKT conditions [Bertsekas. (5. which allows us to perform 75 .1 Solving the M3N QP Let us begin by considering the primal and dual QPs for multiclass SVMs: 2 1 min w2 + C 2 ξi i max i. ∀i. We show that our models signiﬁcantly outperform other approaches by incorporating highdimensional decision boundaries of polynomial kernels over character images while capturing correlations between consecutive characters. We apply our M3 N framework and structured SMO algorithm to a handwriting recognition task. 2004] provide sufﬁcient and necessary criteria for optimality of a dual solution α.t. As we describe below.
76 CHAPTER 6. We can express these conditions as αi (y) = 0 ⇒ w fi (y) + i (y) < max [w fi (y ) + i (y )]. (6. αi (y) can be zero only if vi (y) is at most larger than the all others. are optimal if they satisfy the following two types of constraints: αi (y) = 0 ⇒ w ∆fi (y) > i (y) − ξi . A feasible dual solution α and a primal solution deﬁned by: w = C i. Con versely. This allows us to perform dual blockcoordinate ascent where a block corresponds to . (KKT2). we deﬁne vi (y) = w fi (y) + i (y).y y αi (y)∆fi (y) y (6. αi (y) > 0 ⇒ w ∆fi (y) = i (y) − ξi . we have αi (y) = 0 ⇒ vi (y) < vi (y). Essentially. (KKT1) (KKT2) αi (y) > 0 ⇒ w fi (y) + i (y) = max [w fi (y ) + i (y )].1) ξi = max [ i (y) − w∆fi (y)] = max [ i (y) + w fi (y)] − w fi (y (i) ). With these deﬁnitions. y (KKT1) (KKT2). y =y In practice. we will enforce KKT conditions up to a given tolerance 0 < αi (y) = 0 ⇒ vi (y) ≤ vi (y) + .2) vi (y) = max [w fi (y ) + i (y )]. (KKT1) αi (y) > 0 ⇒ vi (y) ≥ vi (y). y To simplify the notation. αi (y) > 0 ⇒ vi (y) ≥ vi (y) − . M3 N ALGORITHMS AND EXPERIMENTS the search for optimal α by repeatedly considering one example at a time. however. 1. αi (y) can be nonzero only if vi (y) is at most smaller than the all others. Note that the normalization constraints on the dual variables α are local to each example i.
Note that y λ(y) = 0 and αi (y) + λ(y) ≥ 0 so that αi is feasible. Let αi (y) = αi (y) + λ(y). Only the second part of the objective Q(αi . ∀ i. 3. . the objective function can be split into two terms: Q(α) = Q(α−i ) + Q(αi . This allows us to focus on efﬁcient updates to a single block of αi at a time. 6. 7. Find feasible αi such that Q(αi . The algorithm starts with a feasible dual solution α and improves the objective blockwise until all KKT conditions are satisﬁed. the algorithm will converge to the global maximum in a ﬁnite number of steps (within the precision). When optimizing with respect to a single block i. SOLVING THE M3 N QP 77 1. the vector of dual variables αi for a single example i. For each i. Set violation = 1.6. 4. We can write the objective Q(α−i ) + Q(αi . α−i ) in terms of λ and α: αj (y) j (y) + j.y αj (y)∆fj (y) . 6. α−i ) > Q(αi . 5. maintaining the feasibility of the dual. α−i ) matters for optimizing with respect to αi . If αi violates (KKT1) or (KKT2). I(y 2. (6. As long as the local ascent step over αi is guaranteed to improve the objective when KKT conditions are violated. α−i ) and set αi = αi .1).1 is essentially coordinate ascent on blocks αi . If violation = 1 goto 2. y. Figure 6. α−i ). where α−i denotes all dual αk variables for k other than i. The general form of blockcoordinate ascent algorithm as shown in Fig.1.y y 1 λ(y) i (y) − C 2 2 λ(y)∆fi (y) + y j.1: Blockcoordinate dual ascent. Checking the constraints requires computing w and ξ from α according to Eq. Set violation = 0. Initialize: αi (y) = 1 = y (i) ).
t. We address a strategy for selecting the two variables in the next section. y αi (y) + λ(y) ≥ 0.y αj (y)∆fj (y).t. not a full optimization. we have the simplex constraint. we get: 1 − C 2 2 λ(y) i (y) − w y y λ(y)∆fi (y) λ(y)∆fi (y) y . (6. Then we have δ = λ(y ) = −λ(y ) in order to sum to 1. Since y λ(y) = 0. Sequential Minimal Optimization (SMO) approach takes an ascent step that modiﬁes the least number of variables. but for now assume we have picked λ(y ) and λ(y ).78 CHAPTER 6. All that is required is an ascent step. The optimization problem becomes a single variable quadratic program in δ: max s. λ(y)∆fi (y) = y y λ(y)fi (y (i) ) − y λ(y)fi (y) = − y i (y) λ(y)fi (y). 1 [vi (y ) − vi (y )]δ − Cfi (y ) − fi (y )2 δ 2 2 αi (y ) + δ ≥ 0.1 SMO We do not need to solve the optimization subproblem above at each pass through the data. αi (y ) − δ ≥ 0. and making the substitution w=C j. In our case. M3 N ALGORITHMS AND EXPERIMENTS By dropping all terms that do not involve λ. so we must change at least two variables in order to respect the normalization constraint (by moving weight from one dual variable to another).3) . Below we also make the substitution vi (y) = w fi (y) + problem for λ: max y to get the optimization 1 λ(y)vi (y) − C 2 λ(y) = 0. 6.1. ∀y. 2 λ(y)fi (y) y s.
6.1. SOLVING THE M3 N QP
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Figure 6.2: Representative examples of the SMO subproblem. Horizonal axis represents δ with two vertical lines depicting the upper and lower bounds c and d. Vertical axis represents the objective. Optimum either occurs at the maximum of the parabola if it is feasible or the upper or lower bound otherwise.
With a = vi (y ) − vi (y ), b = Cfi (y ) − fi (y )2 , c = −αi (y ), d = αi (y ), we have: b max [aδ − δ 2 ] s.t. c ≤ δ ≤ d, 2 (6.4)
where the optimum is achieved at the maximum of the parabola a/b if c ≤ a/b ≤ d or at the boundary c or d (see Fig. 6.1.1). Hence the solution is given by simply clipping a/b: δ ∗ = max(c, min(d, a/b)). The key advantage of SMO is the simplicity of this update. Computing the coefﬁcients involves dot products (or kernel evaluations) to compute w fi (y ) and w fi (y ) as well as (fi (y ) − fi (y )) (fi (y ) − fi (y )).
6.1.2 Selecting SMO pairs
How do we actually select such a pair to guarantee that we make progress in optimizing the objective? Note that at least one of the assignments y must violate (KKT1) or (KKT2),
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CHAPTER 6. M3 N ALGORITHMS AND EXPERIMENTS
1. Set violation = 0. 2. For each y, 3. 4. 5. 6. 8. 9. 10. 11. 12. KKT1: If αi (y) = 0 and vi (y) > vi (y) + , Set y = y and violation = 1 and goto 7. KKT2: If αi (y) > 0 and vi (y) < vi (y) − , Set y = y and violation = 2 and goto 7. For each y = y , If violation = 1 and αi (y) > 0, Set y = y and goto 13. If violation = 2 and vi (y) > vi (y ), Set y = y and goto 13.
7. If violation > 0,
13. Return y and y . Figure 6.3: SMO pair selection. because otherwise αi is optimal with respect to the current α−i . The selection algorithm is outlined in Fig. 6.3. The ﬁrst variable in the pair, y , corresponds to a violated condition, while the second variable, y , is chosen to guarantee that solving Eq. (6.3) will result in improving the objective. There are two cases, corresponding to violation of KKT1 and violation of KKT2. Case KKT1. αi (y ) = 0 but vi (y ) > vi (y ) + . This is the case where i, y is a not support vector but should be. We would like to increase αi (y ), so we need αi (y ) > 0 to borrow from. There will always be a such a y since
y
αi (y) = 1 and αi (y ) = 0.
Since vi (y ) > vi (y ) + , vi (y ) > vi (y ) + , so the linear coefﬁcient in Eq. (6.4) is a = vi (y ) − vi (y ) > . Hence the unconstrained maximum is positive a/b > 0. Since the upperbound d = αi (y ) > 0, we have enough freedom to improve the objective. Case KKT2. αi (y ) > 0 but vi (y ) < vi (y ) − . This is the case where i, y is a support vector but should not be. We would like to decrease αi (y ), so we need vi (y ) > vi (y ) so that a/b < 0. There will always be a such a y since vi (y ) < vi (y ) − . Since the
6.1. SOLVING THE M3 N QP
81
lowerbound c = −αi (y ) < 0, again we have enough freedom to improve the objective. Since at each iteration we are guaranteed to improve the objective if the KKT conditions are violated and the objective is bounded, we can use the SMO in the blockcoordinate ascent algorithm to converge in a ﬁnite number of steps. To the best of our knowledge, there are no upper bounds on the speed of convergence of SMO, but experimental evidence has shown it a very effective algorithm for SVMs [Platt, 1999]. Of course, we can improve the speed of convergence by adding heuristics in the selection of the pair, as long as we guarantee that improvement is possible when KKT conditions are violated.
6.1.3 Structured SMO
Clearly, we cannot perform the above SMO updates in the space of α directly for the structured problems, since the number of α variables is exponential. The constraints on µ variables are much more complicated, since each µ participates not only in nonnegativity and normalization constraints, but also cliqueagreement constraints. We cannot limit our ascent steps to changing only two µ variables at a time, because in order to make a change in one clique and stay feasible, we need to modify variables in overlapping cliques. Fortunately, we can perform SMO updates on α variables implicitly in terms of the marginal dual variables µ. The diagram in Fig. 6.1.3 shows the abstract outline of the algorithm. The key steps in the SMO algorithm are checking for violations of the KKT conditions, selecting the pair y and y , computing the corresponding coefﬁcients a, b, c, d and updating the dual. We will show how to do these operations by doing all the hard work in terms of the polynomially many marginal µi variables and auxiliary “maxmarginals” variables.
Structured KKT conditions As before, we deﬁne vi (y) = w fi (y) + i (y). The KKT conditions are, for all y: αi (y) = 0 ⇒ vi (y) ≤ vi (y); αi (y) > 0 ⇒ vi (y) ≥ vi (y). (6.5)
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CHAPTER 6. M3 N ALGORITHMS AND EXPERIMENTS
select & lift
SMO update
project
Figure 6.4: Structured SMO diagram. We use marginals µ to select an appropriate pair of instantiations y and y and reconstruct their α values. We then perform the simple SMO update and project the result back onto the marginals.
Of course, we cannot check these explicitly. Instead, we deﬁne maxmarginals for each clique in the junction tree c ∈ T (i) and its values yc , as: vi,c (yc ) = max [w fi (y) + i (y)],
y∼yc
αi,c (yc ) = max αi (y).
y∼yc
We also deﬁne vi,c (yc ) = maxyc =yc vi,c (yc ) = maxy∼yc [w fi (y) + i (y)]. Note that we do not explicitly represent αi (y), but we can reconstruct the maximumentropy one from the marginals µi by using Eq. (5.13). Both vi,c (yc ) and αi,c (yc ) can be computed by using the Viterbi algorithm (one pass propagation towards the root and one outwards from the root [Cowell et al., 1999]). We can now express the KKT conditions in terms of the maxmarginals for each clique c ∈ T (i) and its values yc : αi,c (yc ) = 0 ⇒ vi,c (yc ) ≤ vi,c (yc ); αi,c (yc ) > 0 ⇒ vi,c (yc ) ≥ vi,c (yc ). (6.6)
Theorem 6.1.1 The KKT conditions in Eq. (6.5) and Eq. (6.6) are equivalent. Proof: Eq. (6.5) ⇒ Eq. (6.6). Assume Eq. (6.5). Suppose, we have a violation of KKT1: for some c, yc , αi,c (yc ) = 0, but vi,c (yc ) > vi,c (yc ). Since αi,c (yc ) = maxy∼yc αi (y) = 0,
hence vi. we know that all the yconsistent αi maxmarginals are positive αi. The value of an assignment vi (y) can be decomposed into two parts: vi (y) = vi. Assume Eq.s (ys ) . by Eq.6). (6. we consider any two adjacent nodes in the tree T (i) . Then vi (y) < vi (y). αi. Eq.c (yc ) = vi (y) > vi (y) > vi. we get vi (y) = vi.6).a∪b (ya∪b ) = vi.6). where vi. Note that trivially maxy vi (y ) = max(vi.c (yc ).B (yB ). y(a) ∼ ya with vi (y(a) ) = vi. Hence all the yconsistent αi maxmarginals are positive αi. a contradiction. a contradiction. But vi.c (yc ). (6. αi (y) = 0. vi (y) ≥ vi (y). with a separator s. For that y. SOLVING THE M3 N QP 83 then αi (y) = 0.6) ⇒ Eq.5). By Eq.5). To show that this. ∀y ∼ yc .c (yc ) ≥ vi.c (yc ) > 0.b (yb ) ≥ vi.b (yb ). ∀y ∼ yc .c (yc ) > vi. then maxy vi (y ) = vi. We denote the two subsets of an assignment y as yA and yB (with overlap at ys ). (6. by Eq. By chaining this equality from the root of the tree to all the leaves. (6. ∀c ∈ T (i) . yc . ∀c ∈ T (i) . ∀c ∈ T (i) .c (yc ) = 0. a contradiction. That is. Hence. Since αi (y) > 0. vi. ∀c ∈ T (i) .c (yc ).6.c (yc )) for any clique c and clique assignment yc .c (yc ) > 0 implies there exists y ∼ yc such that αi (y) > 0.1. a contradiction. vi. (6. ∀c ∈ T (i) .c (yc ) ≥ vi.c (yc ) is the optimal value. then we cannot have αi.5). But αi. Now suppose we have a violation of KKT2: for some i.A (yA ) and vi. if vi. but vi.c (yc ) implies the opposite: there exists y ∼ yc such that vi (y) > vi. B} be a partition of the nodes T (i) (cliques of C (i) ) resulting from removing the edge between a and b such that a ∈ A and b ∈ B. yc ∼ y. ∀y ∼ yc . But by Eq.c (yc ).c (yc ).c (yc ) > vi. Take any maximizer. then αi (y) > 0.c (yc ) > 0. We will show that vi (y) = vi.c (yc ). αi (y) > 0. and it follows that all the yconsistent marginals µi are positive as well µi. but vi (y) > vi (y). ∀c ∈ T (i) .b (yb ). Suppose we have a violation of KKT1: for some y.A (yA ) + vi. .c (yc ).B (yB ) only count the contributions of their constituent cliques. which also implies vi (y) > vi (y). so if all the yconsistent marginals are positive. ∀c ∈ T (i) (since sum upperbounds max). But αi (y) = c∈T (i) c∈S (i) µi.a (ya ) ≥ vi.c (yc ) < vi.c (yc ) > 0. (6.c (yc ). This means that y is the optimum of vi (·). Let {A. (6.c (yc ) µi. vi.a (ya ) and any maximizer y(b) ∼ yb with vi (y(b) ) = vi. vi (y) ≤ vi (y). cliques a and b. We need to introduce some more notation to deal with the two parts of the tree induced by cutting the edge between a and b.c (yc ) for any c.a (ya ) = vi.c (yc ). but vi (y) < vi (y). and show that vi. Since vi. Now suppose we have a violation of KKT2: for some y.c (yc ) > 0. which by deﬁnition agree with y .
c (yc ) < vi.c (yc ) = 0 but vi.s (ys ) since they are optimal as we said above. (6. This is the case where i. to guarantee that solving Eq. we enforce approximate KKT conditions in the algorithm in Fig.b (yb ) ≥ vi. We can ﬁnd one by choosing yc for which αi.c (yc ) > 0. the coefﬁcients for the onevariable QP in Eq.3) will result in improving the objective. y . corresponding to a violated condition. (a) (b) (a) (b) (b) (a) (a) (b) (b) (a) (a) (a) (b) (b) (a) (b) (a) (b) (a) (a) (b) (b) Structured SMO pair selection and update As in multiclass problems. Having selected y and y . We have two cases. (6. We have set y = arg maxy∼yc αi (y). We decompose the two associated values into the corresponding parts: vi (y(a) ) = vi (yA )+vi (yB ) and vi (y(b) ) = vi (yA )+vi (yB ). As before. Hence we have vi (yA ) + vi (yB ) = vi (yA ) + vi (yB ) ≥ vi (yA ) + vi (yB ) which implies that vi (yA ) ≥ vi (yA ) and vi (yB ) ≥ vi (yB ). so we need vi (y ) > vi (y ) so that a/b < 0.s (ys ). Now we create another assignment that clamps the value of both a and b: y(a∪b) = yA ∪ yB .c (yc ) > vi. Case KKT1. we have enough freedom to improve the objective.c (yc ) + > vi (y ) + and αi (y ) = 0. b = Cfi (y )−fi (y )2 . Case KKT2.4) are a = vi (y )−vi (y ).c (yc ) > 0 but vi. we will select the ﬁrst variable in the pair. αi. so vi (y ) = vi. vi (y ) ≥ vi (y ) + . This is the case where i. We have set y = arg maxy∼yc vi (y). y is a not support vector but should be. d = αi (y ). We would like to increase αi (y ). 6.c (yc )− . The value of this assignment is optimal vi (y(a∪b) ) = vi (yA ) + vi (yB ) = vi (y(a) ) = vi (y(b) ). corresponding to violation of KKT1 and violation of KKT2. αi (y ) > 0. M3 N ALGORITHMS AND EXPERIMENTS on the intersection s. Now vi. We create a new assignment that combines the best of the two: y(s) = yA ∪ yB . so αi (y ) = αi.4) is a = vi (y ) − vi (y ) > . There will always be a such a y (with yc = yc ) since y αi (y) = 1 and αi (y ) = 0. so the linear coefﬁcient in Eq. while the second variable.c (yc ) − < vi (y ) − . There will always be a such a y since . Note that vi (y(s) ) = vi (yA ) + vi (yB ) = vi. Since vi (y ) ≥ vi (y ) + . which guarantees that for yc = arg maxy∼yc αi (y).c (yc ) < vi.c (yc ) > 0 and vi (y ) < vi.c (yc ) > vi.84 CHAPTER 6. We would like to decrease αi (y ). since we essentially ﬁxed the intersection s and maximized over the rest of the variables in A and B separately. Since the upperbound d = αi (y ) > 0. (6. c = −αi (y ). y is a support vector but should not be. αi. so we need αi (y ) > 0 to borrow from. Hence the unconstrained maximum is positive a/b > 0.c (yc )+ .5. y .a (ya ) = vi.
vi (y ) > vi (y ) − . with average length of ∼ 8 characters. y = arg maxy∼yc αi (y) and violation = 2 and goto 7. Set yc = yc . 13.c (yc ) > vi. yc 3.6. from 150 human subjects. Figure 6. KKT2: If αi. Set yc = arg maxy∼yc αi (y) and goto 13. The only marginal affected are the ones consistent with y and/or y .c (yc ) = 0. and the change is very simple: µi. If violation > 0. 2.c (yc ) − . vi (y ) < vi (y ) − . Return y and y . again we have enough freedom to improve the objective. Having computed new values αi (y ) = αi (y ) + δ and αi (y ) = αi (y ) − δ. we need to project this change onto the marginal dual variables µi . For each c ∈ T (i) . 10.2. 6. y = arg maxy∼yc vi (y) and violation = 1 and goto 7. 5.c (yc ) + δ1 c ∼ y ) − δ1 c ∼ y ).c (yc ) > 0. 11. 8. 9.c (yc ) − . Set y = arg maxy∼yc vi (y) and goto 13.c (yc ) + .c (yc ) = µi.5: Structured SMO pair selection. Since the lowerbound c = −αi (y ) < 0. 7. which guarantees that for yc = arg maxy∼yc vi (y). KKT1: If αi. 4. We can ﬁnd one by choosing yc for which vi. each character was rasterized into an image of 16 by 8 binary . 12.c (yc ) < vi. EXPERIMENTS 85 1. If violation = 2 and vi. and vi.c (yc ) > vi.c (yc ) > 0. from the data set collected by Kassel [1995]. I(y I(y 6. Set violation = 0. Each word was divided into characters. and vi. Set yc = yc . If violation = 1 and αi.c (yc ) > vi.2 Experiments We selected a subset of ∼ 6100 handwritten words.c (yc ). For each yc = yc .
and a labeling for a complete word to Y.35 linear Test error (average percharacter) 0. which do not consider the correlation between neighboring characters — logistic regression. We implemented a selection of stateoftheart classiﬁcation algorithms: independent label approaches.86 CHAPTER 6. summarized in Fig.1 0. 6.05 0 LogReg CRF quadratic cubic m SVM M^3N (a) (b) Figure 6. quadratic. CRFs.6(b). and oneagainstall SVMs (whose performance was slightly lower than multiclass SVMs). using a zeromean diagonal Gaussian prior over the parameters. using linear.9). The data set is divided into 10 folds of ∼ 600 training and ∼ 5500 testing examples.) In our framework. The other methods are trained by margin maximization.15 0. For the sequence approaches (CRFs and M3 ). and our proposed M3 networks. z}. Logistic regression and CRFs are both trained by maximizing the conditional likelihood of the labels given the features. and cubic kernels. . (b) OCR: Average percharacter test error for logistic regression. (2. . are averages over the 10 folds. The accuracy results. . pixels. a label of an individual character to Yj . we used an indicator basis function to represent the correlation between Yj and Yi+1 .3 0.6: (a) 3 example words from the OCR data set. Our features for each label Yj are the corresponding image of ith character. and sequence approaches — CRFs. (See Fig. 6. M3 N ALGORITHMS AND EXPERIMENTS 0. multiclass SVMs. multiclass SVMs as described in Eq. the image for each word corresponds to x. Each label Yj takes values from one of 26 classes {a.25 0.1 and 1.2 0. with a standard deviation between 0. and M3 Ns. .6(a). .
Second. by using kernels. by using sequences.3 Related work The kerneladatron [Friess et al. although using a different setup (e.6. 1998] for largemargin classiﬁers have a similar online optimization scheme. we obtain another signiﬁcant gain in accuracy. 6. the error rate of our method using linear features is 16% lower than that of CRFs. we address the large (though polynomial) size of our quadratic program using an effective optimization procedure inspired by SMO.4 Conclusion In this chapter. it seems that. empirically.. Once we use cubic kernels our error rate is 45% lower than CRFs and about 33% lower than the best previous approach. 6. Although the EG algorithm has attractive convergence properties.3.g. 2004]. Although headtohead comparisons have not been performed. and about the same as multiclass SVMs with cubic kernels. Interestingly. marginbased methods achieve a very signiﬁcant gain over the respective likelihood maximizing methods.. the previously published results. RELATED WORK 87 For marginbased methods (SVMs and M3 ). Using these highdimensional feature spaces in CRFs is not feasible because of the enormous number of parameters. we were able to use kernels (both quadratic and cubic were evaluated) to increase the dimensionality of the feature space. Collins [2001] have applied votedperceptron to structured problems in natural language. particularly in the early iterations through the dataset. are about comparable to those of multiclass SVMs. the Exponentiated Gradient [Kivinen & Warmuth. Recently. Fig. We used the structured SMO algorithm with about 3040 iterations through the data. For comparison.6(b) shows two types of gains in accuracy: First. 1998] and votedperceptron algorithms [Freund & Schapire. it has yet to be shown to learn faster than Structured SMO. less passes (about 3040) are needed for our algorithm than in the perceptron literature. a larger training set). 6.. our sequence model signiﬁcantly outperforms other approaches by incorporating . In our experiments with the OCR task. 1997] algorithm has been adopted to solve our structured QP for maxmargin estimation [Bartlett et al.
Overall. we apply this framework to important classes of Markov networks for spatial and relational data. In the next two chapters. M3 N ALGORITHMS AND EXPERIMENTS highdimensional decision boundaries of polynomial kernels over character images while capturing correlations between consecutive characters.88 CHAPTER 6. . we believe that M3 networks will signiﬁcantly further the applicability of high accuracy marginbased methods to realworld structured data.
AMNs are a natural ﬁt object recognition and segmentation. This subclass. we show that optimal learning is feasible for an important subclass of Markov networks — networks with attractive potentials. in which connected (“associated”) variables tend to have the same label. which is NPhard in general networks suitable in a broad range of practical Markov network structures. the network structure can mirror the hyperlink graph.Chapter 7 Associative Markov networks In the previous chapter.g. the network structure is learned. In many cases. which is usually highly interconnected. [Bach & Jordan. In some cases.. in hypertext. the topology of the Markov network does not allow tractable inference. leading to computationally intractable networks. webpage 89 . Such positive interactions capture the “guilt by association” pattern of reasoning present in many domains. called associative Markov networks (AMNs). For example. contains networks of discrete variables with K labels and arbitrarysize clique potentials with K parameters that favor the same labels for all variables in the clique. 2001]). In other cases (e. In this chapter. including gridtopology networks [Besag. subject to the constraint that inference on these networks is tractable. 1986]. however. which allow very efﬁcient inference and learning. One can address the tractability issue by limiting the structure of the underlying network. The chief computational bottleneck in applying Markov networks for other largescale prediction problems is inference. 1994]. such as the quadtree model used for image segmentation [Bouman & Shapiro. we considered applications of sequencestructured Markov networks. a tractable structure is determined in advance.
