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 Giuseppe Nicosia · Panos Pardalos
Giovanni Giuffrida · Renato Umeton (Eds.)

Machine Learning,
LNCS 10710

Optimization,
and Big Data
Third International Conference, MOD 2017
Volterra, Italy, September 14–17, 2017
Revised Selected Papers

123
Lecture Notes in Computer Science 10710
Commenced Publication in 1973
Founding and Former Series Editors:
Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen

Editorial Board
David Hutchison
Lancaster University, Lancaster, UK
Takeo Kanade
Carnegie Mellon University, Pittsburgh, PA, USA
Josef Kittler
University of Surrey, Guildford, UK
Jon M. Kleinberg
Cornell University, Ithaca, NY, USA
Friedemann Mattern
ETH Zurich, Zurich, Switzerland
John C. Mitchell
Stanford University, Stanford, CA, USA
Moni Naor
Weizmann Institute of Science, Rehovot, Israel
C. Pandu Rangan
Indian Institute of Technology, Madras, India
Bernhard Steffen
TU Dortmund University, Dortmund, Germany
Demetri Terzopoulos
University of California, Los Angeles, CA, USA
Doug Tygar
University of California, Berkeley, CA, USA
Gerhard Weikum
Max Planck Institute for Informatics, Saarbrücken, Germany
More information about this series at http://www.springer.com/series/7409
Giuseppe Nicosia Panos Pardalos
•

Giovanni Giuffrida Renato Umeton (Eds.)

•

Machine Learning,
Optimization,
and Big Data
Third International Conference, MOD 2017
Volterra, Italy, September 14–17, 2017
Revised Selected Papers

123
Editors
Giuseppe Nicosia Giovanni Giuffrida
University of Catania University of Catania
Catania Catania
Italy Italy
Panos Pardalos Renato Umeton
University of Florida Harvard University
Gainesville, FL Cambridge, MA
USA USA

ISSN 0302-9743 ISSN 1611-3349 (electronic)

Lecture Notes in Computer Science
ISBN 978-3-319-72925-1 ISBN 978-3-319-72926-8 (eBook)
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 Preface

MOD is an international conference embracing the fields of machine learning, opti-

mization, and data science. The third edition, MOD 2017, was organized during
September 14–17, 2017 in Volterra (Pisa, Italy), a stunning medieval town dominating
the picturesque countryside of Tuscany.
The key role of machine learning, reinforcement learning, artificial intelligence,
large-scale optimization, and big data for developing solutions to some of the greatest
challenges we are facing is undeniable. MOD 2017 attracted leading experts from the
academic world and industry with the aim of strengthening the connection between these
institutions. The 2017 edition of MOD represented a great opportunity for professors,
scientists, industry experts, and postgraduate students to learn about recent developments
in their own research areas and to learn about research in contiguous research areas, with
the aim of creating an environment to share ideas and trigger new collaborations.
As chairs, it was an honor to organize a premiere conference in these areas and to
have received a large variety of innovative and original scientific contributions.
During this edition, six plenary lectures were presented:
Yi-Ke Guo, Department of Computing, Faculty of Engineering, Imperial College
London, UK. Founding Director of Data Science Institute
Panos Pardalos, Department of Systems Engineering, University of Florida, USA.
Director of the Center for Applied Optimization
Ruslan Salakhutdinov, Machine Learning Department, School of Computer Science
at Carnegie Mellon University, USA. Director of AI Research at Apple
My Thai, Department of Computer and Information Science and Engineering,
University of Florida, USA
Jun Pei, Hefei University of Technology, China
Vincenzo Sciacca, Cloud and Cognitive Division – IBM Rome, Italy
There were also two tutorial speakers:
Domenico Talia, Dipartimento di Ingegneria Informatica, Modellistica, Elettronica
e Sistemistica Università della Calabria, Italy
Xin–She Yang, School of Science and Technology – Middlesex University London,
UK
Moreover, the conference hosted the second edition of the industrial session on
“Machine Learning, Optimization and Data Science for Real-World Applications”:
Luca Maria Aiello, Nokia Bell Labs, UK
Pierpaolo Basile, University of Bari, Italy
VI Preface