90 CHAPTER 7. the inference subtask is one of ﬁnding the best joint (MAP) assignment to all of the variables in a Markov network. maximizing the conditional likelihood of the target labels given the features) require that we compute the posterior probabilities of different label assignments. our method is the ﬁrst to allow training Markov networks of arbitrary connectivity and topology. For binaryvalued Potts models. k) = 1. Thus.g. By constraining the class of Markov networks to AMNs. this linear program provides exact answers. 7. ∀k = l and φij (k. the approximate linear program is not guaranteed to be optimal but we can bound its relative error. We present an AMNbased method for object segmentation of complex from 3D range data. In this setting.. our models can be learned efﬁciently and at runtime. The MAP problem can naturally be expressed as an integer programming problem. and many other applications. where nearby pixels are likely to have the same label [Besag. Greig et al. For L > 2. [1989] show that the MAP problem can be formulated as a mincut in an appropriately constructed graph. Our empirical results suggest that the solutions of the resulting approximate maxmargin formulation work well in practice. 1999b]. a common approach is to use a generalized Potts model [Potts. which penalizes assignments that do not have the same label across the edge: φij (k.. rather than just the MAP. 1986. the MAP problem . For the nonbinary case (K > 2). To our knowledge. for associative Markov networks of over binary variables (K = 2).1 Associative networks Associative interactions arise naturally in the context of image processing. while balancing the spatial coherence modeled by the AMN. where λij ≤ 1. ASSOCIATIVE MARKOV NETWORKS classiﬁcation. l) = λij . Boykov et al. other learning tasks (e. In the maxmargin estimation framework. the MAP problem can be solved exactly for this class of models in polynomial time. The proposed learning formulation effectively and directly learns to exploit a large set of complex surface and volumetric features. 1952]. By contrast. We show that. scale up to tens of millions of nodes and edges. We use a linear program relaxation of this integer program in the minmax formulation.
this probability may increase if they both interact with another protein. A set of potentials φ(y) is associative if φ(y) = eg(y) and g(y) is associative. For example. foreground pixels tend to have locally coherent values while background is much more varied. ∀c ∈ C\V. where V are the nodes and C are the cliques of the graph G. where λij (k) ≥ 1. ∀k = l. 1999].. In particular. with potentials over cliques involving m variables φ(µi1 . and µc (k) for each clique c .1 A function g : Y → IR is associative for a graph G over Kary variables if it can be written as: K K g(y) = v∈V k=1 gv (k)1 v = k) + I(y c∈C\V k=1 gc (k)1 c = k. . where we have a “marginal” variable µv (k) for each node v ∈ V and each label k. we deﬁne associative functions and potentials as follows.7. AMNs allow different labels to have different attraction strength: φij (k.2 LP Inference We can write an integer linear program for the problem of ﬁnding the maximum of an associative function g(y). but a procedure based on a relaxed linear program guarantees a factor 2 approximation of the optimal solution [Boykov et al. . In a second important extension. For example. I(y gc (k) ≥ 0. k) = λc (k) ≥ 1 and the rest of the entries are set to 1. LP INFERENCE 91 is NPhard. This type of transitivity could be modeled by a ternary clique that has high λ for the assignment with all interactions present. AMNs admit nonpairwise interactions between variables. More formally. consider the problem of predicting whether two proteins interact [Vazquez et al. Deﬁnition 7. µim ). AMNs allow us to encode the pattern of (soft) transitivity present in many domains. k). l) = 1. . 7. . which indicates whether node v has value k.2. . k) = λij (k). as different labels can have very diverse afﬁnities. Kleinberg & Tardos. . . . 2003]. Our associative potentials extend the Potts model in several ways. . 1999b. . . . In this case.1. using this additional expressive power. the clique potentials are constrained to have the same type of structure as the edge potentials: There are K parameters φc (k. and φij (k. This additional ﬂexibility is important in many domains. Importantly..
1 for the proof. for any associative function g. Hence at the optimum. This works because the coefﬁcient gc (k) is nonnegative and we are maximizing the objective function. (7. ∀c ∈ C.1) has a solution that is larger than the solution of the integer program by at most the number of variables in the largest clique. ASSOCIATIVE MARKOV NETWORKS (containing more than one variable) and label k. µc (k) ∈ {0. (7. Theorem 7. (7.2 If K > 2.2. µc (k) ≤ µv (k). k.1 If K = 2. these LPs can produce fractional solutions and we use a rounding procedure to get an integral solution.. 1} are replaced by µc (k) ≥ 0). In the nonbinary case (L > 2).1) has an integral optimal solution. regardless of network topology or clique size. ∀c ∈ C \ V. In the appendix. is guaranteed to produce an integer solution when a unique solution exists. we also show that the approximation ratio of the rounding procedure is the inverse of the size of the largest clique (e. the linear relaxation of Eq.1). v ∈ c.2. Theorem 7. Although artiﬁcial examples with fractional solutions can be easily constructed by using symmetry. for any associative function g.92 CHAPTER 7. See Appendix A.1) s. it seems that in real data such symmetries are often broken. µc (k) = minv µv (k) . This result states that the MAP problem in binary AMNs is tractable. v∈c Note that we substitute the constraint µc (k) = µv (k) by linear inequality con straints µc (k) ≤ µv (k). . which represents the event that all nodes in the clique c have label k: K K max v∈V k=1 µv (k)gv (k) + c∈C\V k=1 µc (k)gc (k) K (7. ∀v ∈ V. In fact. (where the constraints µc (k) ∈ {0. when µv (k) are binary. the linear relaxation of Eq. which is equivalent to µc (k) = v∈c µv (k). 1 2 for pairwise networks). 1}. k=1 µv (k) = 1.t. It can be shown that in the binary case. we never encountered fractional solutions. in all our experiments with L > 2 on real data. k. the linear relaxation of Eq.2.g.
along with the 1 and 2 terminals. and later show how to use the local search algorithm developed by Boykov et al. In the ﬁnal (V1 .1) is: max v∈V [µv (1)gv (1) + µv (2)gv (2)] + uv∈E [µuv (1)guv (1) + µuv (2)guv (2)]. MINCUT INFERENCE 93 7. depending on the sign of ∆v . min − v∈V [µv (1)gv (1) + µv (2)gv (2)] − uv∈E [µuv (1)guv (1) + µuv (2)guv (2)].3 Mincut inference We can also use efﬁcient mincut algorithms to perform exact inference on the learned models for K = 2 and approximate inference for K > 2. we focus on the pairwise AMN case. Such a term corresponds to the node potential contribution to our objective function for node v.7.2) 7.1 Graph construction We construct a graph in which the mincut will correspond to the optimal MAP labeling for the above objective. We will show how to deal with the node terms (those depending only on a single variable) and the edge terms (those depending on a pair of variables).3. (7. the objective of the integer program in Eq. (7. The reason for that is that the ﬁnal mincut graph must consist of only positive weights.3) The graph will consist of a vertex for each node in the AMN. (7.3. We then look at ∆v = gv (1) − gv (2). For simplicity. [1999a] to perform (approximate) inference in the general multiclass case. Node terms Consider a node term −µv (1)gv (1) − µv (2)gv (2). we recast the objective as minimization by simply reversing the signs on the value of each θ. and then how to combine the two. binary AMNs. An . For each node term corresponding to node v we add a vertex v to the mincut graph. and create an edge of weight ∆v  from v to either 1 or 2. First. the V1 set will correspond to label 1. V2 ) cut. We ﬁrst consider the case of binary AMNs. and the V2 set will correspond to label 2. For pairwise.
Observe what happens when both nodes are on the V2 side of the cut: the value of the mincut is guv (1). since for each introduced vertex we have only one edge of positive weight to either 1 or 2. ASSOCIATIVE MARKOV NETWORKS 1 v 2 1 u v 1 v 2 2 Figure 7. which must be less than guv (2) or the mincut would have placed them both on the 1 side. From Fig.1. 7. example is presented in Fig.1: Mincut graph construction of node (left) and edge (right) terms. When looking at edge terms in isolation. we see that if the AMN consisted of only node potentials. such cuts will be possible.3.1. 7. To construct a mincut graph for the edge term we will introduce two vertices u and v. We can take the individual graphs we created for node and edge terms and merge them .94 CHAPTER 7. the graph construction above would add an edge from each node to its more likely label. a cut that places each node in different sets will not occur. but when we combine the graphs for node terms and edge terms.3. Thus if we run mincut. we would simply get a cut with cost 0. Edge Terms Now consider an edge term of the form −µuv (1)guv (1) − µuv (2)guv (2).1 shows an example. Fig. connect v to 2 with an edge of weight guv (2) and connect u to v with an edge of weight guv (1) + guv (2). We will connect vertex u to 1 with an edge of weight guv (1).3. 7. and we would always choose not to cut any edges.
Another labeling µ is called an “αexpansion” move (following Boykov et al. and it can be shown that it converges to within a factor of 2 of the global minimum. . or switch to the label α. Expansion Algorithm Consider a current labeling µ and a particular label k ∈ 1. . . but in practice we would often like to handle multiple classes in AMNs. In this new binary problem we will let label 1 represent a node keeping its current label and label 2 will denote a node taking on the new label k.2 Multiclass case The graph construction above ﬁnds the best MAP labeling for the binary case. 7. 7. It can be shown that the resulting graph will represent the same objective (in the sense that running mincut on it will optimize the same objective) as the sum of the objectives of each graph. K. Since our MAPinference objective is simply a sum of node and edge terms. or change to k. It terminates when there is no αexpansion move for any label k that has a lower objective than the current labeling (Fig. The algorithm performs a series of “expansion” moves each of which involves optimization over two labels. merging the node and edge term graphs will result in a graph in which mincut will correspond to the MAP labeling.3.3. MINCUT INFERENCE 95 by adding edge weights together (and treating missing edges as edges with weight 0).) In other words. The key part of the algorithm is computing the best αexpansion labeling for a ﬁxed k and a ﬁxed current labeling µ. . One of the most effective algorithms for minimizing energy functions like ours is the αexpansion algorithm proposed by Boykov et al.2). The αexpansion algorithm cycles through all labels k in either a ﬁxed or random order. and ﬁnds the new labeling whose objective has the lowest value. In order to construct the right coefﬁcients . a kexpansion from a current labeling allows each label to either stay the same.7. [1999a]) from µ if µv = k implies µv = µv (where µv is the label of the node v in the AMN. [1999a]. The mincut construction from earlier allows us to do exactly that since an αexpansion move essentially minimizes a MAPobjective over two labels: it either allows a node to retain its current label.
Note that we ignore nodes with label α altogether since an αexpansion move cannot change their label. . ˆ 3. . Begin with arbitrary labeling µ 2. . we can apply the mincut construction from before to get the optimal labeling within one αexpansion from the current one.α nodes has label α in the current labeling.α 1 we add a new edge potential.k for the new binary objective we need to consider several factors. As noted in Boykov et al. 5.y node whose label is different from α. For each label k ∈ {1. [1999a] and as we have observed in our experiments. If success = 1 goto 2. ASSOCIATIVE MARKOV NETWORKS 1.96 CHAPTER 7. For each edge (i. y α we let θi0 = θi i . If the two nodes of the edge 0 currently have the same label. Below. ◦ Edge Potentials For each edge (i. where yi denotes the current label of node i. j) ∈ E in which exactly one of the α. and if the two nodes currently have 0 different labels we let θij = 0. we add θij . After we have constructed the new binary MAP objective as above. to the node potential θi1 of the y . Set success := 0 3. Veksler [1999] shows that the αexpansion algorithm converges in O(N ) iterations where N is the number of nodes. with weights θij = θij . . we set θij = θiji j . and θyi denotes the coefﬁcient in the multiclass AMN MAP objective. K} 3.2: αexpansion algorithm k.1 Compute µ = arg min −g(µ ) among µ within one αexpansion of µ. α.2 If E(ˆ) < E(µ). and θi1 = θi . let θik and θij denote the node and edge coefﬁcients associated with the new binary objective: ◦ Node Potentials For each node i in the current labeling whose current label is not α. set µ := µ and success := 1 µ ˆ 4. Return µ Figure 7. j) ∈ E whose nodes have labels different from α. the algorithm terminates only after a few iterations with most of the improvement occurring in the ﬁrst 23 expansion moves.
4 Maxmargin estimation The potentials of the AMN are once again loglinear combinations of basis functions. Assumption 7. this restriction is fairly mild. y) is associative for G (i) for all i. and the Hamming loss. MAXMARGIN ESTIMATION 97 7. We will need the following assumption to ensure that w f (x. c > 1. y) is associative for G(x) for any (x.1 ¨ holds and w ≥ 0. We must make similar associative assumption on the loss function in order to guarantee that the LP inference can handle it.1 Basis functions f are componentwise associative for G(x) for any (x. y) is associative: Assumption 7. y) is associative. y ∈ Y.4. y(i) .3 w f (x. which we use in generalization bounds and experiments.4. ˙ Deﬁnition 7. It is easy to verify that any nonnegative combination of associative functions is associative.7.4. c ∈ C(G(x)). is associative. and any combination of basis functions with support only on singleton cliques is also associative. w} = w be the corresponding f subsets of parameters.2 Let f be the subset of basis functions f with support only on singleton cliques: ˙ f = {f ∈ f : ∀ x ∈ X . Let {w. fc (xc .4. y). Recall that this implies that for cliques larger than one.4. In practice. ˙ ˙ ¨ Let ¨ = f \ f be the rest of the basis functions.4. y) whenever Assumption 7. To ensure that w f (x. so we have: Lemma 7. . yc ) = 0}.4 The loss function (x(i) . it is useful to separate the basis functions with support only on nodes from those with support on larger cliques. all basis functions evaluate to 0 for assignments where the values of the nodes are not equal and are nonnegative for the assignments where the values of the nodes are equal.
k. similar to Eq. ∀i.c (k) i.c∈C (i) . there are marginals µ for each node and clique. ¨ w ∆¨i. k.4).c. ¨ ∀i. (7.v (k) ≥ −w ¨i.v (k). (7. . k. However. ∀c ∈ C (i) k=1 (i) µi. c ∈ C (i) \ V (i) .c (k) = i.t.4 and some algebra (see Appendix A. 1 w2 + C 2 ξi. ∀c ∈ C . . (5.v (k). k C µi.4) i. (5. ν ≥ 0.12).c (k. The dual of Eq.c (k) = fi.c∈C (i) . µi.c (k.c.c (k)∆¨i. ASSOCIATIVE MARKOV NETWORKS Using the above Assumptions 7. ¨ w ≥ 0. ∀i. k (i) C ˙ µi. .c.c (k). the constraints are different. ∀i.4.c.4) (see derivation in Sec.v (k) ≥ v∈c − ξi. w ∆fi. \ V .3) is given by: 2 2 max i. k s.v (k) − c⊃v mi.c (k) f i.v (k) ≥ mi. c ∈ C (i) \ V (i) . k. k).4. where fi.3 for derivation). ∀i. .v∈V (i) (7. . we have the following maxmargin QP for AMNs: min s.2. for each value k. The extra constraints are due to the associativity constraints on the resulting model.v .v i.1). k) and i. .c (k) − 2 i. . µi. and not surprisingly.c (k) ≥ 0.v (k) − 2 K ν+ ¨ µi. are essentially the constraints from the inference LP relaxation in Eq. A. the basic structure of the ﬁrst two sets of constraints remains the same: we have local margin requirements and “credit” passed around through messages mi.c (k) + f ∀i. v ∈ c. . ∀v ∈ V (i) . (i) ¨ f mi.t.v (k)∆fi. v ∈ c.2.v (k) = 1.98 CHAPTER 7. While this primal is more complex than the regular M3 N factored primal in Eq.1 and 7. v ∈ V (i) . In the dual.v (k) i.c (k) ≤ µi.c (yc )/c. .v∈V (i) . k.
building. so that Eq. k is negative.c (k)∆¨i. which was fairly noisy because of localization errors.v (k). z) coordinates in an absolute frame of reference. Our task is to classify the laser range points into four classes: ground.v (k) ∆fj. represented as 3D coordinates in an absolute frame of reference Fig. these weights tend to do well in practice. ξ for the original QP may no longer be feasible. maximizing the objective will force the corresponding component of ν to cancel ¨ it out).4) learns exact maxmargin weights for Markov networks of arbitrary topology. Thus. tree. so they can be kernelized. (7. k ˙ µi. f µi. leading to a different choice of weights. the only available information is the location of points. the linear relaxation leads to a strengthening of the constraints on w by potentially adding constraints corresponding to fractional assignments as in the case of untriangualated networks. . the LP inference is exact. k µi. 7. 1 Many thanks to Michael Montemerlo and Sebastian Thrun for sharing the data. and as a preprocessing step for other perceptual tasks.7. For K > 2. represented by its (x. Terrain classiﬁcation is very useful for autonomous mobile robots in realworld environments for path planning. Unfortunately. EXPERIMENTS 99 The dual and primal solutions are related by ˙ w= i.5. the edge basis functions cannot be kernelized because of the nonnegativity constraint.c∈C (i) . For K = 2. ¨ w=ν+ ¨ i. Each reading was a point in 3D space.v∈V (i) . Thus.5.v (k)∆fi. 7.5 Experiments We applied associative Markov networks to the task of terrain classiﬁcation.c (k) f ¨ The ν variables simply ensure that w are positive (if any component ¨ i. y.c (k)∆¨i. 7. the only available information is the location of points. Note that the objective can be written in terms of dot products of node basis func˙ ˙ v ¯ tions ∆fi.c (k). Thus.¯(k). The data consists of around 35 million points. target detection. However. the optimal choice w. The Stanford Segbot Project1 has provided us with a laser range maps of the Stanford campus collected by a moving robot equipped with SICK2 laser sensors Fig.c∈C (i) .5. as our experiments show.
as well as the density of the range scan. We run PCA on these points to get the plane of maximum variance (spanned by the ﬁrst two principal components). we are left with approximately 20 million nonground points. the central plane.3: Segbot: roving robot equipped with SICK2 laser sensors. etc. ASSOCIATIVE MARKOV NETWORKS Figure 7. These features capture the local distribution well and are especially useful in ﬁnding planes. We then partition the cube into 3 × 3 × 3 bins around the point. For each point we sample 100 points in a cube of radius 0. since scans tend to be sparser in regions farther from the robot. Our ﬁrst type of feature is based on the principal plane around it. such as how planar the neighborhood is. oriented with respect to the principal plane. Our second type of feature is based on a column . Since classifying ground points is trivial given their absolute zcoordinate (height). and compute the percentage of points lying in the various subcubes. The features we use require preprocessing to infer properties of the local neighborhood of a point.5 meters. Each point is represented simply as a location in an absolute 3D coordinate system. We use a number of features derived from the cube such as the percentage of points in the central column. the outside corners. we classify them deterministically by thresholding the z coordinate at a value close to 0.100 CHAPTER 7. or how much of the neighbors are close to the ground. The features we use are invariant to rotation in the xy plane. After we do that. and shrubbery.
EXPERIMENTS 101 Figure 7. We considered three different models: SVM. right panel and Fig.. 7.7. Finally. 7. augmented with a quadratic kernel.4: 3D laser scan range map of the Stanford Quad. a tree.g.5. which extends vertically to include all the points in a “column”. All methods use the same set of features. between 2m and 2. This model (Fig. We take a cylinder of radius 0.25 meters. we also use an indicator feature of whether or not a point lies within 2m of the ground.5m). VotedSVM and AMNs. some bushes. The ﬁrst model is a multiclass SVM with a quadratic kernel over the above features. around each point. top panel) achieves reasonable performance .5. We then compute what percentage of the points lie in various segments of this vertical column (e.7. For training we select roughly 30 thousand points that represent the classes well: a segment of a wall. This feature is especially useful in classifying shrubbery.
in many places.5. Each point is connected to 6 of its neighbors: 3 of them are sampled randomly from the local neighborhood in a sphere of radius 0.5m. shrubs/blue. it smooths out trees and some parts of the buildings. middle panel and Fig. but fails to enforce local consistency of the classiﬁcation predictions. Yet it still fails in areas like arches of buildings where the SVM classiﬁer has a locally consistent wrong prediction. 7. The VotedSVM model (Fig.7. 7. trees/green. It is important to ensure vertical consistency since the SVM classiﬁer is wrong in areas that are higher off the . We improved upon the SVM by smoothing its predictions using voting.25m. The ﬁnal model is a pairwise AMN over laser scan points. ground/gray). ASSOCIATIVE MARKOV NETWORKS Figure 7.5: Terrain classiﬁcation results showing Stanford Memorial Church obtained with SVM. For example arches on buildings and other less planar regions are consistently confused for trees. middle panel) performs slightly better than SVM: for example. (Color legend: buildings/red. with associative potentials to ensure smoothness.102 CHAPTER 7. even though they are surrounded entirely by buildings. For each point we took its local neighborhood (we varied the radius to get the best possible results) and assigned the point the label of the majority of its 100 neighbors. and the other 3 are sampled at random from the vertical cylinder column of radius 0. VotedSVM and AMN models.
While we experimented with a variety of edge features including various distances between points.5 x 10 7 Figure 7. The inference over each segment was performed using mincut with αexpansion moves as described above. left panel and Fig. Note the near linear performance of the algorithm and its efﬁciency even for large models.5 1 1.6: The running time (in seconds) of the mincutbased inference algorithm for different problem sizes. it is roughly linear in the size of the problem (number of nodes and number of edges). EXPERIMENTS 103 Mincut inference performance 250 200 Running time (seconds) 150 100 50 0 0 0.5 Problem size (nodes and edges) 2 2. We trained the AMN model using CPLEX to solve the quadratic program. with the actual mincut taking less than two minutes even for the largest segment.6. The problem size is the sum of the number of nodes and the number of edges. The implementation is largely dominated by I/O time. The performance is summarized in Fig. the training took about an hour on a Pentium 3 desktop.5. We used a publicly available implementation of the mincut algorithm. which uses bidirectional search trees for augmenting paths (see Boykov and Kolmogorov [2004]). 7. tree trunks and tree crowns look different).7. 7. we found that even using only a constant feature performs well. 7. We can see that the predictions of the AMN (Fig. bottom panel) are much smoother: for example building arches and tree trunks are predicted . ground (due to the decrease in point density) or because objects tend to look different as we vary their zcoordinate (for example. and as we can see.7.5.
104 CHAPTER 7. In fact. The differences are dramatic: SVM: 68%. a subclass of Markov networks that allows only positive interactions between . 7. Our deﬁnition of associative potentials below also satisﬁes the Kolmogorov and Zabih regularity condition for K = 2.stanford.8) and computed accuracies of the predictions shown in Fig. See more results. including a ﬂythrough movie of the data. our learning formulation provides an exact and tractable optimization algorithm. Kleinberg and Tardos [1999] extend the multiclass Potts model to have more general edge potentials. Kumar and Hebert [2003] train CRFs using a pseudolikelihood approximation to the distribution P (Y  X) since estimating the true conditional distribution is intractable. unlike their work. More recently. the structure of our potentials is simpler to describe and extend for the multiclass case. as long as the parameters satisfy a certain regularity condition. Our terrain classiﬁcation approach is most closely related to work in vision applying conditional random ﬁelds (CRFs) to 2D images.9 (excluding ground. we can extend our maxmargin framework to estimate their more general potentials by expressing inference as a linear program.edu/˜btaskar/3Dmap/. our approach can also handle multiclass problems in a straightforward manner. We also handlabeled around 180 thousand points of the test set (Fig.6 Related work Several authors have considered extensions to the Potts model. under the constraints that negative log of the edge potentials form a metric on the set of labels. Moreover. at http://ai. ASSOCIATIVE MARKOV NETWORKS correctly. However. as well as formal guarantees for binary classiﬁcation problems. which was classiﬁed by preprocessing). 7.7 Conclusion In this chapter. Kolmogorov and Zabih [2002] showed how to optimize energy functions containing binary and ternary interactions using graph cuts. we provide an algorithm for maxmargin training of associative Markov networks. Unlike their work. VotedSVM: 73% and AMN: 93%. They also provide a solution based on a relaxed LP that has certain approximation guarantees. 7. 7.
it would be interesting to see whether we can extend the class of networks we can learn effectively. we are not guaranteed exact solutions. and consider another one (hypertext classiﬁcation) in the next. To our knowledge. which is the key component in the quadratic program associated with the maxmargin formulation. We have explored only a computer vision application in this chapter.g. CONCLUSION 105 related variables. or predicting links in relational data.7. our method is guaranteed to ﬁnd the optimal (marginmaximizing) solution for all binaryvalued AMNs.. We thus provide a polynomial time algorithm which approximately solves the maximum margin estimation problem for any associative Markov network. such as extracting protein complexes from proteinprotein interaction data. In the nonbinary case. it is clear that many applications call for repulsive potentials. and it is an interesting challenge to apply the algorithm to even larger models and develop efﬁcient distributed implementations. While clearly we cannot introduce fully general potentials into AMNs without running against the NPhardness of the general problem. this algorithm is the ﬁrst to provide an effective learning procedure for Markov networks of such general structure. It would be interesting to see whether these bounds provide us with guarantees on the quality (e. Our approach relies on a linear programming relaxation of the MAP problem. It would be very interesting to consider other applications. despite the prevalence of fully associative Markov networks. the margin) of our learned model. However. Importantly. We present largescale experiments with terrain segmentation and classiﬁcation from 3D range data involving AMNs with tens of millions of nodes and edges. Our results in the binary case rely on the fact that the LP relaxation of the MAP problem provides exact solutions. regardless of the clique size or the connectivity. but we can prove constantfactor approximation bounds on the MAP solution returned by the relaxed LP. The class of associative Markov networks appears to cover a large number of interesting applications. .7. The mincut based inference is able to handle very large networks.
.106 CHAPTER 7. ASSOCIATIVE MARKOV NETWORKS Figure 7.7: Results from the SVM. VotedSVM and AMN models.
8: Labeled part of the test set: ground truth (top) and SVM predictions (bottom). . CONCLUSION 107 Figure 7.7.7.
.9: Predictions of the VotedSVM (top) and AMN (bottom) models. ASSOCIATIVE MARKOV NETWORKS Figure 7.108 CHAPTER 7.
Most naively. We provide experimental results on a webpage classiﬁcation task. Entities are related to each other via different types of links. In this chapter. we present a framework that builds on Markov networks and provides a ﬂexible language for modeling rich interaction patterns in structured data. Consider a collection of hypertext documents that we want to classify using some set of labels. hyperlinks that emanate from the same section of the document are even 109 . such as a partition into sections. Many realworld data sets are innately relational: hyperlinked webpages. ignoring the correlations between them. medical records. we can use a bag of words model. hypertext has a very rich structure that this approach loses entirely. In many other supervised learning tasks. Such data consist of entities of different types. the labels of linked pages are highly correlated. where each entity type is characterized by a different set of attributes. we have seen how sequential and spatial correlation between labels can be exploited for tremendous accuracy gains. However. One document has hyperlinks to others. the entities to be labeled are related with each other in very complex ways. classifying each webpage solely using the words that appear on the page. in hypertext classiﬁcation. For example.Chapter 8 Relational Markov networks In the previous chapters. typically indicating that their topics are related. crosscitations in patents and scientiﬁc papers. social networks. A standard approach is to classify each entity independently. showing that accuracy can be signiﬁcantly improved by modeling relational dependencies. not just sequentially or spatially. and the link structure is an important source of information. Each document also has internal structure. and more.
Reference attributes include a special unique key attribute E.HasWordk indicating whether the word k occurs on the page. we can represent a pattern where two linked documents are likely to have the same topic. The graphical structure of an RMN is based on the relational structure of the domain. We propose the use of a joint probabilistic model for an entire collection of related entities.K that identiﬁes each . and thereby can explicitly take advantage of the correlations between the labels of related entities. we restrict label and content attributes to take on categorical values. It thereby allows us tremendous ﬂexibility in representing complex patterns. both of which refer to Doc entities. In general. rather than classifying each document separately. there are two entity types: Doc and Link. . label attributes E. Doc would have a set of boolean attributes Doc.1 Relational classiﬁcation Consider hypertext as a simple example of a relational domain. We can also capture patterns that involve groups of links: for example. . a schema speciﬁes of a set of entity types E = {E1 .To). A relational domain is deﬁned by a schema. Therefore. and can easily model complex patterns over related entities. these are important cues. As we show. The Link entity type has two attributes: Link. Each type E is associated with three sets of attributes: content attributes E. where we simultaneously decide on the class labels of all of the entities together.To. En }. RELATIONAL MARKOV NETWORKS more likely to point to similar documents.Label). and reference attributes E. we want to provide a form of collective classiﬁcation.Label. consecutive links in a document tend to refer to documents with the same label. Doc. their attributes and relations between them.X (for example. 8. Link. the use of an undirected graphical model avoids the difﬁculties of deﬁning a coherent generative model for graph structures in directed models. For simplicity. . which takes on a set of categorical values. We introduce the framework of relational Markov networks (RMNs). . Doc.110 CHAPTER 8.HasWordk ).From and Link. If a webpage is represented as a bag of words. When classifying a collection of documents. In our domain. that can potentially help us achieve better classiﬁcation accuracy. which compactly deﬁnes a Markov network over a relational data set. It would also have the label attribute Doc. For example. which describes entities. indicating the topic of the page.R (for example.Y (for example.
A hypertext instantiation graph speciﬁes a set of webpages and links between them. specifying their labels.HasWordk  Doc. indicating the probability that word k appears in the document given each of the possible topic labels. Other reference attributes E. PRMs [Koller & Pfeffer. but not their words or labels.Y and I.R to denote the content. Given a particular instantiation graph containing some set of documents and links. Taskar et al.1. An instantiation I of a schema E speciﬁes the set of entities I(E) of each entity type E ∈ E and the values of all attributes for all of the entities. In our hypertext example. Getoor et al. which we call an instantiation skeleton or instantiation graph.Label of two documents if there is a link between them. We would have a probabilistic dependency from each document’s label to the words on the document. Friedman et al. speciﬁes the set of entities (nodes) and their reference attributes (edges). This network reﬂects the interactions between related instances by allowing us to represent correlations between their attributes.8.. with a directed edge between Doc. using both the words in the title .K). 2002] are a relational extension of Bayesian networks [Pearl. I. I.R refer to entities of a single type E = Range(E.R) and take values in Domain(E .Label) associated with it.y and I. Taskar et al. and a dependency from each document’s label to the labels of all of the documents to which it points.HadWordk . Given a particular instantiation graph. 1998.x.. We will use I. A PRM speciﬁes a probability distribution over instantiations consistent with a given instantiation graph by specifying a Bayesiannetworklike templatelevel probabilistic model for each entity type. For example. a PRM might use a naive Bayes model for words. 1999. I. RELATIONAL CLASSIFICATION 111 entity.Label to Doc. each of these attributes would have a conditional probability distribution P (Doc. words they contain and links between them. the PRM speciﬁes a Bayesian network over all of the documents in the collection. a PRM can represent the interdependencies between topics of linked documents by introducing an edge from Doc.X.r to denote the values of those attributes. More importantly.r. the PRM induces a large Bayesian network over that instantiation that speciﬁes a joint probability distribution over all attributes of all of the entities. show that this approach works well for classifying scientiﬁc documents. an instantiation of the hypertext schema is a collection of webpages. [2001] suggest the use of probabilistic relational models (PRMs) for the collective classiﬁcation task. label and reference attributes in the instantiation I. 1988].Label and each attribute Doc. The component I.
directed models such as Bayesian networks and PRMs are usually trained to optimize the joint probability of the labels and other attributes. the set of all webpages). a quadratic growth is intractable. This model. For example. Furthermore. The advantage of training a model only to discriminate between labels is that it does not have to trade off between classiﬁcation accuracy and modeling the joint distribution over nonlabel attributes.. leading to cycles in the induced “Bayesian network”. and the cyclicity problem disappears. Such interactions between many overlapping triples of links do not ﬁt well into the generative framework. . Representing more complex patterns involving correlations between multiple edges is very difﬁcult. The model deﬁnes the probability of the link existence as a function of the labels of the two endpoints. it is more likely that they point to each other as well. In this link existence model. has other fundamental limitations. Each two pages have a “potential link”. such as webpages. but rather treat links themselves as random variables. Even more problematic are the inherent limitations on the expressive power imposed by the constraint that the directed graph must represent a coherent generative model over graph structures. is problematic since there are many cycles in the link graph. discriminatively trained models are more robust to violations of independence assumptions and achieve higher classiﬁcation accuracy than their generative counterparts. Getoor et al. In many cases. if two pages point to the same page.g.112 CHAPTER 8. When N is large (e. however. However the application of this idea to other domains. [2001] suggest an approach where we do not include direct dependencies between the labels of linked webpages. In particular. while the goal of classiﬁcation is a discriminative model of labels given the other attributes. This quadratic blowup occurs even when the actual link graph is very sparse. the resulting Bayesian network has a random variable for each potential link — N 2 variables for collections containing N pages. which may or may not exist in the data. which is therefore not a coherent probabilistic model. RELATIONAL MARKOV NETWORKS and abstract and the citationlink structure. labels have no incoming edges from other labels. The link existence model assumes that the presence of different edges is a conditionally independent event.
The potential on the clique will have higher values for assignments that give a common label to the linked pages. we can write the template as a kind of SQL query: SELECT doc1.1. as the unconditional case is a special case where the set of content attributes is empty. a clique between the labels of the source and the target page. A relational Markov network (RMN) speciﬁes a conditional distribution over all of the labels of all of the entities in an instantiation given the relational structure and the content attributes.2 Relational Markov networks We now extend the framework of Markov networks to the relational setting. doc2. We can capture this correlation between labels by introducing. The links follow a common pattern: documents with the same label tend to link to each other more often.2. To specify what cliques should be constructed in an instantiation. so a single model provides a coherent distribution for any collection of instances from the schema. RELATIONAL MARKOV NETWORKS Label 1 Label 2 Label 3 113 Figure 8.Category . For our link example. A relational clique template speciﬁes tuples of variables in the instantiation by using a relational query language. For example. 8. it speciﬁes the cliques and potentials between attributes of related entities at a template level. (We provide the deﬁnitions directly for the conditional case.1: An unrolled Markov net over linked documents.Category.8. for each link. suppose that pages with the same label tend to link to each other. we will deﬁne a notion of a relational clique template. 8. as in Fig.) Roughly speaking.
S) consists of three components: ◦ F = {Fi } — a set of entity variables. W(F. Our deﬁnition of clique templates contains the corresponding three parts.Key and link.S selects the appropriate attributes of the entities.From = doc1.To = doc2. Doc and Link. where an entity variable Fi is of type E(Fi ). ◦ W(F.Key Note the three clauses that deﬁne a query: the FROM clause speciﬁes the cross product of entities to be ﬁltered by the WHERE clause and the SELECT clause picks out the attributes of interest. RELATIONAL MARKOV NETWORKS FROM Doc doc1.Rj = Fk . Doc doc2.Y — a selected subset of content and label attributes in F. This deﬁnition of a clique template is very ﬂexible. It allows modeling complex relational patterns on the instantiation graphs. F consists of doc1. This pattern can be expressed by the following template: SELECT doc1.S ⊆ F. W.r) ensures that the entities are related to each other in speciﬁed ways. the clause W(f . To continue our webpage example. and ﬁnally.F rom = doc1. that is determined by the clique potentials. Note that the clique template does not specify the nature of the interaction between the attributes.S is doc1. .Key ∧ link. A clique template speciﬁes a set of cliques in an instantiation I: C(I) ≡ {c = f . respectively. For the clique template corresponding to the SQL query above. A relational clique template C = (F.Key and F.S : f ∈ I(F) ∧ W(f . ◦ F. consider another common pattern in hypertext: links in a webpage tend to point to pages of the same category. Link link WHERE link. doc2.R) is link.Category and doc2.Category . which will be associated with the template. where f is a tuple of entities {fi } in which each fi is of type E(Fi ).Category.T o = doc2. .114 CHAPTER 8.r)}. doc2 and link of types Doc. × I(E(Fn )) denotes the crossproduct of entities in the instantiation.Category.R) — a boolean formula using conditions of the form Fi . I(F) = I(E(F1 )) × . f . as the WHERE clause of a template can be an arbitrary predicate.Rl .X ∪ F.
Key and not doc1. and f is the vector .x. I. I.x.Key Depending on the expressive power of our template deﬁnition language.x.x.To = doc1. Using the loglinear representation of potentials.r) is the normalizing partition function: Z(I.xc .r) C∈C φC (I. The RMN allows us to associate the same clique potential parameters with all of the subgraphs satisfying the template.x. I.y  I.2.xc .y C∈C c∈C(I) φC (I.y. I.r) where fC (I. I. I. I.To = doc2.yc ) c∈C(I) where Z(I. Doc doc2.From = link2. I. I. I.y  I.r) = c∈C(I) fC (I. the same template can select subgraphs whose structure is fairly different. I.r) = I.x.r) = w f (I.x.r) 1 = Z(I. Link link1.Key and link2. A Relational Markov network (RMN) M = (C.8. thereby allowing generalization over a wide range of different structures. I. Link link2 WHERE link1.xc . Since the clique templates do not explicitly depend on the identities of entities.Key = doc2.yc ) is the sum over all appearances of the template C(I) in the instantiation.yc ) . we can write log P (I.x.y.From and link1. I. we may be able to construct very complex templates that select entire subgraph structures of an instantiation. Φ) speciﬁes a set of clique templates C and corresponding potentials Φ = {φC }C∈C to deﬁne a conditional distribution: P (I. We can easily represent patterns involving three (or more) interconnected documents without worrying about the acyclicity constraint imposed by directed models. RELATIONAL MARKOV NETWORKS 115 FROM Doc doc1.r) − log Z(I. φC (VC ) = exp{wC fC (VC )}.
4 show. and when it does. It is guaranteed to converge to the correct marginal probabilities for each node only for singly connected Markov networks. not just the most likely assignment. 8. 1999] for more details. referring to [Murphy et al. Given a particular instantiation I of the schema.3 Approximate inference and learning Applying both maximum likelihood and maximum margin learning in the relational setting is requires inference in very large and complicated networks. However. We therefore resort to approximate methods. Empirical results [Murphy et al. recent analysis [Yedidia et al. We refer the reader to Yedidia et al.. we assume a pairwise network where all potentials are associated only with nodes and edges given by: . We provide a brief outline of one variant of BP. an RMN with the link basis function described above would deﬁne a Markov net in which. for every link between two pages. Belief Propagation (BP) is a local message passing algorithm introduced by Pearl [1988]. this approach works well in our domain. where exact inference is typically intractable. 8. RELATIONAL MARKOV NETWORKS of all fC ... 8. In our webpage example. Fig. For simplicity.116 CHAPTER 8. for a detailed description of the BP algorithm. As our results in Sec. Maximum likelihood estimation For maximum likelihood learning. including MCMC and variational methods. we need to compute basis function expectations. there is an edge between the labels of these pages. and all of these cliques are associated with the same clique potential φC . 2000] provides some theoretical justiﬁcation. There is a wide variety of approximation schemes for this problem.1 illustrates a simple instance of this unrolled Markov network. We have one clique for each c ∈ C(I). the marginals are a good approximation to the correct posteriors. the RMN M produces an unrolled Markov network over the attributes of entities in I. The cliques in the unrolled network are determined by the clique templates C. We chose to use belief propagation for its simplicity and relative efﬁciency and accuracy. 1999] show that it often converges in general networks.
APPROXIMATE INFERENCE AND LEARNING 117 P (Y1 . At any point in the algorithm. Yj ) = φ(xij . with mij (Yj ) ← α max ψij (yi .3. Yn ) = 1 Z ψij (Yi . ψi (Yi ) = φ(xi . . Yi . Computing the expected basis function expectations involves summing their expected values for each clique using the approximate marginals bi (Yi ) and bij (Yi . this results in less accurate classiﬁcation. . Yj )ψi (Yi )ψj (Yj ) k∈N (i)−j mki (Yi ) l∈N (j)−i mlj (Yj ) These approximate marginals are precisely what we need for the computation of the basis function expectations and performing classiﬁcation. Yj ). Yj )ψi (yi ) k∈N (i)−j mki (Yi ) where α is a (different) normalizing constant. so we use posterior marginal prediction. In our experiments. Similarly. Yj ) ij i ψi (Yi ) where ij ranges over the edges of the network and ψij (Yi . At each iteration. The belief propagation algorithm is very simple. each node Yi sends the following messages to all its neighbors N (i): mij (Yj ) ← α yi ψij (yi . Yj )ψi (yi ) yi k∈N (i)−j mki (Yi ) to compute approximate posterior “max”marginals and use those for prediction. . the marginal distribution of any node Yi is approximated by bi (Yi ) = αψi (Yi ) k∈N (i) mki (Yi ) and the marginal distribution of a pair of nodes connected by an edge is approximated by bij (Yi . Note that we can also max − product variant of loopy BP. .8. This process is repeated until the messages converge. . Yj ) = αψij (Yi . Yj ). Yi ). we use maxyi bi (Yi ) at prediction time.
researchproject (82) and student (542). which always produced integral solutions on test data. we used the LP in Sec. making the number of other pages commensurate with the other categories. For networks with attractive potentials (AMNs). 8. faculty (148). so that a baseline algorithm that simply always selected other as the label would get an average accuracy of 75%.4. Texas (574). representing the type of webpage which is one of course.118 CHAPTER 8. In all of our experiments. but in a relational classiﬁcation setting. Washington (728) and Wisconsin (1614). The data set contains webpages from four different Computer Science departments: Cornell. Hence.2. 1998]. Our goal is to collectively classify webpages into one of these ﬁve categories. Each page has a label attribute. which is an instance of our hypertext example. Texas (292). 7. which we rounded independently for each label. The data set is problematic in that the category other is a grabbag of pages of many different types. student. we have access to the entire html of the page and the links to other pages. other (332). RELATIONAL MARKOV NETWORKS Maximum margin estimation For maximum margin estimation. we used approximate LP inference inside the maxmargin QP. 5. faculty. The number of remaining pages for each school are: Cornell (280). Washington (315) and Wisconsin (454). Texas. The number of pages classiﬁed as other is quite large.4 Experiments We tried out our framework on the WebKB dataset [Craven et al. using commercial Ilog CPLEX software to solve it. we compromised by eliminating all other pages with fewer than three outlinks.. the deleted webpages might be useful in terms of their interactions with other webpages. Washington and Wisconsin. thus evaluating the generalization performance of . The untriangulated LP produced fractional solutions for inference on the test data in several settings. The number of links for each school are: Cornell (574). We could restrict attention to just the pages with the four other labels. For each page. For networks with general potentials. we used the untriangulated LP we described in Sec. project or other. The resulting category distribution is: course (237). we learn a model from three schools and test the performance of the learned model on the remaining school.
linear support vector machines (Svm).8. and logistic regression (Logistic) — using words and metawords.. show that the two discriminative approaches outperform Naive Bayes. We want to capture these correlations in our model and use them for transmitting information between linked pages to provide more accurate classiﬁcation. i. we compare to standard text classiﬁers such as Naive Bayes.1 Flat models The simplest approach we tried predicts the categories based on just the text content on the webpage. and Support Vector Machines. 2002]. 8. EXPERIMENTS 119 the different models. Our ﬁrst experimental setup compares three wellknown text classiﬁers — Naive Bayes. However. are easily incorporated as features. We found that stemming and feature selection did not provide much beneﬁt and simply pruned words that appeared in fewer than three documents in each of the three schools in the training data. 1999]. 10] and took the best setting for all models. We used C ∈ [0.4.2. in anchors of links to the page and in the last header before a link to the page [Yang et al. the resulting classiﬁcation task is still ﬂat featurebased classiﬁcation. Incorporating metadata gives a signiﬁcant improvement. We experimented with several relational models.e. shown in Fig. 8. Logistic and Svm give very similar results.4.1. Logistic Regression. Unfortunately. The results. Note that metadata. We also experimented with incorporating metadata: words appearing in the title of the page. The average error over the 4 schools was reduced by around 4% by introducing the metadata attributes. we cannot directly compare our accuracy results with previous work because different papers use different subsets of the data and different training/test splits. The text of the webpage is represented using a set of binary attributes that indicate the presence of different words on the page. but we can take additional advantage of the correlation in labels of related pages by classifying them collectively. although mostly originating from pages linking into the considered page. . which have been demonstrated to be successful on this data set [Joachims.
The ExistsML model is a (partially) generative model proposed by Getoor et al. Then a simple generative model speciﬁes a probability distribution over the existence of links between pages conditioned on both pages’ labels. with and without metadata features. faculty rarely link to each other.2: Comparison of Naive Bayes.) 8. captures this correlation through links: in addition to the local bag of words and metadata attributes. Maximum likelihood estimation (with regularization) of the generative component is closed . We also compare to a directed graphical model to contrast discriminative and generative models of relational structure. 8. These correlations are very common in our data: courses and research projects almost never link to each other. Concretely. Svm. [2001]. a logistic regression model predicts the page label given the words and metafeatures.2 Link model Our ﬁrst model captures direct correlations between labels of linked pages. students have links to all categories but mostly courses. For each page.3 0.4. and Logistic on WebKB. RELATIONAL MARKOV NETWORKS 0.05 0 Words Words+Meta Naïve Bayes Svm Logistic Figure 8.We train this model using maximum conditional likelihood (labels given the words and the links) and maximum margin.1 0.120 CHAPTER 8.35 0. The Link model.25 Test Error 0.1.2 0. Note that this model does not require inference during learning. (Only averages over the 4 schools are shown here. we learn the probability of existence of a link between two pages given their labels. we introduce a relational clique template over the labels of two pages that are linked.15 0. shown in Fig.
8. Exists model with logistic regression and the Link model estimated using the maximum likelihood (ML) and the maximum margin (MM) criteria. Fig.3 Cocite model The second relational model uses the insight that a webpage often has internal structure that allows it to be broken up into sections.4. since the resulting graphical model includes edges not only for the existing hyperlinks. a faculty webpage might have . By contrast. linked or not.8. but also those that do not exist.3 shows a gain in accuracy from SVMs to the Link model by using the correlations between labels of linked web pages. This can be attributed to the simplicity of the generative model and the difﬁculty of the resulting inference problem. EXPERIMENTS 121 30% 25% 20% ExistsML SVM LinkML LinkMM Error 15% 10% 5% 0% Cor Tex Was Wis Average Figure 8. The Exists model doesn’t perform very well in comparison. the Link model avoids this problem by only modeling the conditional distribution given the existing links. There is also very signiﬁcant additional gain by using maximum margin training: the error rate of LinkMM is 40% lower than that of LinkML. However. observing the link structure directly correlates all page labels in a website.4.3: Comparison of ﬂat versus collective classiﬁcation on WebKB: SVM. 8. For example. Intuitively. the prediction phase is much more expensive. form given appropriate cooccurrence counts of linked pages’ labels. and 51% lower than multiclass SVMs.
they are likely to be on similar topics. with a list of links to all of the projects of the faculty member.To = doc2.To = doc1.Category FROM Doc doc1. To take advantage of this trend. or linked to from the same section. The Cocite model captures this type of correlation.Key and link2. so we can use AMNtype potentials in the maxmargin estimation.Category. Link link1. if two pages are cocited. Intuitively.122 CHAPTER 8.Key and not doc1.Key = doc2. Svm. and Logistic on WebKB.4: Comparison of Naive Bayes. and a third to his advisees.Key We compared the performance of SVM. we need to enrich our schema by adding the attribute Section to Link to refer to the section number it appears in. RELATIONAL MARKOV NETWORKS 25% 20% SVM CociteML CociteMM Error 15% 10% 5% 0% Cor Tex Was Wis Average Figure 8. We can view a section of a webpage as a ﬁnegrained version of Kleinberg’s hub [Kleinberg. with and without metadata features. In the RMN. a second section might contain links to the courses taught by the faculty member. doc2.From and link1.From = link2.Section = link2. 1999] (a page that contains a lot of links to pages of particular category).Section and link1. The results. (Only averages over the 4 schools are shown here. .) one section that discusses research. We deﬁned a section as a sequence of three or more links that have the same path to the root in the html parse tree. Doc doc2. Note that we expect the correlation between the labels in this case to be positive. we have a relational clique template deﬁned by: SELECT doc1. Link link2 WHERE link1. CociteML and CociteMM.