Carlos Castillo, Universitat Pompeu Fabra in Barcelona, Spain

Moderator: Aris Anagnostopoulos, Sapienza University of Rome, Italy
We received 126 submissions from 46 countries and five continents; each manu-
script was independently reviewed by a committee formed by at least five members
through a blind review process. These proceedings contain 49 research articles written
by leading scientists in the fields of machine learning, artificial intelligence, rein-
forcement learning, computational optimization, and data science presenting a sub-
stantial array of ideas, technologies, algorithms, methods, and applications.
For MOD 2017, Springer generously sponsored the MOD Best Paper Award. This
year, the paper by Khaled Sayed, Cheryl Telmer, Adam Butchy, and Natasa
Miskov-Zivanov titled “Recipes for Translating Big Data Machine Reading to Exe-
cutable Cellular Signaling Models” received the MOD Best Paper Award.
This conference could not have been organized without the contributions of these
researchers, and so we thank them all for participating. A sincere thank you also goes to
all the Program Committee, formed by more than 300 scientists from academia and
industry, for their valuable work of selecting the scientific contributions.
Finally, we would like to express our appreciation to the keynote speakers, tutorial
speakers, and the industrial panel who accepted our invitation, and to all the authors
who submitted their research papers to MOD 2017.

September 2017 Giuseppe Nicosia

Panos Pardalos
Giovanni Giuffrida
Renato Umeton
 Organization

General Chair
Renato Umeton Harvard University, USA

Conference and Technical Program Committee Co-chairs

Giuseppe Nicosia University of Catania, Italy and University of Reading,
UK
Panos Pardalos University of Florida, USA
Giovanni Giuffrida University of Catania, Italy

Tutorial Chair
Giuseppe Narzisi New York University Tandon School of Engineering,
USA

Industrial Session Chairs

Ilaria Bordino UniCredit R&D, Italy
Marco Firrincieli UniCredit R&D, Italy
Fabio Fumarola UniCredit R&D, Italy
Francesco Gullo UniCredit R&D, Italy

Organizing Committee
Piero Conca CNR, Italy
Jole Costanza Italian Institute of Technology, Milan, Italy
Giorgio Jansen University of Catania, Italy
Giuseppe Narzisi New York University Tandon School of Engineering,
USA
Andrea Patane’ University of Oxford, UK
Andrea Santoro Queen Mary University London, UK
Renato Umeton Harvard University, USA

Technical Program Committee

Agostinho Agra Universidade de Aveiro, Portugal
Kerem Akartunali University of Strathclyde, UK
Richard Allmendinger The University of Manchester, UK
Aris Anagnostopoulos Università di Roma La Sapienza, Italy
Davide Anguita University of Genoa, Italy
VIII Organization

Takaya Arita Nagoya University, Japan

Jason Atkin The University of Nottingham, UK
Chloe-Agathe Azencott Institut Curie Research Centre, Paris, France
Jaume Bacardit Newcastle University, UK
James Bailey University of Melbourne, Australia
Baski Balasundaram Oklahoma State University, USA
Elena Baralis Politecnico di Torino, Italy
Xabier E. Barandiaran University of the Basque Country, Spain
Cristobal Barba-Gonzalez University of Malaga, Spain
Helio J. C. Barbosa Laboratório Nacional de Computacao Cientifica, Brazil
Roberto Battiti University of Trento, Italy
Lucia Beccai Istituto Italiano di Tecnologia, Italy
Aurelien Bellet Inria Lille, France
Gerardo Beni University of California at Riverside, USA
Khaled Benkrid The University of Edinburgh, UK
Peter Bentley University College London, UK
Katie Bentley Harvard Medical School, USA
Heder Bernardino Universidade Federal de Juiz de Fora, Brazil
Daniel Berrar Tokyo Institute of Technology, Japan
Adam Berry CSIRO, Australia
Luc Berthouze University of Sussex, UK
Martin Berzins SCI Institute, University of Utah, USA
Mauro Birattari IRIDIA, Université Libre de Bruxelles, Belgium
Leonidas Bleris University of Texas at Dallas, USA
Christian Blum Spanish National Research Council, Spain
Paul Bourgine École Polytechnique Paris, France
Anthony Brabazon University College Dublin, Ireland
Paulo Branco Instituto Superior Tecnico, Portugal
Juergen Branke University of Warwick, UK
Larry Bull University of the West of England, UK
Tadeusz Burczynski Polish Academy of Sciences, Poland
Robert Busa-Fekete Yahoo! Research, NY, USA
Sergiy I Butenko Texas A&M University, USA
Stefano Cagnoni University of Parma, Italy
Yizhi Cai University of Edinburgh, UK
Guido Caldarelli IMT Lucca, Italy
Alexandre Campo Université Libre de Bruxelles, Belgium
Angelo Cangelosi University of Plymouth, UK
Salvador Eugenio Caoili University of the Philippines Manila, Philippines
Timoteo Carletti University of Namur, Belgium
Jonathan Carlson Microsoft Research, USA
Celso Carneiro Ribeiro Universidade Federal Fluminense, Brazil
Michelangelo Ceci University of Bari, Italy
Adelaide Cerveira Universidade de Tras-os-Montes e Alto Douro,
Portugal
Uday Chakraborty University of Missouri – St. Louis, USA
 Organization IX