8. we can capture such patterns as well. maximum likelihood trained model CociteML achieves a worse test error than maximum margin CociteMM model. which suggests that the optimization successfully avoided problematic parameterizations of the network. If X’s webpage mentions Y and Z in the same context. 1998]. However there are many patterns that we are difﬁcult to model in PRMs. also demonstrate signiﬁcant improvements of the relational models over the SVM. The improvement is present when testing on each of the schools. By introducing cliques over triples of relations. for example. if Y is Professor X’s advisee. the learned CociteMM weights never produced fractional solutions when used for inference. where objects that share a certain graphbased property are more likely to have the same label. One useful type of pattern type is a similarity template. Note that this type of interaction cannot be accounted for just using pairwise cliques. 1999]. but of course we are limited by the ability of belief propagation . We give some examples here. Getoor et al.5 Related work Our RMN representation is most closely related to the work on PRMs [Koller & Pfeffer.. where the presence of an AB link and of a BC link increases (or decreases) the likelihood of an AC link. then probably so is Z. We note that. Again. RELATED WORK 123 shown in Fig. for example. Later work showed how to efﬁciently learn model parameters and structure (equivalent of clique selection in Markov networks) from data [Friedman et al. in particular those that involve several links at a time. 8. even in the case of the nonoptimal multiclass relaxation. [2002] propose several generative models of relational structure. Our framework accommodates these patterns easily. We can incorporate even more complicated patterns.8. For example. by introducing pairwise cliques between the appropriate relation variables. which shows a 30% relative reduction in test error over SVM. it is likely that the XY relation and the YZ relation are of the same type.4. Another useful type of subgraph template involves transitivity patterns.5. students often assist in courses taught by their advisor. Consider. in our experiments. a professor X and two other entities Y and Z. Their approach easily captures the dependence of link existence on attributes of entities.
Several recent papers have proposed algorithms that use the link graph to aid classiﬁcation. 1990] and hypertext [Kleinberg.124 CHAPTER 8. we can incorporate relational features into standard ﬂat classiﬁcation. 8. For example. it is possible to simply view the presence of particular citations as atomic features. Slattery and Mitchell [2000] tried to identify directory (or hub) pages that commonly list pages of the same topic. where we want to classify multiple entities. In our WebKB example. Chakrabarti et al.. we might consider simply directing the correlation edges between link existence variables arbitrarily. it is not clear how to parameterize a link existence variable for a link that is involved in multiple triangles. for the transitivity pattern. The structure of the relational graph has been used extensively to infer importance in scientiﬁc publications [Egghe & Rousseau.6 Conclusion In this chapter. 1999]. [1998] use systempredicted labels of linked documents to iteratively relabel each document in the test set. achieving a signiﬁcant improvement compared to a baseline of using the text in each document alone. there is no overlap between the webpages in the . In some cases. 2003b]. exploiting the interactions between their labels. RELATIONAL MARKOV NETWORKS to scale up as we introduce larger cliques and tighter loops in the Markov network. For example. none of these approaches provide a coherent model for the correlations between linked webpages. when classifying papers into topics. we propose a new approach for classiﬁcation in relational domains. However. However. Our approach provides a coherent foundation for the process of collective classiﬁcation. signiﬁcantly improving the classiﬁcation accuracy over standard ﬂat classiﬁcation. Attempts to model such pattern in PRMs run into the constraint that the probabilistic dependency graph (Bayesian network) must be a directed acyclic graph. with no formal justiﬁcation. and used these pages to improve classiﬁcation of university webpages. A similar approach was used by Neville and Jensen [2000] in a different domain. We describe and exploit these patterns in our work on RMNs using maximum likelihood estimation [Taskar et al. However. this approach is limited in cases where some or even all of the relational features that occur in the test data are not observed in the training data. applying combinations of classiﬁers in a procedural way. We have shown that we can exploit a very rich set of relational patterns in classiﬁcation.
8. social networks provide extensive information about interactions among people and organizations. Incorporating basic features (e... Hypertext is the most easily available source of structured data. In particular. CONCLUSION 125 different schools. but cannot exploit the strong correlation between the labels of related entities that RMNs capture. . it is particularly interesting to explore the problem of inducing them automatically.g. RMNs offer a principled method for learning to predict communities of and hierarchical structure between people and organizations based on both the local attributes and the patterns of static and dynamic interaction. so we cannot learn anything from the training data about the signiﬁcance of a hyperlink to/from a particular webpage in the test data. RMNs are generally applicable to any relational domain. however. words) from the related entities can aid in classiﬁcation. The results in this chapter represent only a subset of the domains we have worked on (see [Taskar et al. 2003b]). Given the wealth of possible patterns.6.
126 CHAPTER 8. RELATIONAL MARKOV NETWORKS .
matching.Part III Broader applications: parsing. clustering 127 .
9. we condition on the words in a sentence to produce a model of the syntactic structure.1(a) shows a parse tree for the sentence The screen was a sea of 128 . However. 9. The terminal symbols are usually words of the sentence. The nonterminal symbols correspond to syntactic categories such as noun phrase (NP) or verbal phrase (VP). We show that this framework allows highaccuracy parsing in cubic time by exploiting novel kinds of lexical information. we restrict our grammars to be in Chomsky normal form as in Sec. 3. u For clarity of presentation. For example.1 Context free grammar model CFGs are one of the primary formalisms for capturing the recursive structure of syntactic constructions. Instead. in the discriminative framework that we adopt. Our models can condition on arbitrary features of input sentences. Terminal symbols for our purposes are partofspeech tags like nouns (NN). thus incorporating an important kind of lexical information not usually used by conventional parsers. although many others have also been proposed [Manning & Sch¨ tze. verbs (VBD). Fig.4. 1999].Chapter 9 Context free grammars We present a novel discriminative approach to parsing using structured maxmargin criterion based on the decomposition properties of context free grammars. we are not concerned with deﬁning a distribution over sequences of words (language model). determiners (DT). We show experimental evidence of the model’s improved performance over a natural baseline model and a lexicalized probabilistic contextfree grammar.
9. and this triple of nodes can be labeled as A. VBD) are added to conform to the CNF restrictions. For convenience.n is constrained to be in NS . or dominates. DT. This tree representation seems quite different from the graphical models we have been considering thus far. N ◦ A designated set of start symbols. B and C. CONTEXT FREE GRAMMAR MODEL 129 red.4 here: Deﬁnition 9. PU = {A → D : A ∈ N . For each span starting with s and an ending with e.1 (CFG) A CFG G consists of: ◦ A set of nonterminal symbols.1. The root’s label set is NS . T ◦ A set of productions. we can use an equivalent representation that essentially encodes a tree as an assignment to a set of appropriate variables. hence 0 ≤ s < e ≤ n for a sentence of length n. The nonterminal symbols with bars (for example.2 (CFG tree) A CFG tree is a labeled directed tree. we introduce a variable Ys. PB = {A → B C : A. the words of the sentence from s to e. Additionally. left and right. rather than to words themselves. In general. The value ⊥ is assigned if no subtree dominates the span. P = {PB . 1993]. respectively. C ∈ N } and Unary productions. since it represents . divided into Binary productions. Indices s and e refer to positions between words. NN.1. The set of symbols we use is based on the Penn Treebank [Marcus et al. PU }. respectively. there are exponentially many parse trees that produce a sentence of length n. B. All other internal nodes have two children.1. if and only if there is a binary production A → B C ∈ PB . D ∈ T }.e taking values in N ∪⊥ to represent the label of the subtree that exactly covers.. where the set of valid labels of the internal nodes other than the root is N and the set of valid labels for the leaves is T . each preleaf node has a single child and this pair of nodes can be labeled as A and D. 3. A CFG deﬁnes a set of valid parse trees in a natural manner: Deﬁnition 9. we repeat our deﬁnition of a CFG from Sec. NS ⊆ N ◦ A set of terminal symbols. if and only if there is a unary production A → D ∈ PU . However. The “top” symbol Y0.
Y6. The row and column number in the grid correspond to the beginning and end of the span. If Ys. The row and column number are the beginning and end of the span. respectively. We also introduce variables Ys. While any parse tree corresponds to an assignment to this set of variables in a straightforward manner.130 CHAPTER 9. Empty squares correspond to nonconstituent spans.1(a) as a grid where each square corresponds to Ys.e = ⊥.1(b) shows the representation of the tree in Fig. and (b) grid of labeled spans.s taking values in T to represent the terminal symbol (partofspeech) between s and s + 1. In order to characterize the set of valid assignments Y. respectively. CONTEXT FREE GRAMMARS (a) (b) Figure 9. Y3. The gray squares on the diagonal represent partofspeech tags. The gray squares on the diagonal represent the terminal variables. the starting symbol of the sentence.6 = NN.5 = NP and Y1. the converse is not true: there are assignments that do not correspond to valid parse trees. Empty squares correspond to ⊥ values.e .1: Two representations of a binary parse tree: (a) nested tree structure. 9. 9. consider the . the ﬁgure shows Y0.0 = DT.4 = ⊥. For example. it is often called a constituent. Fig.
1) A→B C∈PB 1 s. Conversely.e = (A.m.s+1 = A ∧ ys. y0.m and ym.3 and 9. CONTEXT FREE GRAMMAR MODEL 131 constraints that hold for a valid assignment y: 1 s. D)). will produce the rest of the tree down to the preterminals. B.9.s.e = (A. Similarly.1. Recursing on the two subtrees. A. then there must be a unique production starting with A and some split point m. if ys. We denote the set of assignments y satisfying (9. (9.4) A→D∈PU A→D∈PU The notation ys. ∀A ∈ N . 0 ≤ s < n. B.s = D) = I(y 1 s. D) abbreviates ys. then there must be a (unique) production that generated it: either starting before s or after e. The last two sets of constraints (9.1) holds because if the span from s to e is dominated by a subtree starting with A (that is.s+1 = A) = I(y 1 s. The ﬁrst set of constraints (9.4) hold since the terminals are generated using valid unary productions. I(y 1 s .e = A).1.s+1 = (A. I(y e<e ≤n 0 ≤ s < e ≤ n.s = D. ys. Starting from the root symbol.3) (9. say splitting at m and specifying the values for y0.m and ym .2) holds because that if the span from s to e is dominated by a subtree starting with A (ys.n .e = (B. ∀A ∈ N . C)). A)).3 If y ∈ Y. Proof sketch: It is straightforward to construct a parse tree from y ∈ Y in a topdown manner.n .s+1 = (A. C. the ﬁrst set of constraints (9.m.n . for m = m are labeled by ⊥.s.2) B→C A∈PB 1 s. (9.3 and 9. ∀D ∈ T .e = A). s < m < e.1) ensures that a unique production spans 0 to n.19.s. C) abbreviates ys.e = A) = I(y s<m<e 1 s. I(y (9.e = (B.s.e = A. The second set of constraints (9. the third and fourth set of constraints (9. C)) I(y 0≤s <s 0 ≤ s < e ≤ n. that produces that subtree.e = A) = I(y + B→A C∈PB 1 s. The second set of constraints (9. In fact the converse is true as well: Theorem 9. ∀A ∈ N .4) as Y. 0 ≤ s < n.e = C and ys. no productions start with A and cover s to e.m = B ∧ ym.m and ym. y0. then y represents a valid CFG tree.e = A ∧ ys.e.4) .n .2) ensures that all other spans y0. I(y 1 s.s+1 = (A. D)).
e = ⊥ ∨ ys. (9.m. ∗ ∗ Ss. 0 ≤ s < n. The probability of a tree is simply the product of probabilities of the productions used in the tree. Using the arg max’s of the max’s in .m.n (A).e (A.e ) + 0≤s<n Ss. C) + Ss.5).m (B) + Sm. D). then the tree score is the tree log probability.s+1 (A. a weighted CFG assigns a score to each production (this score may depend on the position of the production s.m.e ) = 0 if (ys. where Ss. weighted CFGs do not have the local normalization constraints Eq. 1967.s+1 (ys. A→B C∈PB max s<m<e ∗ The highest scoring tree has score maxA∈NS S0.e (A) = A→D∈PU max Ss.e (C). 1999]. m.132 CHAPTER 9. ∀A ∈ N . If the production scores are production log probabilities.5) 0 ≤ s < e ≤ n. B. ∀A ∈ N . This can be done simply by assigning a probability to each production and making sure that the sum of probabilities of all productions starting with each symbol is 1: P (A → B C) = 1.e (ys.m. We can use a Viterbistyle dynamic programming algorithm called CKY to compute the highest score parse tree in O(Pn3 ) time [Younger.m. (9. 9. ∀A ∈ N . u The algorithm computes the highest score of any subtree starting with a symbol over each span 0 ≤ s < e ≤ n recursively: ∗ Ss. More generally.e = ⊥).m = ⊥ ∨ ym. Manning & Sch¨ tze. However. B.s+1 (A) = ∗ Ss.2 Context free parsing A standard approach to parsing is to use a CFG to deﬁne a probability distribution over parse trees.s+1 ).C:A→B C∈PB D:A→D∈PU P (A → D) = 1. e) such that the total score of a tree is the sum of the score of all the productions used: S(y) = 0≤s<m<e≤n Ss.e (ys. CONTEXT FREE GRAMMARS ensure that the terminals are generated by an appropriate unary productions from the preterminals.
f (xs.g.e ).e are the relevant subsets of the sentence the basis functions depend on. yc ).m. where the basis functions consist of the counts of the productions used in the parse.e .3 Discriminative parsing models We cast parsing as a structured classiﬁcation task. We could also include functions that identify the label of the span . y).m. m. We assume that score ties are broken in a predetermined way. The functions we consider take the following linear discriminant form: hw (x) = arg max w f (x. C. and Y is a set of valid parse trees according to a ﬁxed CFG grammar.m. we introduce the set of indices.9. and neighboring positions in the sentence x (e. 9. e.e = S. To simplify notation.3. e) : 0 ≤ s ≤ m < e ≤ n}. VP) ∧ I(y mth word(x) = was)). y) = c∈C f (xc . where we want to learn a function h : X → Y. For example.e ) + 0≤s≤m<e≤n f (xs. f (x.m. y where w ∈ IRd and f is a basis function representation of a sentence and parse tree pair f : X × Y → IRd . and the parameters w are the logprobabilities of those productions. m. ys. where X is a set of sentences.e and xs. which includes both spans and span triplets: C = {(s. ys. Hence. ys.e ) = 1 s.e . say according to some lexicographic order of the symbols. where n is the length of the sentence x and xs. m) : 0 ≤ s ≤ e ≤ n} ∪ {(s. Note that this class of discriminants includes PCFG models. We assume that the basis functions decompose with the CFG structure: f (x.e . NP. f could include functions which identify the production used together with features of the words at positions s. y) = 0≤s≤e≤n f (xs. DISCRIMINATIVE PARSING MODELS 133 the computation of S ∗ .m.m. we can backtrace the highest scoring tree itself.
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from s to e together with features of the word (e.g. f (xs,m , ys,m ) = 1 s,m = NP) ∧ I(y sth word(x) = the)).
9.3.1 Maximum likelihood estimation
The traditional method of estimating the parameters of PCFGs assumes a generative model that deﬁnes P (x, y) by assigning normalized probabilities to CFG productions. We then maximize the joint loglikelihood
i
log P (x(i) , y(i) ) (with some regularization). We com
pare to such a generative grammar of Collins [1999] in our experiments. A alternative probabilistic approach is to estimate the parameters discriminatively by maximizing conditional loglikelihood. For example, the maximum entropy approach [Johnson, 2001] deﬁnes a conditional loglinear model: Pw (y  x) = where Zw (x) = the sample,
i
1 exp{w f (x, y)}, Zw (x)
y
exp{w f (x, y)}, and maximizes the conditional loglikelihood of
log P (y(i)  y(i) ), (with some regularization). The same assumption that
the basis functions decompose as sums of local functions over spans and productions is typically made in such models. Hence, as in Markov networks, the gradient depends on the expectations of the basis functions, which can be computed in O(Pn3 ) time by dynamic programming algorithm called insideoutside, which is similar to the CKY algorithm. However, computing the expectations over trees is actually more expensive in practice than ﬁnding the best tree for several reasons. CKY works entirely in the logspace, while insideoutside needs to compute actual probabilities. Branchandprune techniques, which save a lot of useless computation, are only applicable in CKY. A typical method for ﬁnding the parameters is to use Conjugate Gradients or LBFGS methods [Nocedal & Wright, 1999; Boyd & Vandenberghe, 2004], which repeatedly compute these expectations to calculate the gradient. Clark and Curran [2004] report experiments involving 479 iterations of training for one model, and 1550 iterations for another using similar methods.
9.3. DISCRIMINATIVE PARSING MODELS
135
9.3.2
Maximum margin estimation
We assume that loss function also decomposes with the CFG structure: ˆ (x, y, y) = (xs,e , ys,e , ys,e ) + ˆ ˆ (xs,m,e , ys,m,e , ys,m,e ) =
c∈C
ˆ (xc , yc , yc ).
0≤s≤e≤n
0≤s≤m<e≤n
One approach would be to deﬁne (xs,e , ys,e , ys,e ) = 1 s,e = ys,e ). This would lead to ˆ I(y ˆ ˆ ˆ (x, y, y) tracking the number of “constituent errors” in y. Another, more strict deﬁnition ˆ ˆ would be to deﬁne (xs,m,e , ys,m,e , ys,m,e ) = 1 s,m,e = ys,m,e ). This deﬁnition would lead I(y ˆ ˆ to (x, y, y) being the number of productions in y which are not seen in y. The constituent loss function does not exactly correspond to the standard scoring metrics, such as F1 or crossing brackets, but shares the sensitivity to the number of differences between trees. We have not thoroughly investigated the exact interplay between the various loss choices and the various parsing metrics. We used the constituent loss in our experiments. As in the maxmargin estimation for Markov networks, we can formulate an exponential size QP: min s.t. 1 w2 + C 2 ξi
i
(9.6)
w ∆fi (y) ≥ i (y) − ξi ∀i, y,
where ∆fi (y) = f (x(i) , y(i) ) − f (x(i) , y), and i (y) = (x(i) , y(i) , y). The dual of Eq. (9.6) (after normalizing by C) is given by: max
i,y
1 αi (y) i (y) − C 2 αi (y) = 1,
2
αi (y)∆fi (y)
i,y
(9.7)
s.t.
y
∀i; αi (y) ≥ 0, ∀i, y.
Both of the above formulations are exponential (in the number of variables or constraints) in the lengths (ni ’s) of the sentences. But we can exploit the contextfree structure of the basis functions and the loss to deﬁne a polynomialsize dual formulation in terms of
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marginal variables µi (y): µi,s,e (A) ≡
y:ys,e =A
αi (y), 0 ≤ s ≤ e ≤ n, ∀A ∈ N ; αi (y),
y:ys,s =D
µi,s,s (D) ≡ µi,s,m,e (A, B, C) ≡
0 ≤ s ≤ e ≤ n, ∀D ∈ T ; αi (y), 0 ≤ s < m < e ≤ n, ∀A → B C ∈ PB , 0 ≤ s < n, ∀A → D ∈ PU .
y:ys,m,e =(A,B,C)
µi,s,s,s+1 (A, D) ≡
y:ys,s,s+1 =(A,D)
αi (y),
There are O(PB n3 + PU ni ) such variables for each sentence of length ni , instead of i exponentially many αi variables. We can now express the objective function in terms of the marginals. Using these variables, the ﬁrst set of terms in the objective becomes: αi (y) i (y) =
i,y i,y
αi (y)
c∈C (i)
i,c (yc )
=
i,c∈C (i) ,yc
µi,c (yc )
i,c (yc ).
Similarly, the second set of terms (inside the 2norm) becomes: αi (y)∆fi (y) =
i,y i,y
αi (y)
c∈C (i)
∆fi,c (yc ) =
i,c∈C (i) ,yc
µi,c (yc )∆fi,c (yc ).
As in M3 Ns, we must characterize the set of marginals µ that corresponds to valid α. The constraints on µ are essentially based on the those that deﬁne Y in (9.19.4). In addition, we require that the marginals over the root nodes, µi,0,ni (y0,ni ), sums to 1 over the possible start symbols NS .
9.3. DISCRIMINATIVE PARSING MODELS
137
Putting the pieces together, the factored dual is:
2
max
i,c∈C (i)
µi,c (yc )
i,c (yc )
+C
i,c∈C (i)
µi,c (yc )∆fi,c (yc ) µi,c (yc ) ≥ 0; ∀i, ∀c ∈ C (i) ; ∀i, 0 ≤ s < e ≤ ni , ∀A ∈ N ;
(9.8)
s.t.
A∈NS
µi,0,ni (A) = 1, µi,s,e (A) =
s<m<e
∀i;
µi,s,m,e (A, B, C), µi,s ,s,e (B, A, C)
0≤s <s
A→B C∈PB
µi,s,e (A) = + µi,s,s+1 (A) = µi,s,s (D) =
B→A C∈PB
µi,s,e,e (B, C, A), ∀i, 0 ≤ s < e ≤ ni , ∀A ∈ N ; µi,s,s,s+1 (A, D), µi,s,s,s+1 (A, D), ∀i, 0 ≤ s < ni , ∀A ∈ N ; ∀i, 0 ≤ s < ni , ∀D ∈ T .
B→C A∈PB e<e ≤ni
A→D∈PU
A→D∈PU
The constraints on µ is necessary, since they must correspond to marginals of a distribution over trees. They are also sufﬁcient: Theorem 9.3.1 A set of marginals µi (y) satisfying the constraints in Eq. (9.8) corresponds to a valid distribution over the legal parse trees y ∈ Y (i) . A consistent distribution αi (y) is given by αi (y) = µi,0,ni (y0,ni )
0≤s≤m<e≤ni
µi,s,m,e (ys,m,e ) , µi,s,e (ys,e )
where 0/0 = 0 by convention. Proof sketch: The proof follows from insideoutside probability relations [Manning & Sch¨ tze, 1999]. The ﬁrst term is a valid distribution of starting symbols. Each u
µi,s,m,e (ys,m,e ) µi,s,e (ys,e )
term for m > s corresponds to a conditional distribution over binary productions (ys,e → ys,m ym,e ) that are guaranteed to sum to 1 over split points m and possible productions. Similarly, each
µi,s,s,s+1 (ys,s,s+1 ) µi,s,s+1 (ys,s+1 )
term for corresponds to a conditional distribution over
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CHAPTER 9. CONTEXT FREE GRAMMARS
unary productions (ys,s+1 → ys,s ) that are guaranteed to sum to 1 over possible productions. Hence, we have deﬁned a kind of PCFG (where production probabilities depend on the location of the symbol), which induces a valid distribution αi over trees. It straightforward to verify that this distribution has marginals µi .
9.4 Structured SMO for CFGs
We trained our maxmargin models using the Structured SMO algorithm with blockcoordinate descent adopted from graphical models (see Sec. 6.1). The CKY algorithm computes similar maxmarginals in the course of computing the best tree as does Viterbi in Markov networks. vi,c (yc ) = max [w fi (y) + i (y)],
y∼yc
αi,c (yc ) = max αi (y).
y∼yc
We also deﬁne vi,c (yc ) = maxyc =yc vi,c (yc ) = maxy∼yc [w fi (y) + i (y)]. Note that we do not explicitly represent αi (y), but we can reconstruct the maximumentropy one from the marginals µi as in Theorem 9.3.1. We again express the KKT conditions in terms of the maxmarginals for each span and span triple c ∈ C (i) and its values yc : αi,c (yc ) = 0 ⇒ vi,c (yc ) ≤ vi,c (yc ); αi,c (yc ) > 0 ⇒ vi,c (yc ) ≥ vi,c (yc ). (9.9)
The algorithm cycles through the training sentences, runs CKY to compute the maxmarginals and performs an SMO update on the violated constraints. We typically ﬁnd that 2040 iterations through the data are sufﬁcient for convergence in terms of the objective function improvements.
9.5 Experiments
We used the Penn English Treebank for all of our experiments. We report results here for each model and setting trained and tested on only the sentences of length ≤ 15 words. Aside
9.5. EXPERIMENTS
139
from the length restriction, we used the standard splits: sections 221 for training (9753 sentences), 22 for development (603 sentences), and 23 for ﬁnal testing (421 sentences). As a baseline, we trained a CNF transformation of the unlexicalized model of Klein and Manning [2003] on this data. The resulting grammar had 3975 nonterminal symbols and contained two kinds of productions: binary nonterminal rewrites and tagword rewrites. Unary rewrites were compiled into a single compound symbol, so for example a subjectgapped sentence would have label like S + VP. These symbols were expanded back into their source unary chain before parses were evaluated. The scores for the binary rewrites were estimated using unsmoothed relative frequency estimators. The tagging rewrites were estimated with a smoothed model of P (wt), also using the model from Klein and Manning [2003]. In particular, Table 9.2 shows the performance of this model (GENERATIVE): 87.99 F1 on the test set. For the
BASIC
maxmargin model, we used exactly the same set of allowed rewrites
(and therefore the same set of candidate parses) as in the generative case, but estimated their weights using the maxmargin formulation with a loss that counts the number of wrong spans. Tagword production weights were ﬁxed to be the log of the generative P (wt) model. That is, the only change between GENERATIVE and BASIC is the use of the discriminative maximummargin criterion in place of the generative maximum likelihood one for learning production weights. This change alone results in a small improvement (88.20 vs. 87.99 F1 ). On top of the basic model, we ﬁrst added lexical features of each span; this gave a
LEXICAL
model. For a span s, e of a sentence x, the base lexical features were:
◦ xs , the ﬁrst word in the span ◦ xs−1 , the preceding adjacent word ◦ xe−1 , the last word in the span ◦ xe , the following adjacent word ◦ xs−1 , xs ◦ xe−1 , xe ◦ xs+1 for spans of length 3
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CHAPTER 9. CONTEXT FREE GRAMMARS
Model GENERATIVE BASIC LEXICAL LEXICAL+AUX
P 87.70 87.51 88.15 89.74
R 88.06 88.44 88.62 90.22
F1 87.88 87.98 88.39 89.98
Table 9.1: Development set results of the various models when trained and tested on Penn treebank sentences of length ≤ 15.
Model GENERATIVE BASIC LEXICAL LEXICAL+AUX COLLINS 99
P 88.25 88.08 88.55 89.14 89.18
R F1 87.73 87.99 88.31 88.20 88.34 88.44 89.10 89.12 88.20 88.69
Table 9.2: Test set results of the various models when trained and tested on Penn treebank sentences of length ≤ 15.
These base features were conjoined with the span length for spans of length 3 and below, since short spans have highly distinct behaviors (see the examples below). The features are lexical in the sense than they allow speciﬁc words and word pairs to inﬂuence the parse scores, but are distinct from traditional lexical features in several ways. First, there is no notion of headword here, nor is there any modeling of wordtoword attachment. Rather, these features pick up on lexical trends in constituent boundaries, for example the trend that in the sentence The screen was a sea of red., the (length 2) span between the word was and the word of is unlikely to be a constituent. These nonhead lexical features capture a potentially very different source of constraint on tree structures than headargument pairs, one having to do more with linear syntactic preferences than lexical selection. Regardless of the relative merit of the two kinds of information, one clear advantage of the present approach is that inference in the resulting model remains cubic (as opposed to O(n5 )), since the dynamic program need not track items with distinguished headwords. With the addition of these features, the accuracy moved past the generative baseline, to 88.44.
The generative model incorrectly considers Libya today to be a base NP. last. in isolation. These features represent the preference of the word today for being the ﬁrst and last word in constituent spans of length 1. pairs of tags such as precedingﬁrst. Another kind of feature that can usefully be incorporated into the classiﬁcation process is the output of other.94 / F1 70.62 each. the resulting maxmargin model (LEXICAL + AUX) scored 89.1 In the LEXICAL model. Two features relevant to this trend are: (CONSTITUENT ∧ ﬁrstword = today ∧ length = 1) and (CONSTITUENT ∧ lastword = today ∧ length = 1). However. Note also that the features are conjoined with only one generic label class “constituent” rather than speciﬁc constituent types. To ensure that such features are as noisy on the training data as the test data. To situate these numbers with respect to other models. but also the following: the preceding. and following tag in the span. these features have quite large positive weights: 0. 2003]. and using their predictions as features on the other fold. giving a prediction feature for each span (these classiﬁers predicted only the presence or absence of a bracket over that span. The second feature was the output of a ﬂat classiﬁer which was trained to predict whether single spans. were constituents or not. one must take care that its reliability on the training not be vastly greater than its reliability on the test set. precedingfollowing. The auxiliary classiﬁers were then retrained on the entire training set. this analysis is counter to the trend of today to be a oneword constituent. Tag features on the test sets were taken from a pretagging of the sentence by the tagger described in [Toutanova et al. and their predictions used as features on the development and test sets. we split the training into two folds.5.. this model makes this parse decision correctly. its weight will be artiﬁcially (and detrimentally) high. Otherwise.While the ﬂat classiﬁer alone was quite poor (P 78. auxiliary classiﬁers. We used two such auxiliary classiﬁers. but made the learning phase faster. consider the sentence The Egyptian president said he would visit Libya today to resume the talks. 1 . this feature added little information. The ﬁrst feature was the prediction of the generative baseline.12 F1 . lastfollowing. ﬁrstlast. the parser in [Collins. not bracket labels). based on a bundle of features including the list above.77 / R 63. and the entire tag sequence. 1999]. ﬁrst. We then trained the auxiliary classiﬁers on each fold.which In this length 1 case.58). For this kind of feature.9. these are the same feature. As a result. EXPERIMENTS 141 As a concrete (and particularly clean) example of how these features can sway a decision.
2004]. 2000.69 over the same train/test conﬁguration. 2001. 2004. Unlike reranking methods. CONTEXT FREE GRAMMARS is generative. . Moreover. 2002. Clark & Curran.. where variants of the insideoutside algorithm can be used to efﬁciently calculate gradients of the loglikelihood function.142 CHAPTER 9. despite the exponential number of trees represented by the parse forest. Shen et al. and intricately smoothed scores 88. an initial parser is used to generate a number of candidate parses. reranking and dynamic programming approaches. Clark & Curran. lexicalized. 2003]. 9. in the work of Collins [2000]. A discriminative model is then used to choose between these candidates. For example. Collins. 41% of the correct parses were not in the candidate pool of ∼30best parses. 2002.. Kaplan et al. several approaches [Johnson. Geman & Johnson. 2004] are based on conditional loglinear (maximum entropy) models. our method incorporates an articulated loss function which penalizes larger tree discrepancies more severely than smaller ones. Unlike previous dynamic programming approaches. The method we presented has several compelling advantages. For example. 1999. This distinction can be very signiﬁcant.6 Related work A number of recent papers have considered discriminative approaches for natural language parsing [Johnson et al. Geman & Johnson.. 2000. Broadly speaking. 2001. the structured SMO we use requires only the calculation of Viterbi trees. Johnson. 2002. which consider only a prepruned selection of “good” parses. 1999. Collins. these approaches fall into two categories. the decoding and parameter estimation problems can be solved using dynamic programming algorithms. 2004. In reranking methods [Johnson et al. Given sufﬁciently “local” features. a large number of candidate parse trees are represented compactly in a parse tree forest or chart. rather than expectations over all trees (for example using the insideoutside algorithm). 2004. Miyao & Tsujii. our method is an endtoend discriminative model over the full space of parses. 2002. Collins.. Miyao & Tsujii. which were based on maximum entropy estimation. In dynamic programming methods.. as the set of nbest parses often does not contain the true parse. Kaplan et al.
. 2040 iterations were generally required for convergence (except the iterations.7. and the current feature set allows limited lexicalization in cubic time.7 Conclusion We have presented a maximummargin approach to parsing. This tradeoff between the complexity. Generative approaches are vastly cheaper to train. which means parsing the training set (usually many times). At training time.) BASIC model. On the other hand. while still decomposing in a way that exploits the shared substructure of parse trees in the standard way. In our experiments. which took about 100 9. CONCLUSION 143 This allows a range of optimizations that prune the space of parses (without making approximations) not possible for maximum likelihood approaches which must extract basis function expectations from the entire set of parses. since they must only collect counts from the training set. the maxmargin approach does have the potential to incorporate many new kinds of features over the input. which allows a discriminative SVMlike objective to be applied to the parsing problem. since they all involve iteratively checking current model performance on the training set. discriminative methods are inherently expensive. accuracy and efﬁciency of a parsing model is an important area of future research. Our framework permits the use of a rich variety of input features. unlike other lexicalized models (including the Collins model which it outperforms in the present limited experiments).9. It is worth considering the cost of this kind of method.
In this chapter. quadratic program. We use kernels to efﬁciently learn very rich (infact. convex. we focus on a more complex problem of nonbipartite matchings.Chapter 10 Matchings We address the problem of learning to match: given a set of input graphs and corresponding matchings. We provide some background on this problem. Throughout this chapter. 4. to ﬁnd marker correspondences in vision problems. Bipartite matchings are used in many ﬁelds. but nonbipartite matchings can be used for many other tasks. to identify functional genetic analogues in different organisms. 144 . We exploit combinatorial properties of the perfect matching problem to deﬁne a compact. to map words of a sentence in one language to another. disulﬁde connectivity prediction. showing that our framework achieves stateoftheart performance on the task. inﬁnitedimensional) models and present experiments on standard protein databases. we use the problem of disulﬁde connectivity prediction as an example. Recently proposed models have formulated this prediction task as a maximum weight perfect matching problem in a graph containing cysteines as nodes with edge weights measuring the attraction strength of the potential bridges. ﬁnd a parameterized edge scoring function such that the correct matchings have the highest score. for example. Identifying disulﬁde bridges formed by cysteine residues is critical in determining the structure of proteins. We motivate this problem using an application in computational biology. We have shown a compact maxmargin formulation for bipartite matchings in Ch.
2003. Vullo & Frasconi. Klepeis & Floudas. 1994]. They do so mostly by imposing strict structural constraints due to the resulting links between distant regions of the protein sequence [Harrison & Sternberg. which may or may not participate in disulﬁde bonds. Thus. 2001. etc. secondary structure or solvent accessibility information. as well as the protein datasets. the development of efﬁcient. We parameterize the this attraction strength via a linear combination of features. We thank Pierre Baldi and Jianlin Cheng for introducing us to the problem of disulﬁde connectivity prediction and providing us with preliminary draft of their paper and results of their model.10.. the task of predicting the connectivity pattern is typically decomposed into two subproblems: predicting the bonding state of each cysteine in the sequence. and predicting the exact connectivity among bonded cysteines. since the disulﬁde connectivity pattern imposes structure constraints. 1989].. DISULFIDE CONNECTIVITY PREDICTION 145 10. Fariselli et al. 2001]. 2004]. 2004. Recently. scalable and accurate methods for the prediction of disulﬁde bonds has numerous practical applications. and each edge represents the “attraction strength” between the cysteines it connects [Fariselli & Casadio. which can include the protein sequence around the two residues.1 Disulﬁde connectivity prediction Proteins containing cysteine residues form intrachain covalent bonds known as disulﬁde bridges. Alternatively. there are methods [Baldi et al. 1 . there has been increased interest in applying computational techniques to the task of predicting the intrachain disulﬁde connectivity [Fariselli & Casadio. 2004] that predict the connectivity pattern without knowing the bonding state of each cysteine1 . We predict the connectivity pattern by ﬁnding the maximum weighted matching in a graph in which each vertex represents a cysteine residue.. 2002. Since a sequence may contain any number of cysteine residues.. Furthermore. Such bonds are a very important feature of protein structure since they enhance conformational stability by reducing the number of conﬁgurational states and decreasing the entropic cost of folding a protein into its native state [Matsumura et al. Baldi et al. evolutionary information in the form of multiple alignment proﬁles. it can be used to reduce the search space in both protein folding prediction as well as protein 3D structure prediction. Knowledge of the exact disulﬁde bonding pattern in a protein provides information about protein structure and possibly its function and evolution.1.
MATCHINGS 10. we seek a function h : X → Y that maps inputs x ∈ X to output matchings y ∈ Y. but very little needs to be changed to handle sparse graphs. y(i) )}m of input graphs and i=1 output matchings. For simplicity.2) . In a perfect matching. in fact. each node is connected to at most one other node. The space of matchings Y is very large. given a protein sequence. and summing contact potentials for pairs of residues.1) For disulﬁde connectivity prediction. superexponential in 2 ni ). We consider a simple but very general class of attraction scoring functions deﬁned by a weighted combination of features or basis functions: sjk (x) = d wd fd (xjk ) = w f (xjk ). If example i has Li nodes. the number of possible perfect matchings is (2ni )! 2ni ni ! (i) (which is Ω(( ni )ni ). then for complete graphs with even number of vertices Li . We represent each possible edge between nodes j and k (j < k) in example i using a binary variable yjk . Their model assigns an attraction strength sjk (x) to each pair of cysteines. Let ni = Li /2.2 Learning to match Formally. each node is connected exactly one other node. 15 potential bonds (edges) and 15 possible perfect matchings. calculated by assuming that all residues in the local neighborhoods of the two cysteines make contact. However.146 CHAPTER 10. (10. for example. Our hypothesis class is maximum weight matchings: hs (x) = arg max y∈Y jk sjk (x)yjk . The training data consists of m examples S = {(x(i) . we assume complete graphs. 1ANS protein in Fig. For example. this model was used by Fariselli and Casadio [2001]. 10.1 has 6 cysteines (nodes). (10. we construct a complete graph where each node corresponds to a cysteine. Y has interesting and complex combinatorial structure which we exploit to learn h efﬁciently. X is the space of protein sequences and Y is the space of matchings of their cysteines. For example. then there are Li (Li − 1)/2 edge variables. We assume that the input x deﬁnes the space of possible matchings using some deterministic procedure. superexponential in the number of nodes in a graph. so y(i) is a binary vector of dimension Li (Li − 1)/2. In nonperfect matchings.
4).4) The number of constraints in this formulation is superexponential in the number of nodes in each example. is: min jk w f (xjk )yjk . 10.t. ∀y ∈ Y (i) . (10. for the model: hw (x) = arg max y∈Y jk w f (xjk )yjk . In the following sections we present two maxmargin formulations. and then with a polynomial one (Sec. ﬁrst with an exponential set of constraints (Sec.3).10. We assume that the user provides the basis functions. and graph of potential disulﬁde bonds. 3D structure. 2 (10.2. 10.3) Below. y) ≡ matchings for each example i. y). the basis functions can represent arbitrary information about the two cysteine neighborhoods: the identity of the residues at speciﬁc positions around the two cysteines.1: PDB protein 1ANS: amino acid sequence. or the predicted secondary structure in the neighborhood of each cysteine. ∀i. For example. The naive formulation of the maxmargin estimation. fd (xjk ) is a realvalued basis function and wd ∈ IR. and w fi (y) ≡ w f (x(i) . where xjk is the portion of the input x that directly relates to nodes j and k. w fi (y(i) ) ≥ w fi (y) + i (y). we will abbreviate w f (x. . LEARNING TO MATCH 147 RSCCPCYWGGCPWGQNCYPEGCSGPKV 1 2 3 4 5 6 2 3 1 4 5 6 Figure 10. Actual disulﬁde connectivity is shown in yellow in the 3D model and the graph of potential bonds. which enumerates all perfect 1 w2 s. and that our goal is to learn the weights w.
these constraints are changed to µi. k (i) (i) (10. 1965]. max jk (i) (i) (i) µi.jk = 1 to ensure exactly one bond. the maximum weight matching where edge jk has weight w f (xjk )+(1 −2yjk ) (plus the constant 1 y(i) ) gives the value of maxy∈Y (i) [w fi (y) + i (y)].148 CHAPTER 10. Lawler. The subset constraints (in the last line of Eq. 2 V ⊆ {1. 1 ≤ j < k ≤ Li . 2003]. The constraints k µi.5) The key to solving this problem efﬁciently is the lossaugmented inference maxy∈Y (i) [w fi (y) + i (y)]. 2 y∈Y (i) (10. we have a single max constraint for each i: min 1 w2 s. 1976]. MATCHINGS 10. the Hamming distance between y(i) and y can be written as (1 − y) y(i) + (1 − y(i) ) y = 1 y(i) + (1 − 2y(i) ) y. This problem can be solved in O(L3 ) time [Gabow. (10.t.jk ≥ 0. 1973. Under the assumption of Hamming distance loss (or any loss function that can be written as a sum of terms corresponding to edges). 4.6)) ensure that solutions to the LP are integral [Edmonds.jk instead of binary variables yjk . 1 ≤ j ≤ Li .jk ≤ 1 require that the number of bonds incident on a node is less k or equal to one. this maximization is equivalent (up to a constant term) to a maximum weighted matching problem. . Li }.6) µi. For perfect matchings. ∀i.3 Minmax formulation Using the minmax formulation from Ch.k∈V 1 µi. Note that since the y variables are binary. . It is an open problem to derive a polynomial sized LP formulation for perfect matchings [Schrijver. where we introduce continuous variables µi. Hence. w fi (y(i) ) ≥ max [w fi (y) + i (y)]. s. but this number is asymptotically smaller than the number of possible matchings . It can also be solved as a linear program. j.jk ≤ (V  − 1). . Note that we have an exponential number of constraints (O(2(Li −1) )).jk [w f (xjk ) + (1 − 2yjk )] µi.jk ≤ 1. V  ≥ 3 and odd. .t. .
Note that the dependence on w is linear and occurs only in the objective of the LP.3. (10. (10.t. λi ≥ 0. The dual of the LP in Eq. µi is a vector of length Li (Li − 1)/2 indexed by bond jk.6) is min λi bi s. ∀i.6): max [w fi (y) + i (y)] = di + max µi [Fi w + ci ]. respectively. ∀i. The parameter C allows the user to trade off violations of the constraints with ﬁt to the . MINMAX FORMULATION 149 We can write the lossaugmented inference problem in terms of the LP in Eq.9) w fi (y ) + ξi ≥ di + λi bi . 1 w2 + C 2 (i) ξi i (10. Fi is a matrix of basis function coefﬁcients such that the component jk of the vector Fi w is w f (xjk ) and ci = (1 − 2y(i) ).7) (i) We plug it into Eq. Ai µi ≤bi µi ≥0 y∈Y (i) where: di = 1 y(i) . Ai and bi are the appropriate constraint coefﬁcient matrix and right hand side vector. ∀i. (10. ∀i. λi ≥ 0. ∀i. Ai λi ≥ Fi w + ci . (10.5) and combine the minimization over λ with minimization over w.8) In case that our basis functions are not rich enough to predict the training data perfectly.10. ξi ≥ 0. Ai λi ≥ Fi w + ci .t. ∀i.t. λi ≥ 0. 1 w2 2 w fi (y(i) ) ≥ di + λi bi . (10. Ai λi ≥ Fi w + ci . ∀i. min s. we can introduce a slack variable ξi for each example i to allow violations of the constraints and minimize the sum of the violations: min s.
In an alternating cycle/path in G with respect to M . we can focus on ﬁnding a compact certiﬁcate of optimality that guarantees that y(i) = arg maxy [w fi (y) + i (y)].4. 10. Theorem 10. 1965] A perfect matching M is a maximum weight perfect matching if and only if there are no augmenting alternating cycles. An alternating cycle is augmenting with respect to M if the score of the edges in the matching M is smaller that the score of the edges not in the matching M .2: Log of the number of QP constraints (yaxis) vs. albeit with an exponential number of constraints. Let M be a perfect matching for a complete undirected graph G = (V. We consider perfect matchings and then provide a reduction for the nonperfect case. we develop an equivalent polynomial size formulation.150 CHAPTER 10. E). number of bonds (xaxis) in the three formulations (perfect matching enumeration.1 [Edmonds. data. the edges alternate between those that belong to M and those that do not.4 Certiﬁcate formulation Rather than solving the lossaugmented inference problem explicitly. minmax and certiﬁcate). . Our formulation is a linearlyconstrained quadratic program. In the next section. MATCHINGS 30 Perfect Matchings 25 Minmax Certificate 20 LogNumber of Constraints 15 10 5 0 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Number of Bonds Figure 10.
The length of the path is s(C) = s1. denote the length of the shortest distance alternating path from r to j. / (Only if) Suppose a distance function {de } satisﬁes the constraints in Eq. the edge (j. kj ∈ M . (10. Then let d0 and d1 be the length of those paths. j + 1) is in M . (1. we can rule out such cycles by considering shortest paths. k j sjk ≥ d1 − d0 .10) Theorem 10. For each odd j.4. j j k k so the constraint is satisﬁed. We begin by negating the score of those edges not in M . We renumber the nodes such that the cycle passes through nodes 1. 1}. Similarly for jk. so simply enumerating all of them will not do. In the discussion below we assume that each edge score sjk has been modiﬁed this way. k j sjk ≥ d0 − d1 . Pick an arbitrary root node r. Conj sider an alternating cycle C. the shortest path to j ending with an edge not in M plus the edge jk (or kj) is an alternating path to k ending with an edge in M . An alternating cycle is augmenting if and only if its length is negative. j k sjk ≥ d1 − d0 . j k ∀ jk ∈ M . This path is longer or same length as the shortest path to k ending with an edge in M : sjk + d0 ≥ d1 (or skj + d0 ≥ d1 ).j+1 . j e ∈ {0. (If) Suppose there are no augmenting alternating cycles. Let de .2 There exists a distance function {de } satisfying the constraints in j Eq. 0 otherwise. The following constraints capture this distance function.4.l + l−1 j=1 sj. . We also refer to the score sjk as the length of the edge jk.10) if and only if no augmenting alternating cycles exist. where e = 1 if the last edge of the path is in M . . / ∀ jk ∈ M. 2). l and the ﬁrst edge. sjk ≥ d0 − d1 . 2. Instead. A condition ruling out negative length alternating cycles can be stated succinctly using a kind of distance function. the two shortest paths to j (one ending with M edge and one not) contain no cycles. set d0 = d1 = 0). . For j j+1 . Since any alternating paths from r to j can be shortened (or left the same length) by removing the cycles they contain. is in M . Then for j j r r any jk (or kj) in M . (10. These shortest distances are welldeﬁned if and only if there are no negative alternating cycles.10). CERTIFICATE FORMULATION 151 The number of alternating cycles is exponential in the number of vertices. (10. with j ∈ V .10. so sj. .j+1 ≥ d1 − d0 . Proof. for all j (for j = r.
1 w2 2 H i w + G i di ≥ q i . Finally. We create a new graph by making a copy of the nodes and the edges and adding edges between each node and the corresponding node in the copy. (10. we have: 1 l l−1 l−1 s(C) ≥ d0 1 − d1 l + j=1. we can introduce a slack variable vector ξi to allow violations of the constraints. 2003]. (i) (i) (i) Once again. We deﬁne f (xjk ) ≡ 0 for edges between the original and the copy. (1. . j+1 j j=2.even Hence all alternating cycles have nonnegative length. the edge (j. Then the following joint convex program in w and d computes the maxmargin parameters: min s. minmax and certiﬁcate) is shown in Fig.odd [d1 j+1 − d0 ] j + [d0 − d1 ] = 0. The case of nonperfect matchings can be handled by a reduction to perfect matchings as follows [Schrijver. Hi and Gi be matrices j of coefﬁcients and qi be a vector such that Hi w + Gi di ≥ qi represents the constraints in Eq. 10. so sj. The xaxis is the number of edges in the matching (number of nodes divided by two). so s1.l ≥ d0 − d1 .j+1 ≥ d0 − d1 . l).t. MATCHINGS even j. The comparison between the lognumber of constraints for our three equivalent QP formulations (enumeration of all perfect matchings. (10. We extend the matching by replicating its edges in the copy and for each unmatched node. In our learning formulation we have the lossaugmented edge weights sjk = (2yjk − 1)(w f (xjk )+1−2yjk ). Let di be a vector of distance variables de .11) ∀i.10) for example i. the last edge. Perfect matchings in this graph projected onto the original graph correspond to nonperfect matchings in the original graph.152 CHAPTER 10. j + 1) is not in M . Summing the edges.2. j+1 j is not in M . introduce an edge to its copy. in case that our basis functions are not rich enough to predict the training data perfectly.
5 Kernels Instead of directly optimizing the primal problem in Eq. we can apply the kernel trick and let f (xkl ) f (xmn ) = K(xkl . (10. The primal and dual solutions are related by: w= i jk (Cyjk − αjk )f (xjk ) (i) (i) (i) (10.8). and αjk is the dual variable associated with the features corresponding to the edge jk. Each training example i has Li (Li − 1)/2 dual variables. (10. The only occurrence of feature vectors is in the expansion of the squarednorm term in the objective: Cyjk − αjk f (xkl ) f (x(j) ) Cyjk − αjk mn i. ∀i. ∀i.t.13) Therefore.5. xmn ). The dual quadratic optimization problem has the form: 2 (i) max i ci α(i) − 1 2 Cyjk − αjk f (xjk ) i jk∈E (i) (i) (i) (i) (10. Ai α(i) ≤ Cbi . we can work with its dual.11) is similarly kernelizable.14) can be used to compute the attraction strength sjk (x) in a kernelized manner at prediction time. The polynomialsized representation in Eq.10.14) Eq. we can efﬁciently map the original features f (xjk ) to a highdimensional space.j kl∈E (i) mn∈E (j) (i) (j) (i) (j) (i) (i) (i) (j) (j) (10. Thus. . α(i) ≥ 0.12) s. KERNELS 153 10. (10. Let α(i) be the vector of dual variables for example i.