Xu Chang University of Sydney, Australia

W. Art Chaovalitwongse University of Washington, USA
Antonio Chella Università di Palermo, Italy
Ying-Ping Chen National Chiao Tung University, Taiwan
Haifeng Chen NEC Labs, USA
Keke Chen Wright State University, USA
Gregory Chirikjian Johns Hopkins University, USA
Silvia Chiusano Politecnico di Torino, Italy
Miroslav Chlebik University of Sussex, UK
Sung-Bae Cho Yonsei University, South Korea
Anders Christensen Lisbon University Institute, Portugal
Dominique Chu University of Kent, UK
Philippe Codognet University Pierre and Marie Curie – Paris 6, France
Carlos Coello Coello CINVESTAV-IPN, Mexico
George Coghill University of Aberdeen, UK
Pietro Colombo University of Insubria, Italy
David Cornforth University of Newcastle, UK
Luís Correia University of Lisbon, Portugal
Chiara Damiani University of Milan-Bicocca, Italy
Thomas Dandekar University of Würzburg, Germany
Ivan Luciano Danesi Unicredit Bank, Italy
Christian Darabos Dartmouth College, USA
Kalyanmoy Deb Michigan State University, USA
Nicoletta Del Buono University of Bari, Italy
Jordi Delgado Universitat Politecnica de Catalunya, Spain
Ralf Der MPG, Germany
Clarisse Dhaenens Université Lille, France
Barbara Di Camillo University of Padua, Italy
Gianni Di Caro IDSIA, Switzerland
Luigi Di Caro University of Turin, Italy
Luca Di Gaspero University of Udine, Italy
Peter Dittrich Friedrich Schiller University of Jena, Germany
Federico Divina Pablo de Olavide University of Seville, Spain
Stephan Doerfel Kassel University, Germany
Devdatt Dubhashi Chalmers University, Sweden
George Dulikravich Florida International University, USA
Juan J. Durillo University of Innsbruck, Austria
Omer Dushek University of Oxford, UK
Marc Ebner Ernst-Moritz-Arndt-Universität Greifswald, Germany
Pascale Ehrenfreund The George Washington University, USA
Gusz Eiben VU Amsterdam, The Netherlands
Aniko Ekart Aston University, UK
Talbi El-Ghazali University of Lille, France
Michael Elberfeld RWTH Aachen University, Germany
Michael T. M. Emmerich Leiden University, The Netherlands
Andries Engelbrecht University of Pretoria, South Africa
X Organization

Anton Eremeev Sobolev Institute of Mathematics, Russia

Harold Fellermann Newcastle University, UK
Chrisantha Fernando Queen Mary University, UK
Cesar Ferri Universidad Politecnica de Valencia, Spain
Paola Festa University of Naples Federico II, Italy
Jose Rui Figueira Instituto Superior Tecnico, Lisbon, Portugal
Grazziela Figueredo The University of Nottingham, UK
Alessandro Filisetti Explora Biotech Srl, Italy
Christoph Flamm University of Vienna, Austria
Enrico Formenti Nice Sophia Antipolis University, France
Giuditta Franco University of Verona, Italy
Piero Fraternali Politecnico di Milano, Italy
Valerio Freschi University of Urbino, Italy
Enrique Frias Martinez Telefonica Research, Spain
Walter Frisch University of Vienna, Austria
Rudolf M. Fuchslin Zurich University of Applied Sciences, Switzerland
Claudio Gallicchio University of Pisa, Italy
Patrick Gallinari LIP6 – University of Paris 6, France
Luca Gambardella IDSIA, Switzerland
Jean-Gabriel Ganascia Pierre and Marie Curie University – LIP6, France
Xavier Gandibleux Université de Nantes, France
Alfredo G. Hernandez-Diaz Pablo de Olvide University – Seville, Spain
Jose Manuel Garcia Nieto University of Malaga, Spain
Paolo Garza Politecnico di Torino, Italy
Romaric Gaudel Inria, France
Nicholas Geard University of Melbourne, Australia
Philip Gerlee Chalmers University, Sweden
Mario Giacobini University of Turin, Italy
Onofrio Gigliotta University of Naples Federico II, Italy
Giovanni Giuffrida University of Catania, Italy
Giorgio Stefano Gnecco University of Genoa, Italy
Christian Gogu Université Toulouse III, France
Faustino Gomez IDSIA, Switzerland
Michael Granitzer University of Passau, Germany
Alex Graudenzi University of Milan-Bicocca, Italy
Julie Greensmith University of Nottingham, UK
Roderich Gross The University of Sheffield, UK
Mario Guarracino ICAR-CNR, Italy
Francesco Gullo Unicredit Bank, Italy
Steven Gustafson GE Global Research, USA
Jin-Kao Hao University of Angers, France
Simon Harding Machine Intelligence Ltd., Canada
Richard Hartl University of Vienna, Austria
Inman Harvey University of Sussex
Jamil Hasan University of Idaho, USA
Mohammad Hasan Indiana University – Purdue University, USA
 Organization XI