After redundance reduction there are a total of 1018 sequences. 1981] (with the BLOSUM65 scoring matrix. Even though our method is applicable to both sequences with a high number of bonds or sequences in which the bonding state of cysteine residues is unknown. The DIPRO2 dataset2 was compiled and made publicly available by Baldi et al. 2004.. 2004..154 CHAPTER 10. [2004]. The same dataset was used in earlier work [Baldi et al. We split SP39 into 4 different subsets. The DIPRO2 contains 567 such sequences. SP39 contains 446 sequences containing between 2 and 5 bonds. 2001]. MATCHINGS 10. Vullo & Frasconi. and has a total of 726 proteins. Fariselli & Casadio. gap penalty 12 and gap extension 4). In addition. with the constraint that proteins no proteins with sequence similarity of more than 30% belong to different subsets. Sequence similarity was derived using an allagainstall rigorous SmithWaterman local pairwise alignment [Smith & Waterman.. which contain intrachain disulﬁde bonds.ics. 2004.html . 2000]. It consists of all proteins from PDB [Berman et al. In order to avoid biases during testing.uci. Baldi et al. It contains only sequences with experimentally veriﬁed disulﬁde bridges. so we are able to perform learning on over 90% of all proteins.6 Experiments We assess the performance of our method on two datasets containing sequences with experimentally veriﬁed bonding patterns: DIPRO2 and SP39. The SP39 dataset is extracted from the SwissProt database of proteins [Bairoch & Apweiler. we report results for the case where the bonding state is known. and only 53 sequences with a higher number of bonds. 2004]. 2000]. the sequences are annotated with secondary structure and solvent accessibility information derived from the DSSP database [Kabsch & Sander. and we have followed the same procedure for extracting sequences from the database. There are 430 proteins with 2 and 3 bonds and 137 with 4 and 5 bonds. we adopt the same dataset splitting procedure as the one used in previous work [Fariselli & Casadio.edu/bridge. release 39. 1983]. Pairs of chains whose alignment is less than 30 residues were considered unrelated. and the number of bonds is between 2 and 5 (since the case of 1 bond is trivial). 2001. The DIPRO2 dataset was split similarly into 5 folds. as of May 2004. Vullo & Frasconi. although the procedure had less effect due to the redundance reduction applied by the authors of the 2 http://contact.
EXPERIMENTS 155 dataset. xlm ) = exp( xjk −xlm γ 2 ). The ﬁrst model. Training time took around 70 minutes for 450 examples. The ﬁnal set of features for each {j. counting from the left end of the window. augmented with the linear distance between the cysteine residues. For each pair of candidate cysteines {j.10. . 10. The features we experimented with were all based on the local regions around candidate cysteine pairs. As in Baldi et al. Below. using a sequential optimization procedure which solves QP subproblems associated with blocks of training examples. 1997].. the actual sequence is expanded to a 20 × n binary vector. with γ ∈ [0. We are currently working on an implementation of the certiﬁcate formulation Sec. we extract the aminoacid sequence in windows of size n centered at j and k. k} pair of cysteines is simply the two local windows concatenated together. the input at each position of a local window is the frequency of occurrence of each of the 20 aminoacids in the alignments. we use multiple sequence alignment proﬁle information. Models The experimental results we report use the dual formulation of Sec. uses the features described above: for each window. [2004]. 10. the 21st entry in the vector represents whether or not the aminoacid Alanine occurs at position 2 of the local window. we augment the features of each model with the number of residues between j and k. we describe several models we used. except that instead of using the actual protein sequence. it is more efﬁcient due to the low constants in the exponential problem size. SEQUENCE.4 to handle longer sequences and nonperfect matchings (when bonding state is unknown). where j < k.1. Thus. in which the entries denote whether or not a particular amino acid occurs at the particular position.6.5 and an RBF kernel K(xjk . For example. The second model. We use the exponential sized represen tation of Sec.3 since for the case of proteins containing between two and ﬁve bonds. is the same as SEQUENCE. Multiple alignments were computed by running PSIBLAST using default settings to align the sequence with all sequences in the NR database [Altschul et al. 10]. 10. k}. The models below use windows of size n = 9. PROFILE. We used commercial QP software (CPLEX) to train our models.
PROFILESS.70 / 0.70 / 0.156 CHAPTER 10. which represent the current topperforming system.62 / 0. MATCHINGS K 2 3 4 5 PROFILE 0.74 / 0. with similar or better levels of precision for all bond numbers. the evolutionary information captured by the aminoacid alignment frequencies plays an important role in increasing the performance of the algorithm.73 / 0.75 / 0.79 / 0. (a) Performance of PROFILE model on SP39 vs.75 0.69 0. The third model.48 0. [2004]. As Table 10.17 (b) PROFILESS 0.24 0.60 / 0.73 0. the best performance is in bold.43 / 0. whereas precision measures the number of correctly predicted bonds as a fraction of the total number of possible bonds.16 (a) DAGRNN 0.27 0. (b) Performance of SEQUENCE.11 K 2 3 4 5 SEQUENCE 0.06 PROFILE 0.1: Numbers indicate Precision / Accuracy. so we augment each local window of size n with an additional length 8 × n binary vector.1(b).62 / 0.67 / 0.52 0. augments the PROFILE model with secondary structure and solventaccessibility information.44 / 0. In another experiment. 2004] which represent the best currently published results.59 / 0. Results and discussion We evaluate our algorithm using two metrics: accuracy and precision.27 Table 10. The ﬁrst set of experiments compares our model to preliminary results reported in Baldi et al.21 0.61 / 0. and slightly lower accuracies for the case of 2 and 3 bonds. preliminary results of the DAGRNN model [Baldi et al.59 0. We perform 4fold crossvalidation on SP39 in order to replicate their setup. As we can see from Table 10. as well as a length n binary vector representing the solvent accessibility at each position.51 0. the PROFILE model achieves comparable results. PROFILE.79 0. The DSSP program produces 8 types of secondary structure.44 0. In each row. we show the performance gained by using multiple alignment information by comparing the results of the SEQUENCE model with the PROFILE.43 / 0.44 / 0..41 / 0.74 / 0. PROFILESS models on the DIPRO2 dataset. The accuracy measure counts how many full connectivity patterns were predicted correctly.1 shows.56 0. .46 / 0.29 / 0.70 0.74 0.
∞.1(b) shows that the gains are signiﬁcant. The trend is more pronounced for sequences with 4 and 5 bonds because they are sparsely distributed in the dataset. both accuracy and precision increase as the amount of data grows. RELATED WORK 157 2 and 3 bonds 100% 90% 80% 70% 60% 50% 40% 30% 20% 100 150 200 250 300 Training Set Size 350 Accuracy (2 Bonds) Precision (3 Bonds) Accuracy (3 Bonds) 4 and 5 bonds 85% 75% 65% 55% 45% 35% 25% 15% 5% Precision (4 Bonds) Accuracy (4 Bonds) Precision (5 Bonds) Accuracy (5 Bonds) 400 450 100 150 200 250 300 Training Set Size 350 400 450 (a) (b) Figure 10.3 shows the performance of the PROFILE model as training set size grows. 4. We can see that for sequences of all bond numbers. Table 10. This highlights the importance of developing even richer features.7 Related work The problem of inverse perfect matching has been studied by Liu and Zhang [2003] in the inverse combinatorial optimization framework we describe in Sec.7. especially for sequences with 3 and 4 bonds.10. which is not a maximum one with respect to w0 . perhaps through more complex kernels. 10. ﬁnd a new weight vector w that makes M optimal and minimizes w0 − wp for p = 1. since it validates the applicability of our algorithm as the availability of highquality disulﬁde bridge annotations increases with time. Fig. The same phenomenon is observed by Vullo and Frasconi [2004] in their comparison of sequence and proﬁlebased models. Such behavior is very promising.3: Performance of PROFILE model as training set size changes for proteins with (a) 2 and 3 bonds (b) 4 and 5 bonds. They do not provide a compact optimization problem for this related but . 10. As a ﬁnal experiment.3: Given a set of nominal weights w0 and a perfect matching M . we examine the role that secondary structure and solventaccessibility information plays in the model PROFILESS.
The method is computationally limited to sequences of 2 to 5 bonds. The problem of disulﬁde bond prediction ﬁrst received comprehensive computational treatment in Fariselli and Casadio [2001]. 1998] to score candidate patterns. the authors switch to using a neural network for learning edge weights and achieve better performance. the approach can be used to predict disulﬁde bonds with no knowledge of bonding state. It also uses multiple alignment proﬁle information and demonstrates its beneﬁts over sequence information. especially for the case of 2 and 3 disulﬁde bonds. Residuetoresidue contacts (which include disulphide bridges) are predicted by solving a series of constrained integer programming problems. MATCHINGS different task. In Baldi et al. At prediction time the pattern scores are used to perform an exhaustive search on the space of all matchings. The method in Vullo and Frasconi [2004] takes a different approach to the problem. [2004]. It scores candidate connectivity patterns according to their similarity with respect to the correct pattern. Their method performs better than the one in Vullo and Frasconi [2004] and is also the only one which can cope with sequences with more than 5 bonds. Their method is only applicable to the case when bonding state is known.. but the results are not comparable with those in other publications. SVMs. The problem of learning the edge weights was addressed using a simulated annealing procedure. A different approach to predicting disulﬁde bridges is reported in Klepeis and Floudas [2003]. the authors achieve the current stateoftheart performance on the task. and HMMs . In Fariselli et al. [2002]. where bond prediction occurs as part of predicting βsheet topology in proteins. relying instead on the ellipsoid method with constraint generation. and uses a recursive neural network architecture [Frasconi et al. Interestingly. 2003] to predict bonding probabilities between cysteine pairs.158 CHAPTER 10. They modeled the prediction problem as ﬁnding a perfect matching in a weighted graph where vertices represent bonded cysteine residues. and edge weights correspond to attraction strength. It also improves on previous methods by not assuming knowledge of bonding state. Their method uses Directed Acyclic Graph Recursive Neural Networks [Baldi & Pollastri. The task of predicting whether or not a cysteine is bonded has also been addressed using a variety of machine learning techniques including neural networks. The prediction problem is solved using a weighted graph matching based on these probabilities.
2000. In the future. While we have developed the framework to handle that task. and one which develops a certiﬁcate of matching optimality for a compact polynomialsized representation. Furthermore. requiring an exponential number of constraints. Our experimental results show that the method can achieve performance comparable to current topperforming systems. will affect performance. 1999. we derive a compact convex quadratic program for the problem of learning to match. 2003] Currently the top performing systems have accuracies around 85%.. formulated as a weighted matching problem. such as convolution kernels for protein sequences. Ceroni et al. Frasconi et al. Our approach learns a parameterized scoring function that reproduces the observed matchings in a training set. We present two formulations: one which is based on a linear programming approach to matching. 2002. Martelli et al. which have already addressed the more challenging setting. the use of kernels makes it easy to incorporate rich sets of features such as secondary structure information.. CONCLUSION 159 [Fariselli et al. or extended local neighborhoods of the protein sequence.8. it will be worthwhile to examine how other kernels. 2004]. We apply our framework to the task of disulﬁde connectivity prediction..10.. 10. We also hope to explore the more challenging problem of disulﬁde connectivity prediction when the bonding state of cysteines is unknown. Fiser & Simon. it remains to experimentally determine how well the method performs. . 2002.8 Conclusion In this chapter. especially in comparison to existing methods [Baldi et al..
a novel clustering method that has recently enjoyed signiﬁcant attention from the theoretical computer science community [Bansal et al. Learning to cluster considers the problem of ﬁnding desirable clusterings on new data. and minimize the weight of intercluster edges. 2003. several algorithms based on linear programming and positivesemideﬁnite 160 . Recently. For example. Emanuel & Fiat. These properties make correlation clustering a promising approach to many clustering problems. in machine learning.. encouraging those vertices to belong to a common cluster. Images can be segmented by hue or object boundaries. 2003]. both of these parameters are effectively chosen to be the best possible by the problem deﬁnition. Unlike most clustering formulations. it has been successfully applied to coreference resolution for proper nouns [McCallum & Wellner. negative weights encourage the vertices to belong to different clusters. Positive edge weights represent correlations between vertices.Chapter 11 Correlation clustering Data can often be grouped in many different reasonable clusterings. 2003]. It is formulated as a vertex partitioning problem: Given a graph with realvalued edge scores (both positive and negative). one user may organize her email messages by project and time. given example desirable clusterings on training data. another by sender and topic. partition the vertices into clusters to maximize the score of intracluster edges. correlation clustering does not require the user to specify the number of clusters nor a distance threshold for clustering. there might be only one of these clusterings that is desirable. Demaine & Immorlica. For a given application. We focus on correlation clustering. 2002.
For notational convenience. which will be constrained to have the same value. We also introduce yjj variables.1. CLUSTERING FORMULATION 161 programming relaxations have been proposed to approximately solve this problem. that represent whether node j and k belong to the same cluster. (j < k). we can make it fully connected by adding appropriate edges jk with sjk = 0). [2002] consider two related problems: max y∈Y jk:sjk >0 sjk yjk − jk:sjk <0 sjk (1 − yjk ). Let Y be the space of assignments y that deﬁne legal partitions. In this chapter.1 Clustering formulation An instance of correlation clustering is speciﬁed by an undirected graph G = (V.11. sjk yjk . In . we minimize the disagreement: the weight of positive excluded edges minus the weight of negative included edges. In M AX AGREE. We formulate the approximate learning problem as a compact convex program with quadratic objective and linear or positivesemideﬁnite constraints. we introduce both yjk and ykj variables. 11. The best score is obviously achieved by including all the positive and excluding all the negative edges. Bansal et al. Experiments on synthetic and realworld data show the ability of the algorithm to learn an appropriate clustering metric for a variety of desired clusterings. We assume that the graph is fully connected (if it is not. E) with N nodes and edge score sjk for each jk in E. we employ these relaxations to derive a maxmargin formulation for learning the edge scores for correlation clustering from clustered training data. one for each edge jk. jk:sjk <0 (M AX AGREE) (M IN D IS AGREE) min y∈Y jk:sjk >0 sjk (1 − yjk ) − The motivation for the names of the two problems comes from separating the set of edges into positive weight edges and negative weight edges. but this will not generally produce a valid partition. In M IN D IS AGREE. we maximize the “agreement” of the partition with the positive/negative designations: the weight of the positive included edges minus the weight of negative excluded edges. and ﬁx them to have value 1 and set sjj = 0. We deﬁne binary variables yjk .
The optimal partition for the two problems is of course the same (if it is unique). s− = jk:sjk <0 sjk . With these deﬁnitions. Note that the constraints imply that yab = yba for any two nodes a and b. ∀j. Any symmetric. [2002] show that both of these problems are NPhard (but have different approximation hardness).1 Linear programming relaxation In order to insure that y deﬁnes a partition. k = . which we consider in the next sections. Then the value of M AX AGREE is s∗ − s− and the value of M IN D IS AGREE s+ − s∗ . ∀j. Bansal et al. 2003. (11. s. transitive binary relation induces a partition of the objects. To see this. we can express the M AX AGREE problem as an integer linear program (ignoring the constant −s− ): max jk sjk yjk yjk + ykl ≤ ylj + 1. 2003. let s∗ = max y∈Y sjk yjk . l. yjl + ykl ≤ yjk + 1. Emanuel & Fiat. Several approximation algorithms have been developed based on Linear and Semideﬁnite Programming [Charikar et al. l = b and j = b. yjj = 1.1. yjk + yjl ≤ ykl + 1. Demaine & Immorlica.1) The triangle inequality enforces transitivity: if j and k are in the same cluster (yjk = 1) and k and l are in the same cluster (ykl = 1). ∀j. it is sufﬁcient to enforce a kind of triangle inequality for each triple of nodes j < k < l: yjk + ykl ≤ yjl + 1. 1}.. CORRELATION CLUSTERING particular. (11. s+ = jk:sjk >0 sjk . M AX AGREE. consider the inequalities involving node a and b with j = a. k. 2003].2) yjk ∈ {0.162 CHAPTER 11. 11. k = b.t. k. The other two cases are similar. then j and l will be forced to be in this cluster (yjl = 1). We will concentrate on the maximization version.
(11. 1} in Eq.. k. we have µjk ≤ 1. consider any clustering solution.t. The score of the clustering . . yba + yaa ≤ yab + 1. If vertices j and k are in the same cluster. The LP solution.1. ∀j. vj vk = 0. l. µjk ≥ 0. Since yaa = ybb = 1. Charikar et al. µjj = 1. Choose a collection of orthogonal unit vectors {v1 . ∀j. if not. (11. µjj = 1. CLUSTERING FORMULATION 163 a. l = a: yab + ybb ≤ yba + 1. µjk + µkl ≤ µlj + 1. We are not guaranteed that this relaxation will produce integral solutions. then vj vk = 1. Every vertex j in the cluster is assigned the unit vector vj corresponding to the cluster it is in. sLP . . Let mat(µ) denote the variables µjk arranged into a matrix. we substituted the triangle inequalities by the semideﬁnite constraint. [2003] show that the integrality gap of this upper bound is at least 2/3: s∗ − s− 2 < .4) s. In effect.2 Semideﬁnite programming relaxation An alternative formulation [Charikar et al. ∀j. (11. . The LP relaxation is obtained by replacing the binary variables yjk ∈ {0. k.1. ∀j. ∀j. k. one for each cluster in the solution. To motivate this relaxation. and since µjj = 1 and µjk = µkj .3) Note that µjk ≤ 1 is implied since the triangle inequality with j = l gives µjk + µkj ≤ µjj + 1. µjk ≥ 0. . is an upper bound on the s∗ . max jk sjk µjk mat(µ) 0. LP − s− s 3 11.11.2) with continuous variables 0 ≤ µjk ≤ 1. vK }. 2003] is the SDP relaxation. we have yab = yba .
CORRELATION CLUSTERING solution can now be expressed in terms of the dot products vj vk . Speciﬁcally. We assume f (xjj ) = 0 so that sjj = 0.jk (0). they do not necessarily form a set of orthogonal vectors. For example. [2003] show that the integrality gap of this upper bound is at least 0. where xjk is a set of features associated with nodes j and k. f (xjk ) ∈ IRn . into a sum of edge losses i (y) i.4). w. Furthermore.2 Learning formulation The score for an edge is commonly derived from the characteristics of the pair of nodes. However. is also an upper bound on the s∗ and Charikar et al. sSDP − s− 11.82843: s∗ − s− ≤ 0. The SDP solution.82843.jk (1) − i.jk (yjk ) = jk yjk i. the Hamming loss counts the number of . features might be distances along different dimensions.164 CHAPTER 11. where i. we assume that the loss function decomposes over the edges.jk = i. while if one is clustering points in IRn . y) = jk yjk w f (xjk ).jk (1) + (1 − yjk ) i.jk . The vectors generating the inner products are unit vectors by the requirement µjj = 1.jk (0) = i (0) + jk yjk i. In document clustering.jk (yjk ): = jk i. which can be decomposed into a sum of outer products vj vj . the entries of fxjk might be the words shared by the documents j and k. The entries µjk correspond to inner products vj vk . we parameterize the score as a weighted combination of basis functions sjk = w f (xjk ). sSDP . In the SDP relaxation in Eq. Hence we write w f (x. (11. we have mat(µ) mat(µ) = j 0.
LEARNING FORMULATION 165 edges incorrectly cut or uncut by a partition.j for the identity on the diagonal.jk . where i. The dual of the LP based upper bound for example i is i (0)+ min jkl λi.t. (11.klj ] ≥ w f (xjk ) + zi. H i (y) = jk 1 jk = yjk ) = I(y jk (i) (i) yjk + jk (i) yjk (1 − 2yjk ) = (i) H i (0) + jk yjk i.jlj ] ≥ i.jkl for each triangle inequality and zi. ∀j.jk = 1 − 2yjk .jkl + j zi. (11.jk ].ljk − λi. (11. the loss augmented maximization is i (0) + max y∈Y jk yjk [w f (xjk ) + (i) i.4) as upper bounds on Eq. s. λi.jk . k. we introduced a dual variable λi.j + l [λi. (11. l [λi. Above.2.5). (11. Note the righthandside of the second set of inequalities follows from the assumption f (xjj ) = 0.jj .5) We can now use the LP relaxation in Eq. ∀j.j (i) i.3) and the SDP relaxation in Eq.jkl ≥ 0. l. .ljj − λi.11.jkl + λi.6) ∀j = k. With this assumption.jjl + λi. We use these upperbounds in the minmax formulation to achieve approximate maxmargin estimation.
j −λi. ∀j.jkl + j (i) f (xjk ) i.9) zi. y(i) ) + ξi ≥ i (0) + jkl (11.t.jkl + λi.jlj ] ≥ ∀i. we have: min s. zi.jj . the dual of the SDP based upper bound is i (0)+ min j zi. λi.t. ∀j.166 CHAPTER 11.jjl + λi.jk . ∀i.jj ≥ mat(λi ) 0. ∀i.8) ∀j = k.7) λi.ljj − λi.jj ≥ mat(λi ) i. 0.jk ≥ w f (xjk ) + zi.j − λi. ∀j = k. l. s. ∀j. we have: min s. ∀i. . (11.klj ] ≥ w l + ∀i. l. 1 w2 + C ξi 2 w f (x(i) . ∀i.jj (i) i. (i) i. ∀i. i.jkl ≥ 0.jk ≥ w f (xjk ) + zi.j . zi. y(i) ) + ξi ≥ i (0) + j (11. ∀i. [λi. k. Plugging the SDP dual into the minmax formulation. CORRELATION CLUSTERING Plugging this dual into the minmax formulation. ∀j. −λi. i.j . ∀j = k. 1 w2 + C ξi 2 w f (x(i) .jj .jk . k.ljk − λi.t.j − λi.jk . Similarly.j + l [λi. ∀j.
µi. . m). mat(µi ) µi. Therefore.jk 1 i. k. The dual of Eq. µjk + µkl ≤ µlj + 1. ∀i. and measures the similarity between the relation between the nodes of each pair.jk (yjk − µjk )f (xjk ). (11. we can use kernels K(xjk . ∀j.jk 1 i.jk − C 2 0.jk ∀i.t. k.7): max i. xlm ) to deﬁne the space of basis functions.jk − C 2 2 (i) (yjk i. ∀i. ∀j. l. ∀j. The dual objective can be expressed in terms of dotproducts f (xjk ) f (xlm ). (j.10) One important consequence of this relationship is that the edge parameters are all support vector expansions. Here we give the dual of Eq. DUAL FORMULATION AND KERNELS 167 11.jk ≥ 0. µi.jk ≥ 0. except that the linear transitivity constraints µjk + µkl ≤ µlj + 1. µi. 2 (i) (yjk i. ∀i.jk )f (xjk ) s. k. l are replaced by the corresponding mat(µi ) µi.jk µi. for example.jj = 1. (11.jk )f (xjk ) s. ∀i.jj = 1.jk − (i) µi. ∀i. ∀j. a polynomial kernel over their lengths and angle between them.3. If we are clustering points in Euclidian space.7) and Eq. k.t.jk 0: − (i) µi. k) and (l. (11. ∀j.9) is very similar. max i. This kernel looks at two pairs of nodes.3 Dual formulation and kernels The dual of Eq.11. (i) (i) (11. ∀i. ∀j. the kernel could be a function of the two segments corresponding to the pairs of points. The relation between the primal and dual solution is w = C i.9) provide some insight into the structure of the problem and enable efﬁcient use of kernels. (11.
email clustering and image segmentation. 1 http://www.4 Experiments We present experiments on a synthetic problem exploring the effect of irrelevant basis functions (features). We used a basis function for each dimension fd (xjk ) = e−(xj [d]−xk [d]) .1(b) illustrate the capability of our algorithm to learn to ignore irrelevant dimensions. Let xj denote each point and xj [d] denote the dth dimension of the point.1(a) shows the projection of a data sample onto the ﬁrst two dimensions and on two irrelevant dimensions. CORRELATION CLUSTERING 11. The noise is independently generated for each dimension.sri. from a mixture of Gaussians with same difference in means and variance as for the relevant dimension. where each mixture component corresponds to a cluster. Then we add noise components in D additional (irrelevant) dimensions. we explore on a synthetic example how our algorithm deals with irrelevant features. 11. 11. with an average of 34 folders.2 Email clustering We also test our approach on the task of clustering email into folders.1 Our dataset consisted of email from seven users (approximately 100 consecutive messages per user). The number of folders for each users varied from two to six.1 Irrelevant features In this section. The training and test data consists of a 100 samples from the model. This ﬁrst dimension is thus the relevant feature. The results in Fig. We gathered the data from the SRI CALO project.ai. In particular. plus an additional constant basis function. we generate data (100 points) from a mixture of two onedimensional Gaussians.168 CHAPTER 11.4. We are interested in the problem of learning to cluster emails. Figure 11. which the users had manually ﬁled into different folders.com/project/CALO .4. 2 11. and two real data sets. The comparison with kmeans is simply a baseline to illustrate the effect of the noise on the data. Random clustering will give an accuracy of 50%. The accuracy is the fraction of edges correctly predicted to be between/within cluster.
The basis functions f (xjk ) measured the similarity between the text of the messages. Learning to cluster is the solid line. One feature was used for each common word in the pair of emails (except words that appeared in more than half the messages. the similarity between the “From:” ﬁeld. subject and body ﬁelds. additional features captured the proportion of shared tokens for each email ﬁeld. Accuracy is the fraction of edges correctly predicted to be between/within cluster. and “Cc:” ﬁeld. Also. EXPERIMENTS 169 4 3 0. kmeans the dashed line. as well as importance of meaningful words versus common.11. Errorbars denote one standard deviation. including the from.75 0. to.85 0. The algorithm is therefore able to automatically learn the relative importance of certain email ﬁelds to ﬁling two messages together. we use each user as a training set in turn. averages are over 20 runs.95 test accuracy 0. Speciﬁcally. Cc.4. We then use the learned parameters to cluster the other users’ mail. “To:” ﬁeld.65 0. what score function sjk causes correlation clustering to give clusters similar to those that human users had chosen? To test our learning algorithm. irrelevant ones. We compare our method to the kmeans clustering algorithm using with the same word . (c) Performance on 2 cluster problem as function of the number of irrelevant noise dimensions.45 1 2 4 8 16 32 64 128 lcc kmeans 2 1 0 −1 −2 −3 −4 −4 4 −3 −2 −1 0 1 2 3 3 2 1 0 −1 −2 # noise dimensions −3 −2 −1 0 1 2 3 4 −3 −4 −4 (a) (b) Figure 11.55 0.1: (a) Projection onto ﬁrst two dimensions (top) and two noise dimensions (bottom). which were deemed “stop words” and omitted). learning the parameters from the partition of a single user’s mailbox into folders.
a standard metric in information retrieval [BaezaYates & RibeiroNeto. It is precisely this kind of variability in the similarity judgements that . 11. and one much ﬁner.3 0. We made this comparison somewhat easy for kmeans by giving it the correct number of clusters k. and took the best clustering out of ﬁve tries. We selected images from the Berkeley Image Segmentation Dataset [Martin et al. We performed a simple binary search on this additional bias weight parameter to ﬁnd the number of clusters comparable to k. Depending on the task at hand.2 show the average F 1 measure (harmonic mean of precision and recall.170 CHAPTER 11. we may prefer the ﬁrst over the second or viceversa. features. based on the hue and intensity. 11. We also informed our algorithm of the number of clusters by uniformly adding a positive weight to the edge weights to cause it to give the correct number of clusters.3 Image segmentation We also test our approach on the task of image segmentation.4. For example.4 0.2: Average Pair F1 measure for clustering user mailboxes.6 0. mostly based of overall hue.2 0.3(a) and (b) show two distinct segmentations: one very coarse.7 0. CORRELATION CLUSTERING 0..5 Pair F1 lcc kmeans 0.8 0. 11. Our algorithm signiﬁcantly outperforms kmeans on several users and does worse only for one of the users. The results in Fig. 2001] for which two users had signiﬁcantly different segmentations. 1999]) computed on the pairs of messages that belonged to the same cluster.1 0 1 2 3 4 User 5 6 7 Figure 11. Fig.
) There is a rich space of possible features we can use in our models: for each pair of regions. 11. as well as the distance in pixels between the bounding boxes and the area of the smaller of the two regions. All features were normalized to have zero mean and variance 1. we calculated the bounding box. In our experiments. which covered 8090% of the pixels. area and average color (averaging the pixels in the RGB space). we ﬁrst divided it contiguous regions of approximately the same color by running connected components on the pixels. distance. (We then use the learned metric to greedily assign the remaining small regions to the large adjoining regions.4. For each region. one using Fig. etc.3(a) and the other using Fig.3: Two segmentations by different users: training image with (a) coarse segmentation and (b) ﬁne segmentation.3(b) and .B channel). we want our algorithm to capture.11. 11. we used a fairly simple set of features that are very easy to compute. EXPERIMENTS 171 (a) (b) Figure 11. presence of edges between them. In order to segment the image. we can consider their shape. These regions are the objects that our algorithm learns to cluster. color distribution. We connected two adjacent pixels by an edge if their RGB value was the same at a coarse resolution (4 bits per each of the R. We trained two models. We then selected about a hundred largest regions. We then computed three distances (one for each HSV channel).G.
. 11.5 Related work The performance of most clustering algorithms depends critically on the distance metric that they are given for measuring the similarity or dissimilarity between different datapoints.4(a).4(b) and (c). we will instead seek to learn a good metric for the clustering algorithm. Recently. a number of algorithms have been proposed for automatically learning distance metrics as a preprocessing step for clustering [Xing et al. (b) segmentation based on coarse training data (c) segmentation based on ﬁne training data.4: Test image: (a) input. In contrast to algorithms that learn a metric independently of the algorithm that will be used to cluster the data. which is more efﬁcient than correlation clustering. 11. However the objective in the learning . instead of using an externallydeﬁned criterion for choosing the metric. respectively.. Thus. rocks and grass are segmented very coarsely based on hue in (b) while the segmentation in (c) is more detailed and sensitive to saturation and value of the colors. 2002. 2003]. for which we use LP or SDP formulations. Note that mountains. we describe a formulation that tightly integrates metric learning with the clustering algorithm. 11. An example of work in a similar vein is the algorithm for learning a distance metric for spectral clustering [Bach & Jordan. tuning one to the other in a joint optimization. 2003]. tested on the image in Fig. CORRELATION CLUSTERING (a) (b) (c) Figure 11.172 CHAPTER 11. The results are shown in Fig. The clustering algorithm essentially uses an eigenvector decomposition of an appropriate matrix derived from the pairwise afﬁnity matrix. BarHillel et al.
11. The main limitation of the correlation clustering is scalability: the number of constraints (V3 ) in the LP relaxation and the size of the positivesemideﬁnite constraint in the SDP relaxation. We showed results on a synthetic dataset..6. . On the theoretical side. and attempts to learn a good metric speciﬁcally for the clustering algorithm. It would be very interesting to explore constraint generation or similar approaches to speed up learning and inference.6 Conclusion We looked at correlation clustering. it would be interesting to work out a PAClike bound for generalization of the learned score metric. Our approach ties together the inference and learning algorithm. Experiments on the CALO email and image segmentation experiments show the potential of the algorithm on realworld data. showcasing robustness to noise dimensions. and how to learn the edge weights from example clusterings. CONCLUSION 173 formulation proposed in Bach and Jordan [2003] is not convex and difﬁcult to optimize. 11.
174 CHAPTER 11. CORRELATION CLUSTERING .
Part IV Conclusions and future directions 175 .
disulﬁde connectivity in protein structure prediction.Chapter 12 Conclusions and future directions This thesis presents a novel statistical estimation framework for structured models based on the large margin principle underlying support vector machines. 3D terrain classiﬁcation. email organization and image segmentation. For some of these models. alternative estimation methods are intractable. The framework results in several efﬁcient learning formulations for complex prediction tasks.1 Summary of contributions We view a structured prediction model as a mapping from the space of inputs x ∈ X to a discrete vector output y ∈ Y. Essentially. Our class of models has the following linear form: hw (x) = arg max w f (x. we rely on the expressive power of convex optimization problems to compactly capture inference or solution optimality in structured models. Fundamentally. a model deﬁnes a compact. hypertext categorization. y : g(x. y). parameterized scoring function w f (x. We develop theoretical foundations for our approach and show a wide range of experimental applications. y) and prediction using the model reduces to ﬁnding the highest scoring output y given the input x. including handwriting recognition.y)≤0 176 . 12. Directly embedding this structure within the learning formulation produces compact convex problems for efﬁcient estimation of very complex models. natural language parsing.
∀i. Although the space of outputs {y : g(x. y) ≤ 0} is usually immense. which is generally exponential in the number of variables in each y(i) . ∀i. This deﬁnition covers a broad range of models. 7 and Ch. .1. 10). The naive formulation1 uses i Y (i)  linear constraints.t. we assume that the inference problem arg maxy : g(x. we provide exact maximum margin solutions (Ch.12. y) ∈ IRk deﬁne the space of feasible outputs y given the input x and basis functions f (x. y) ∈ IRn represent salient features of the input/output pair. from probabilistic models such as Markov networks and context free grammars to more unconventional models like weighted graphcuts and matchings.y)≤0 w f (x. 1 For simplicity.1 Structured maximum margin estimation Given a sample S = {(x(i) . min s. y) ≤ 0}. y(i) )}m . We propose two general approaches that transform the above exponential size QP to an exactly equivalent polynomial size QP in many important classes of models. These formulations allow us to ﬁnd globally optimal parameters (with ﬁxed precision) in polynomial time using standard optimization software. we omit the slack variables in this summary. y) ≈ y(i) . constraints g(x. SUMMARY OF CONTRIBUTIONS 177 where w ∈ IRn is the vector of parameters of the model. we develop methods for ﬁnding parameters w such i=1 that: arg max w f (x(i) . ∀y ∈ Y (i) . 1 w2 2 w fi (y(i) ) ≥ w fi (y) + i (y). 12. y) can be solved (or closely approximated) by an efﬁcient algorithm that exploits the structure of the constraints g and basis functions f . In many models where maximum likelihood estimation is intractable.1. y∈Y (i) where Y (i) = {y : g(x(i) .
For example. QP. contextfree grammars. we can embed the maximization inside the minmax formulation to get a compact convex program equivalent to the naive exponential formulation. associative Markov networks over binary variables. maximum weight perfect (nonbipartite) matching and spanning tree problems can be expressed as linear programs with exponentially many constraints. 1997. We show that if we can express the (lossaugmented) inference as a compact convex optimization problem (e. ∀i. can be solved in polynomial time using combinatorial algorithms. but no polynomial formulation is known [Bertsimas & Tsitsiklis. LP. y∈Y (i) The key to solving the estimation problem above efﬁciently is the lossaugmented inference problem maxy∈Y (i) [w fi (y) + i (y)]. Even if maxy∈Y (i) w fi (y) can be solved in polynomial time using convex optimization. Schrijver. 1 w2 2 w fi (y(i) ) ≥ max [w fi (y) + i (y)].). Certiﬁcate formulation There are several important combinatorial problems which allow polynomial time solution yet do not have a compact convex optimization formulation.. y . SDP. In some cases.g. We typically use a natural loss function which is essentially the Hamming distance between y(i) and h(x(i) ): the number of variables predicted incorrectly. the form of the loss term i (y) is crucial for the lossaugmented inference to remain tractable. bipartite matchings. 2003]. CONCLUSIONS AND FUTURE DIRECTIONS Minmax formulation We can turn the above problem into an equivalent minmax formulation with i nonlinear maxconstraints: min s. and many other models. we can ﬁnd a compact certiﬁcate of optimality that guarantees that y(i) = arg max[w fi (y) + i (y)].178 CHAPTER 12. Both of these problems.t. etc. however. though. We show that this approach leads to exact polynomialsize formulations for estimation of lowtreewidth Markov networks.
1979]. we can derive a compact certiﬁcate for the spanning tree problem. 1993. 2004]. maximum margin estimation can be formulated as a compact QP with linear constraints. Zhu & Hastie. which makes the use of kernels much more efﬁcient. Because of the hingeloss. Because our approach only relies on using the maximum in the model for prediction. Lafferty et al. This observation allows us to apply our framework to an even broader range of models with combinatorial structure than the minmax formulation. 1979... This simple set of linear constraints scales linearly with the number of edges in the graph. SUMMARY OF CONTRIBUTIONS 179 For perfect (nonbipartite) matchings. Altun et al. Maximum likelihood models with kernels are generally nonsparse and require pruning or greedy support vector selection methods [Wahba et al.12. The certiﬁcate formulation relies on the fact that verifying optimality of a solution is often easier than actually ﬁnding one. By contrast. Maximum margin vs. We can express this condition by deﬁning an auxiliary distance function on the nodes an a set of linear constraints that are satisﬁed if and only if there are no negative cycles.1. maximum margin estimation can be tractable when maximum likelihood is not. our approach has an additional advantage. context free grammars. 10). maximum likelihood There are several theoretical advantages to our approach in addition to the empirical accuracy improvements we have shown experimentally. which is #Pcomplete [Valiant. In models that are tractable for both maximum likelihood and maximum margin (such as lowtreewidth Markov networks. this certiﬁcate is a condition that ensures there are no augmenting alternating cycles (see Ch. Similar results hold for an important subclass of Markov networks and nonbipartite matchings. 2004.. For example. . Garey & Johnson. many other problems in which inference is solvable by dynamic programming). to learn a probabilistic model P (y  x) over bipartite matchings using maximum likelihood requires computing the normalizing partition function. and does not require a normalized distribution P (y  x) over all outputs. Similarly. 2001. the solutions to the estimation are relatively sparse in the dual space (as in SVMs).
representational extensions. several advantages to maximum likelihood estimation. of course. ◦ Scalable online algorithm Although our convex formulation is a QP with linear number of variables and constraints in the size of the data. convex learning formulation. QPs or SDPs often provide excellent approximation algorithms and ﬁt well within our framework. the maximization problem we are interested in may be NPhard. The dual formulation allows efﬁcient integration of kernels with graphical models that leverages rich highdimensional representations for accurate prediction in realworld tasks. graphpartitioning in Ch. multiway cuts in Ch. We show empirically that these approximations are very effective in many applications. maximum likelihood is much more appropriate. in training settings with missing data and hidden variables. CONCLUSIONS AND FUTURE DIRECTIONS There are. Relaxations of such integer programs into LPs. 12. ◦ Lowtreewidth Markov networks We use a compact LP for MAP inference in Markov networks with sequence and other lowtreewidth structure to derive an exact. particularly the minmax formulation. Approximations In many problems. generalization analysis and experimental validation for Markov networks.180 CHAPTER 12. In applications where probabilistic conﬁdence information is a must.. associative.2 Markov networks: maxmargin. 8. Many such problems can be written as integer programs. relational The largest portion of the thesis is devoted to novel estimation algorithms. 7. 1977].1. we consider MAP inference in large treewidth Markov networks in Ch. for large datasets (millions of examples). compact. Our onlinestyle algorithm uses . it is very difﬁcult to solve using standard software. Also. probabilistic interpretation permits the use of wellunderstood algorithms such as EM [Dempster et al. 11. for example. We present an efﬁcient algorithm for solving the estimation problem called Structured SMO.
For the nonbinary case. for which likelihood methods are believed to be intractable. We apply this class of models to classiﬁcation of hypertext using hyperlink structure to deﬁne relations between webpages. ◦ Learning associative Markov networks (AMNs) We deﬁne an important subclass of Markov networks that captures positive correlations present in many domains. We present an AMNbased method for object segmentation from 3D range data. for associative Markov networks over binary variables. in which exact inference is intractable. our models are learned efﬁciently and. 1952] often used in computer vision and allows exact MAP inference in the case of binary variables. We show how to express the inference problem using an LP which is exact for binary networks.g. our framework allows exact estimation of networks of arbitrary connectivity and topology. which compactly deﬁne templates for Markov networks for domains with relational structure: objects. and can easily model complex interaction patterns over related entities. to derive an approximate maxmargin formulation. SUMMARY OF CONTRIBUTIONS 181 inference in the model and analytic updates to solve extremely large estimation problems. at runtime. proportion of mislabeled pixels in an image). ◦ Representation and learning of relational Markov networks We introduce relational Markov networks (RMNs).. This is the ﬁrst bound to address structured error (e. By constraining the class of Markov networks to AMNs. ◦ Generalization analysis We analyze the theoretical generalization properties of maxmargin estimation in Markov networks and derive a novel marginbased bound for structured prediction. 2002]. relations. can scale up to tens of millions of nodes and edges by using graphcut based inference [Kolmogorov & Zabih. We use a compact approximate MAP LP in these complex Markov networks.1. .12. As a result. This class of networks extends the Potts model [Potts. attributes. The graphical structure of an RMN is based on the relational structure of the domain. we provide an approximation that works well in practice.
clustering The other large portion of the thesis addresses a range of prediction tasks with very diverse models: context free grammars for natural language parsing. matching. graph partitions for clustering documents and segmenting images. . we describe a formulation that tightly integrates metric learning with the clustering algorithm. ◦ Learning to match We use a combinatorial optimality condition.182 CHAPTER 12. including email folder organization and image segmentation.3 Broader applications: parsing. to derive an exact. We build on a recently proposed “unlexicalized” grammar that allows cubic time parsing and we show how to achieve highaccuracy parsing (still in cubic time) by exploiting novel kinds of lexical information. In contrast to algorithms that learn a metric independently of the algorithm that will be used to cluster the data. The algorithm we propose uses kernels. We apply our framework to prediction of disulﬁde connectivity in proteins using perfect matchings. namely the absence of augmenting alternating cycles.1. tuning one to the other in a joint optimization. perfect matchings for disulﬁde connectivity in protein structure prediction. ◦ Learning to parse We exploit dynamic programming decomposition of context free grammars to derive a compact maxmargin formulation. we use the minmax formulation to learn a parameterized scoring function for clustering. We show experimental evidence of the model’s improved performance over several baseline models. efﬁcient certiﬁcate formulation for learning to match. ◦ Learning to cluster By expressing the correlation clustering problem as a compact LP and SDP. which makes it possible to efﬁciently embed input features in very highdimensional spaces and achieve stateoftheart accuracy. We formulate the approximate learning problem as a compact convex program. Experiments on synthetic and realworld data show the ability of the algorithm to learn an appropriate clustering metric for a variety of desired clusterings. CONCLUSIONS AND FUTURE DIRECTIONS 12.
For example. An open question is to translate these error bounds on inference into error bounds on the resulting maxmargin formulations.2 Extensions and open problems There are several immediate applications. 5.d. novel prediction tasks. y(i) ) being i. These approximate inference programs have strong relative error bounds.12. 7 and correlation clustering in Ch.1 Theoretical analysis and optimization algorithms ◦ Approximation bounds In several of the intractable models. Similar assumptions may be made for some “degree of separation” in relational domains. we used approximate convex programs within the minmax formulation.e. 12. scaling . relying only on the samples (x(i) .i. This distributionfree assumption leads to a worst case analysis. We organize these ideas into several sections below.2. EXTENSIONS AND OPEN PROBLEMS 183 12. a label variable is independent of the rest given a large enough ball of labels around it. less immediate extensions and open problems for our estimation framework. it would be interesting to exploit such conditional independence assumptions or asymptotic bounds on entropy of P (y  x) to get generalization guarantees even from a single structured example (x. while some assumptions about the approximate decomposition P (y  x) may be warranted. the next label is independent of the labels more than k in the past). we presented a bound on the structured error in Markov networks. including further theoretical analysis and new optimization algorithms. ◦ Problemspeciﬁc optimization methods Although our convex formulations are polynomial in the size of the data. y). More generally. like multiclass AMNs in Ch.. 11. In spatial prediction tasks. for sequential prediction problems. ◦ Generalization bounds with distributional assumptions In Ch. and more general learning settings. without any assumption about the distribution of P (y  x).2. given the input and previous k labels. the Markov assumption of some ﬁnite order is reasonable (i.
perhaps using novel string kernels [Haussler. For lowtreewidth Markov networks and context free grammars. 1970. we can consider a whole range of problems where the prediction variables are continuous. Leslie et al.. Both algorithms rely on dynamic programming decompositions. CONCLUSIONS AND FUTURE DIRECTIONS up to larger datasets will require problemspeciﬁc optimization methods.184 CHAPTER 12. generalizing classiﬁcation models to multivariate. 2004]. ◦ Sequence alignment In standard pairwise alignment of biological sequences..2 Novel prediction tasks ◦ Bipartite matchings Maximum weight bipartite matchings are used in a variety of problems to predict mappings between sets of items. 2000]. Our framework provides an exact. . efﬁcient alternative to the maximum likelihood estimation for learning the matching scoring function.. In 2D shape matching. such as graphcuts. a string edit distance is used to determine which portions of the sequences align to each other [Needleman & Wunsch.. Our framework can be applied (just as in context free grammar estimation) to efﬁciently learn a more complex edit function that depends on the contextual string features. 1998]. matchings. Lodhi et al. 1999. 2002. Another algorithm useful for such models is Exponentiated Gradient [Bartlett et al. ◦ Continuous prediction problems We have addressed estimation of models with discrete output spaces. 2004]. structured classiﬁcation. matchings are used to map words of the two languages in aligned sentences [Matusov et al. points on two shapes are matched based on their local contour features [Belongie et al. and many others. 12. we have presented the Structured SMO algorithm. In machine translation. Finding the best alignment involves a dynamic program that generalizes the longest common subsequence algorithm..2. models which do not permit such decompositions.. However. 2002]. Similarly. Durbin et al. create a need for new algorithms that can effectively use combinatorial optimization as a subroutine to eliminate the dependence on generalpurpose convex solvers.
It would be interesting to use observed equilibria data under different conditions to learn what “objective” the cell is maximizing. In this setting. there is a wealth of possible structures (cliques in the network) one can use to model a problem. However.12. 1997]. 12. Developing effective loss functions and maxmargin formulations for the continuous setting could provide a novel set of effective models for structured multivariate realvalued prediction problems. not concave (it turns out that it is actually possible to use L∞ loss). 1991. especially in spatial and relational domains. Hamming distance equivalent. interconstrained realvalued outputs. no longer produces a maximization of a concave objective with convex constraints since L1 .2. Luenberger. EXTENSIONS AND OPEN PROBLEMS 185 Such problems are a natural generalizations of regression. L1 loss (or L2 loss). involving correlated. Details of this are beyond the scope of this thesis. L2 are convex. one could learn a user’s return projection and risk assessment function from observed portfolio allocations by the user. but it sufﬁces to say that lossaugmented inference using. It is particularly interesting to explore the problem of inducing these cliques automatically from data. 1994]. for example. In ﬁnancial modeling. The standard method of greedy stepwise selection followed by reestimation is very . In the case of Markov networks. with stoichiometric constraints [Varma & Palsson. there are obstacles to directly applying the minmax or certiﬁcate formulations. convex programs are often used to model portfolio management. These problems are similar to the discrete structured prediction models we have considered: inference in the model can formulated as a convex optimization problem.3 More general learning settings ◦ Structure learning We have focused on the problem of learning parameters of the model (even though our kernelized models can be considered nonparametric). For example. several recent models of metabolic ﬂux in yeast use linear programming formulations involving quantities of various enzymes. Markowitz portfolio optimization is formulated as a quadratic program which minimizes risk and maximizes expected return under budget constraints [Markowitz.2.
This assumption often limits us to relatively small training sets where data has been carefully annotated. Recent work on selecting input features in Markov networks (or CRFs) uses several approximations to learn efﬁciently with millions of candidate features [McCallum. The simplest setting is a mix of labeled and unlabeled examples. may permit more efﬁcient clique selection methods. 1998. 2003]. However. 2003]. Similarly. 1977.. extensions of our framework allow opportunities for problemspeciﬁc convex approximations to be exploited.. Szummer & Jaakkola. 1997. There has been much research in this setting for classiﬁcation [Blum & Mitchell. Discriminative methods have been explored far less. . in machine translation. 2003.. we may not have each letter segmented out but instead just get a word or sentence as a label for the entire image. A more complex and rich setting involves presence of hidden variables in each example. while much of the easily accessible data is not at all or suitably labeled. Especially in the case of combinatorial structures. 1999]. Nigam et al.186 CHAPTER 12. This setting has been studied mainly in the probabilistic. 2001]. word correspondences between pairs of sentences are usually not manually annotated (at least not on a large scale). Although most of this work has been done in a probabilistic setting. Bach & Jordan. 2001. 2000. in handwriting recognition. Cowell et al. generative models often using the EM algorithm [Dempster et al.. CONCLUSIONS AND FUTURE DIRECTIONS expensive in general networks [Della Pietra et al. There are several more general settings we would like to extend our framework. These correspondence variables can be treated as hidden variables. clique selection is still relatively unexplored. ◦ Semisupervised learning Throughout the thesis we have assumed completely labeled data. It is possible that AMNs. by restricting the network to be tractable under any structure. For example. where a small supervised dataset is augmented by a large unsupervised one. Chapelle et al. the principle of regularizing (discouraging) decision boundaries near densely clustered inputs could be applicable to our structured setting. Corduneanu & Jaakkola.. Zhu et al. 2002..
3 Future We have presented a supervised learning framework for a large class of prediction models with rich and interesting structure.3. Our approach has several theoretical and practical advantages over standard probabilistic models and estimation methods for structured prediction.12. . We hope that continued research in this framework will help tackle evermore sophisticated prediction problems in the future. FUTURE 187 12.
His analysis is based on the upper bounds on the covering number for the class of linear functions FL (w. 1998].1 The proof of Theorem 5.) Zhang provides generalization guarantees for linear binary classiﬁers of the form hw (x) = sgn(w x).g. Intuitively. Here. the covering number of an inﬁnite class of functions (e. we will only deﬁne the ∞norm covering number.5.. The covering number is a key quantity in measuring function complexity. We reproduce the relevant deﬁnitions and theorems from Zhang [2002] here to highlight the necessary extensions for structured classiﬁcation.5. Marginbased analysis of generalization error uses the margin achieved by a classiﬁer on the training set to approximate the original function class of the classiﬁer by a ﬁnite covering with precision that depends on the margin.Appendix A Proofs and derivations A.1 Proof of Theorem 5. z) = w z where the norms of the vectors w and z are bounded. 188 . parameterized by a set of weights w) is the number of vectors necessary to approximate the values of any function in the class on a sample.1 uses the covering number bounds of Zhang [2002] (in the DataDependent Structural Risk Minimization framework [ShaweTaylor et al.
v(r) }. the corresponding γmargin loss is f γ (v) = 1 ≤ 2γ). 1] be a loss function. The next theorem bounds the expected f loss in terms of the γmargin loss. S) with precision under the metric ρ.t. z(i) )) ≤ . In binary classiﬁcation. y (i) }m . Theorem A. we let f (v) = 1 ≤ 0) be the step function.1. . marginbased loss on the training sample that measures the worst loss achieved by the approximate covering based on this margin. . ρ.v )<2γ f (v ) be the γmargin loss for a metric ρ. on the training sample. The covering number of a sample S is the size of the smallest covering: N∞ (F. Let γ1 > γ2 > . . . . . ρ. z)). v ) = v − v .1 189 A. log2 N∞ (FL . Deﬁnition A.1. m) = supS: S=m N∞ (F.2 (Theorem 4 from Zhang [2002]) If w > 0. . We also deﬁne the covering number for any sample of size m: N∞ (F. where X = IRn and Y is mapped to ±1. When the norms of w and z are bounded.1. V (j) is a covering of F(w. be a covering of a function class F(w.1 (Covering Number) Let V = {v(1) . f γ (v) = supρ(v. 1] be a loss function and f γ (v) = supρ(v.A. the bounds below use a stricter. be . Let f : IR → [0. if for all w there exists a v(j) such that for each data sample z(i) ∈ S: ρ(vi . For 01 loss and linear metric ρL . we are given a sample S = {x(i) .1. ρ.v )<2γ f (v ). . I(v Theorem A. S).1 Binary classiﬁcation In binary classiﬁcation. In order to use the classiﬁer’s margin to bound its expected loss.3 (Corollary 1 from Zhang [2002]) Let f : IR → [0. we have the following upper bound on the covering number of linear functions under the linear metric ρL (v. so we can fold x and y into z = yx. from distribution D over i=1 X × Y.5. ρL . S). . m) ≤ 36 a2 b2 2 2 ≤ a and z 2 ≤ b. S) = inf V  s.1. PROOF OF THEOREM 5. F(w. so that 01 loss of I(v sgn(w x) is f (FL (w. . where v(j) ∈ IRm . then ∀ log2 (2 4ab/ + 2 m + 1) .
. PROOFS AND DERIVATIONS a decreasing sequence of parameters. we use i to denote the smallest index s. . . y). . z) = min w ∆fi (y). z) by deﬁning an appropriate loss function fM . since y is a vector. A.1. y: H (y)=d Deﬁnition A. z). . We deﬁne a new function class FM (w. . . ρ. .190 APPENDIX A. then for all δ > 0. Md (w. In order for our loss function to compute average perlabel loss. z).1. We will bound the corresponding covering number by building on the bound in Theorem A. L} is given by: Md (w. z))] ≤ ES [f γ (F(w.2. γi . z).4 (dtherrorlevel function) The dtherrorlevel function Md (w. z) for d ∈ {1. and pi be a sequence of positive numbers such that ∞ i=1 pi = 1. it is convenient to make our function class vectorvalued (instead of scalarvalued as above). z))] + for all w and γ. which is a vector of minimum values of w ∆fi (y) for each error level H (y) from 1 to L as described below. . z) is given by: FM (w. S) + ln m pi δ ED [f (F(w.2 Structured classiﬁcation We will extend this framework to bound the average perlabel loss H (y)/L for structured classiﬁcation by deﬁning an appropriate loss f and a function class F (as well as a metric ρ) such that f (F) computes average perlabel loss and f γ (F) provides a suitable γmargin loss.1. Deﬁnition A. z)) . with probability of at least 1 − δ over data: 32 1 ln 4N∞ (F. so we let z = (x. where for each ﬁxed γ.t. . z) = (M1 (w. . . . ML (w. We can no longer simply fold x and y.5 (Multierrorlevel function class) The multierrorlevel function class FM (w. γi ≤ γ. We can now compute the average perlabel loss from FM (w.1.
d We now deﬁne the corresponding γmargin loss using the new metric: Deﬁnition A. d:vd ≤0 L . one that maximizes the Hamming distance from y.1. z) ≥ d:Md (w.z)≤2dγ 1 arg min vd .1. Since the margin of the hypothesis grows with the number of mistakes. Combining the two deﬁnitions. we deﬁne arg mind:vd ≤0 vd ≡ 0. y ).v )≤2γ fM (v ). our metric can become “looser” with the number of mistakes. z)) = 1 1 arg min Md (w. v ) = max d vd − vd  . 1] is given by: fM (v) = 1 arg min vd .1. We now need to deﬁne an appropriate metric ρ that in turn deﬁnes γmargin loss for structured classiﬁcation. as there is more room for error.6 (Average perlabel loss) The average perlabel loss fM : IR L → [0. y Note that the case ∀d. 1] is given by: γ fM (v) = sup ρM (v.5. we get: γ fM (FM (w. Deﬁnition A.8 (γmargin average perlabel loss) The γmargin average perlabel loss γ fM : IR L → [0.1 191 Deﬁnition A. d:vd ≤0 L where in case ∀d.1.z)≤0 L L H arg max w fi (y) . we have an upper bound on the average perlabel loss fM (FM (w. z) > 0 corresponds to the classiﬁer making no mistakes: arg maxy w fi (y) = y.A. it is adversarial: it picks from all y which are better (w f (y) ≤ w f (y )). vd > 0. With the above deﬁnitions. z)) = sup v:vd −Md (w. Otherwise. Md (w. This upper bound is tight if y = arg maxy w f (x.7 (Multierrorlevel metric) Let the multierrorlevel metric ρM : IRL × IRL → IR for a vector in IR L be given by: ρM (v. PROOF OF THEOREM 5.
. Vc is the maximum number of values in a clique Yc . q. if for all w there exists a V(j) such that for each data We provide a bound on the covering number of our new function class in terms of a covering number for the linear function class. and currentnext edge clique. ρL . Note that this is sufﬁcient since N∞ (FL . ρM . S ) ≤ N∞ (FL . z(i) )) ≤ . . . mNc (Vc − 1)). . ρM . . . . mNc (Vc − 1)). ρM . and Rc is an upperbound on the 2norm of clique basis functions. . m) = sup N∞ (FM . V is a covering of FM (w.9 (Multierrorlevel covering number) Let V = {V(1) . by deﬁnition. node clique. m) = sup N∞ (FM . ρL . V(r) }. PROOFS AND DERIVATIONS We also deﬁne the corresponding covering number for our vectorvalued function class: Deﬁnition A. where V(j) = (V1 . S ) for any sample S of size m.t.1. ρM .1. Consider a ﬁrstorder sequence model as an example. ρM . S) ≤ N∞ (FL . . m) ≤ N∞ (FL . . . where we construct the sample S of size mNc (Vc − 1) in order to cover the clique potentials as described below. FM (w. ρM . . q is the maximum number of cliques that have a variable in common. be a covering of FM (w. ρM . Lemma A. S). S: S=m (j) (j) (j) (j) (j) ∈ IRL . We also deﬁne N∞ (FM . S) ≤ N∞ (FL . Recall that Nc is the maximum number of cliques in G(x). . S).192 APPENDIX A. Vi . The covering number of a sample S is the size of the smallest covering: N∞ (FM . . . Proof: We will show that N∞ (FM . ρL . . ρL . . with  precision under the metric ρM . S:S=m . Then Nc = 2L−1 since we have L node cliques and L − 1 edge cliques.10 (Bound on multierrorlevel covering number) N∞ (FM . with L as the maximum length. so N∞ (FM . S) = inf V s. q. . S). and V the number of values a variable takes. Vm ) and Vi sample z(i) ∈ S: ρM (Vi . and q = 3 since nodes in the middle of the sequence participate in 3 cliques: previouscurrent edge clique. . Vc = V 2 because of the edge cliques. ρL . q. . q. mNc (Vc − 1)).
Md (v(j) . Vm ) (j) (j) and Vi (j) ∈ IRL . PROOF OF THEOREM 5. . .1 193 The construction of S below is inspired by the proof technique in Collins [2001]. S ) under ρL . and (j) Md (vi .c (yc ) = 0. (j) (j) (j) (A. For each sample z ∈ S. as ∆fi. By combining this fact with Eq. . . . Vi . .c (yc ) − w ∆fi. . ∀c ∈ C (i) . we deﬁne vi. V(r) }. while his is exponential in the total number of label variables per example.c (yc ). ρL .A. as each label can appear in at most q cliques. This reduction in size comes about because our covering approximates the values of clique potentials w ∆fi. (A. we obtain: vi (y) − w ∆fi (y) ≤ dq .5. .c (yc ). . . Let vi (y) = (j) (j) c vi. . we create Nc (Vc − 1) samples ∆fi. z(i) ). We can now use V to construct a covering V = {V(1) . mNc (Vc −1)).c (yc ) will be nonzero. z(i) ) = miny: H (y)=d vi (y).1.1) By Deﬁnition A.2) (i) Note that vi. For convenience. one for each clique c and each assignment yc = yc . z(i) )) . . we require that for any w there exists a v such that for each sample z : vi.c (yc ) ≤ . for our multierrorlevel function FM . the number of vectors in V is given by r = N∞ (FL . ML (v(j) . then i Vi = (M1 (v(j) . .c (yc ) = 0 for correct label assignments. . We construct a set of vectors (j) (i) V = {v(1) . at most dq vi. (A. . . Thus for an assignment y with d mistakes. (j) (j) ∀i. The component of v(j) corresponding to the sample z(i) and the assignment yc to the labels of the clique c will be denoted by vi. but the key difference is that our construction is linear in the number of cliques Nc and exponential in the number of label variables per clique.c (yc ). ∀y : H i (y) = d. where (j) V(j) = (V1 .c (yc ) is zero for all cliques c for which the assignment is correct: yc = yc . . .c (yc ) for each clique c and clique assignment yc as opposed to the values of entire assignments w ∆fi (y). . .1). z(i) ). . (j) (i) (j) (i) (i) V an (j) ∈V (A. where v(j) ∈ IRmNc (Vc −1) . ∀yc . To make ∞norm covering of FL (w.1.3) .1. v(r) }. . . . .
z)) + ∞ i=1 pi = 1. Proof: Substitute Theorem A. ρM . We must now bound: (j) ρM (Vi .10. The last step is a direct consequence of Eq. m) ≤ 36 2 Rc w 2 2 2 (j) q2 log2 1 + 2 4 Rc w 2 q + 2 mNc (Vc − 1) . γ Theorem A.1). (A. we use i to denote the smallest index s.1. since vi (yd ) ≤ vi (yd ).3). . with probability of at least 1 32 ln 4N∞ (FM . FM (w.11 (Numeric bound on multierrorlevel covering number) log2 N∞ (FM . PROOFS AND DERIVATIONS We conclude the proof by showing that V is a covering of FM under ρM : For each w.1. (j) (j) (j) (j) (A. γi ≤ γ. .t. Let yd = arg miny: H (y)=d vi (y) and yd = arg miny: H (y)=d w ∆fi (y).1. z)) ≤ ES fM (FM (w. Lemma A. be a decreasing sequence of parameters.1. S) + ln m pi δ for all w and γ.3) Let fM and fM (v) be as deﬁned above. then for all δ > 0. FM (w. and pi be a sequence of positive numbers such that 1 − δ over data: γ Ez fM (FM (w. ρM . (A. 2002] where in Step 3 (derandomization) we substitute the vectorvalued FM and the metric ρM .4) v v w where the ﬁrst step follows from deﬁnition of yd .1. Proof: Similar to the proof of Zhang’s Theorem 2 and Corollary 1 [Zhang. . w v Fix any i. Let γ1 > γ2 > .12 (Multilabel analog of Theorem A. Coni i w v sider the case where vi (yd ) ≥ w ∆fi (yd ) (the reverse case is analogous). pick V(j) ∈ V such that the corresponding v(j) ∈ V satisﬁes the condition in Eq. γi . Hence ρM (Vi . z(i) )) ≤ q .1 follows from above theorem with γi = Rc w 2 /2i and pi = 1/2i using an .5. we must (j) prove that: v w w w vi (yd ) − w ∆fi (yd ) ≤ vi (yd ) − w ∆fi (yd ) ≤ dq . where for each ﬁxed γ.2 into Lemma A.194 APPENDIX A. Theorem 5. z(i) )) = max d  miny: H (y)=d vi (y) − miny: H (y)=d w ∆fi (y) i i d (j) (j) .
µc (k) ≥ 0.1) Consider any fractional. we need µv (1) + µv (2) = 1. µc (k) ≤ µv (k). 2. v ∈ c. I(0 µv (2) = µv (2) + λ1 < µv (2) < 1).2. I(0 Now consider the smallest fractional µv (k). I(0 µc (1) = µc (1) − λ1 < µc (1) < 1). Since gc (k) ≥ 0. Thus if we can show that the update results in a feasible and better scoring assignment. A. We construct an assignment µ from µ by leaving integral values unchanged and uniformly shifting fractional values by λ: µv (1) = µv (1) − λ1 < µv (1) < 1).2 AMN proofs and derivations In this appendix. k=1 (A. We show that we can construct a new feasible assignment µ which increases the objective (or leaves it unchanged) and furthermore has fewer fractional entries. Recall that the LP relaxation for ﬁnding the optimal maxy g(y) is: K K max v∈V k=1 µv (k)gv (k) + c∈C\V k=1 K µc (k)gc (k) µv (k) = 1. .1 Binary AMNs Proof (For Theorem 7. we can apply it repeatedly to get an optimal integer solution. µv (k) ≥ 0 and µc (k) = mini∈c µv (k). ∀c ∈ C. we present proofs of the LP inference properties and derivations of the factored primal and dual maxmargin formulation from Ch. ∀c ∈ C \ V. feasible µ. I(0 µc (2) = µc (2) + λ1 < µc (2) < 1).5) s. we can assume that µc (k) = minv∈c µv (k).t. 7. k. k. AMN PROOFS AND DERIVATIONS 195 argument identical to the proof of Theorem 6 in Zhang [2002]. otherwise we could increase the objective by increasing µc (k). λ(k) = minv : µv (k)>0 yv (k) for k = 1. To show that µ is feasible. Note that if λ = λ(1) or λ = −λ(2). µ will have at least one more integral µv (k) than µ.2. ∀v ∈ V.A. A.2.
λ = λ(1) or λ = −λ(2). since µv (1) + µv (2) = 1. PROOFS AND DERIVATIONS First. so is µv (2). I(0 Hence the new assignment µ is feasible. I(0 Dv (k) = gv (k)1 < µv (k) < 1). we prove minv µv (k) = 0. will necessarily increase the objective (or leave it unchanged). Lastly. µc (1) = µc (1) − λ1 < µc (1) < 1) I(0 = (min µv (1)) − λ1 < min µv (1) < 1) = min µv (1). min µv (k) = min µv (k) − ( min µv (k))1 < µv (k) < 1) I(0 v v i:µv (k)>0 = min min µv (k).2 [µc (k) − µc (k)]gc (k) c∈C\V k=1. I(0 i∈c i∈c i∈c µc (2) = µc (2) + λ1 < µc (1) < 1) I(0 = (min µv (2)) + λ1 < min µv (2) < 1) = min µv (2). we show µc (k) = mini∈c µv (k). Above we used the fact that if µv (1) is fractional. and it remains to show that we can improve the objective. and .196 APPENDIX A. we show that µv (1) + µv (2) = 1.2 = λ v∈V [Dv (1) − Dv (2)] + c∈C\V [Dc (1) − Dc (2)] = λD Dc (k) = gc (k)1 < µc (k) < 1). µv (1) + µv (2) = µv (1) − λ1 < µv (1) < 1) + µv (2) + λ1 < µv (2) < 1) I(0 I(0 = µv (1) + µv (2) = 1. The change in the objective is: [µv (k) − µv (k)]gv (k) + v∈V k=1. This implies that one of the two cases. min i i:µv (k)>0 µv (k) − min µv (k) i:µv (k)>0 = 0. We can show that the change in the objective is always λD for some constant D that depends only on µ and g. To show that µv (k) ≥ 0. does not decrease the objective function. I(0 i∈c i∈c i∈c We have established that the new µ are feasible.
(They can also be assigned label k as a result of several phases. the probability that all nodes in a clique c are assigned label k if none of the nodes were previously assigned is 1 K mini∈c µv (k) = that at least one of the nodes will be assigned label k in a phase 1− 1 K K k=1 1 µ (k). Lemma A.2 Multiclass AMNs For K > 2.2. By symmetry.A.2.2. losing at most a factor of m = maxc∈C c in the objective function. Proof The probability that an unassigned node is assigned label k during one phase is 1 µ (k). K v which is proportional to µv (k). The procedure terminates when all nodes have been assigned a label. Our analysis closely follows that of Kleinberg and Tardos [1999]. we pick a label k. The basic idea of the rounding procedure is to treat µv (k) as probabilities and assign labels according to these probabilities in phases.2 The probability that all nodes in a clique c are assigned label k by the procedure is at least 1 µ (k). A. The probability K c 1 is K (maxi∈c µv (k)). AMN PROOFS AND DERIVATIONS 197 has strictly fewer fractional entries.1 The probability that a node i is assigned label k by the randomized procedure is µv (k).) The probability that all the . and a threshold α ∈ [0. the probability that a node is as signed label k over all phases is exactly µv (k). Lemma A. 1] uniformly at random. The probability that none of the nodes in the clique will be assigned any label in one phase is maxi∈c µv (k). Nodes in the clique c will be assigned label k by the procedure if they are assigned label k in one phase. but we can ignore this possibility for the purposes of the lower bound. c c Proof For a single phase. we assign the label k if µv (k) ≥ α. For each node i which has not yet been assigned a label. In each phase. uniformly at random.2. we use the randomized rounding procedure of Kleinberg and Tardos [1999] to produce an integer solution for the linear relaxation.
2. we have that the rounded solution is at most m times worse than the optimal solution produced by the LP of Eq. c 1 . PROOFS AND DERIVATIONS nodes in c will be assigned label k by the procedure in a single phase is: ∞ j=1 1 1 µc (k) 1 − K K µc (k) K k=1 i∈c K j−1 max µv (k) k=1 i∈c = = µc (k) K k=1 maxi∈c µv (k) ≥ µv (k) = i∈c µc (k) K k=1 µv (k) ∞ i=0 µc (k) . using the method of conditional probabilities. Along similar lines. di = and then upperbounded Theorem A. we note that the constant factor approximation is smaller for smaller cliques. . we observe. the potentials associated with large cliques are typically smaller in magnitude. Note that the approximation factor of m applies.5). again. only to the clique potentials.3 The expected cost of the assignment found by the randomized procedure given a solution µ to the linear program in Eq. reducing further the actual error in practice. As node potentials are often larger in magnitude than clique potentials.5) is at least 1 c∈C\V c K k=1 v∈V K k=1 gv (k)µv (k) + gc (k)µk . we ﬁrst used the fact that for d < 1. 1−d Above. We can also derandomize this procedure to get a deterministic algorithm with the same guarantees. c Proof This is immediate from the previous two lemmas. Thus. (A. the terms corresponding to the logpartitionfunction and the node potentials are identical. the max of the set of positive µv (k)’s by their sum. By picking m = maxc∈C c. The only difference between the expected cost of the rounded solution and the (non1 integer) optimal solution is the c factor in the second term.198 APPENDIX A. We obtain an additive error (in logprobability space) only for the clique potentials. (A. similar in spirit to the approach of Kleinberg and Tardos [1999]. if we compare the logprobability of the optimal MAP solution and the logprobability of the assignment produced by this randomized rounding procedure. in fact. the fact that we incur no loss proportional to node potentials is likely to lead to smaller errors in practice.
c. v∈V (i) w fi (y ) + ξi ≥ −w fi. v ∈ V (i) .v (k) ≥ mi.v (k) ≥ 0.v = ξi. ∀i. .3 Derivation of the factored primal and dual maxmargin QP Using Assumptions 7. . we have a variable ξi.t.2. Reexpressing the above QP in terms of these new variables. i.c (k. ∀i.v (k) i. ∀i. (7. k. (3.v (k) for each of the Substituting this dual into Eq.7) ξi.v (k) ≥ 0. i. mi.t.v for each normalization constraint in Eq.1 and 7. .v (k) ≥ v∈c − ξi.v + w fi. ¨ f −w ¨i.c.c (k) = i. we have the dual of the LP used to represent the interior max subproblem maxy w fi (y) + i (y) in Eq. . .c.c (yc )/c and mi.c (k).c.1) and variables mi. where fi.v −w fi. AMN PROOFS AND DERIVATIONS 199 A.c.v .c.4.c. we obtain: min s.A.c (k) + mi. ∀i. c ∈ C (i) \ V (i) .v (k) − c⊃v (A.6) mi. k. c ∈ C (i) \ V (i) .1).c (k). k).c (k. .v (k) ≥ v∈c i. v ∈ V (i) . ¨ w ≥ 0. k. (5. k.v (k) ≥ mi.2): min v∈V ξi.v .c. v ∈ c.v (k) − c⊃v ∀i. . s. . k) and inequality constraints. In the dual.c. 1 w2 + C 2 (i) ξi i (A. c ∈ C (i) \ V (i) . − ξi. c ∈ C (i) \ V (i) .v .v (k) + (i) ¨ f w ¨i.2. k.v (yv ) + c⊃v w ¨i. ∀i.4. ¨ f −w ¨i. ∀i.c (k) + mi.c (yc )/c. we get: . k. (i) (i) ¨ f Now let ξi.c (k) = fi. v ∈ c.4.v (k) = mi.v (k) i.
c. mi. repeated here for reference: min s.4).v .v (k) ≥ ∀i.c (yc )/c.9) i. k. ¨ w ≥ 0. ∀i.v∈V (i) (A. k. (7. k.v .c.v (k) i. ∀i.t. ∀i. v ∈ c.c. k. ∀i.v (k) − c⊃v mi.v (k) ≥ −w ¨i. 1 w2 + C 2 ξi.v (k) ≥ v∈c − ξi.v∈V (i) ξi.v (k) ≥ mi. . ¨ w ≥ 0.c.v (k) − ¨ w ∆¨i.v . 1 w2 + C 2 ξi ≥ v∈V (i) ξi i (A.c (k).8) ξi.v at the optimum.c (k).v (k) ≥ c⊃v i. v ∈ c. ∀i.c (k) + f v∈c − ξi.c. k. PROOFS AND DERIVATIONS min s.c. (i) ¨ f mi. v ∈ V (i) . c ∈ C (i) \ V (i) . Since ξi = i.200 APPENDIX A.c (k) + f ∀i. ¨ w ∆¨i.v (k) i. v ∈ V (i) .v i. mi. we can eliminate ξi and the corresponding set of constraints to get the formulation in Eq. w ∆fi.c (yc )/c.v (k) ≥ −w ¨i.t. (i) ¨ f mi. c ∈ C (i) \ V (i) . w ∆fi. c ∈ C (i) \ V (i) . c ∈ C (i) \ V (i) . k.
and reexpress the above QP as: 2 2 max i.v∈c. ∀i.10) 2 (i) λi.c. v ∈ c. ∀v ∈ V (i) . k.c (yc )/c f ¨ and the fact that λi.c (k)∆¨i. k s.v (k)¨i.c.v i. ∀i.v∈V (i) .c (k) i. µi. ∀c ∈ C (i) \ V (i) . k (A.v (k)¨i. v ∈ c.c.c. k 1 µi. ν ≥ 0.v (k).c (yc ) ≥ 0. k. ∀i.v (k) ≥ 0 τ ≥ 0. µi. k=1 µi. In this dual.t. Using the substitution ν=τ+ ¨ ¨ i.9) is given by: 2 max i. ¨ . ∀i.c (k) f i. while λ and τ correspond ¨ to third and fourth set of constraints. µi. ∀c ∈ C . v ∈ c.v∈V (i) .v (k)∆fi.v (k) ≥ 0 and ¨i.v (k) = C. µi. ∀i.v (k) = 1. λi.v (k).v (k) = λi. k (i) λi. k.c (k) ≥ 0.c (k) − C 2 ˙ µi.c (k) i. µ correspond to the ﬁrst two sets of constraints. k.c (k) − µi.t. ¨ ∀i.c∈C (i) .c (k) − 2 1 τ+ ¨ − 2 ˙ µi.c (k) f i. as well as divide f (i) µ’s by C. k (i) i. ∀c ∈ C (i) k=1 (i) µi.c∈C (i) . k 1 µi.c (k)∆¨i.v (k)∆fi. AMN PROOFS AND DERIVATIONS 201 Now the dual of Eq. k. k K 1 ¨ − C ν+ 2 µi.2.A.c∈C (i) \V (i) . ∀c ∈ C (i) \ V (i) . ∀i.c (yc )/c + f K µi.v∈c.c∈C (i) .c∈C (i) \V (i) . \ V .v i. (A. ∀c ∈ C (i) .c (k) ≥ 0.c∈C (i) . we can eliminate λ and τ . ∀v ∈ V (i) . k s.c (k) ≤ µi.c.
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