Geir Hasle SINTEF ICT, Norway

Carlos Henggeler Antunes University of Coimbra, Portugal
Francisco Herrera University of Granada, Spain
Arjen Hommersom Radboud University, The Netherlands
Vasant Honavar Pennsylvania State University, USA
Fabrice Huet University of Nice Sophia Antipolis, France
Hiroyuki Iizuka Hokkaido University, Japan
Takashi Ikegami University of Tokyo, Japan
Bordino Ilaria Unicredit Bank, Italy
Hisao Ishibuchi Osaka Prefecture University, Japan
Peter Jacko Lancaster University Management School, UK
Christian Jacob University of Calgary, Canada
Yaochu Jin University of Surrey, UK
Colin Johnson University of Kent, UK
Gareth Jones Dublin City University, Ireland
Laetitia Jourdan Inria/LIFL/CNRS, France
Narendra Jussien Ecole des Mines de Nantes/LINA, France
Janusz Kacprzyk Polish Academy of Sciences, Poland
Theodore Kalamboukis Athens University of Economics and Business, Greece
George Kampis Eotvos University, Hungary
Dervis Karaboga Erciyes University, Turkey
George Karakostas McMaster University, Canada
Istvan Karsai ETSU, USA
Jozef Kelemen Silesian University, Czech Republic
Graham Kendall Nottingham University, UK
Didier Keymeulen NASA – Jet Propulsion Laboratory, USA
Daeeun Kim Yonsei University, South Korea
Zeynep Kiziltan University of Bologna, Italy
Georg Krempl University of Magdeburg, Germany
Erhun Kundakcioglu Ozyegin University, Turkey
Renaud Lambiotte University of Namur, Belgium
Doron Lancet Weizmann Institute of Science, Israel
Pier Luca Lanzi Politecnico di Milano, Italy
Sanja Lazarova-Molnar University of Southern Denmark, Denmark
Doheon Lee KAIST, South Korea
Jay Lee Center for Intelligent Maintenance Systems – UC, USA
Eva K. Lee Georgia Tech, USA
Tom Lenaerts Université Libre de Bruxelles, Belgium
Rafael Leon Universidad Politecnica de Madrid, Spain
Shuai Li Cambridge University, UK
Lei Li Florida International University, USA
Xiaodong Li RMIT University, Australia
Joseph Lizier The University of Sydney, Australia
Giosue’ Lo Bosco Università di Palermo, Italy
Daniel Lobo University of Maryland Baltimore County, USA
Fernando Lobo University of Algarve, Portugal
XII Organization

Daniele Loiacono Politecnico di Milano, Italy

Jose A. Lozano University of the Basque Country, Spain
Paul Lu University of Alberta, Canada
Angelo Lucia University of Rhode Island, USA
Dario Maggiorini University of Milan, Italy
Gilvan Maia Universidade Federal do Cear, Brazil
Donato Malerba University of Bari, Italy
Lina Mallozzi University of Naples Federico II, Italy
Jacek Mandziuk Warsaw University of Technology, Poland
Vittorio Maniezzo University of Bologna, Italy
Marco Maratea University of Genoa, Italy
Elena Marchiori Radboud University, The Netherlands
Tiziana Margaria University of Limerick and Lero, Ireland
Omer Markovitch University of Groningen, The Netherlands
Carlos Martin-Vide Rovira i Virgili University, Spain
Dominique Martinez LORIA, France
Matteo Matteucci Politecnico di Milano, Italy
Giancarlo Mauri University of Milan-Bicocca, Italy
Mirjana Mazuran Politecnico di Milano, Italy
Suzanne McIntosh NYU Courant Institute, and Cloudera Inc., USA
Peter Mcowan Queen Mary University, UK
Gabor Melli Sony Interactive Entertainment Inc., Japan
Jose Fernando Mendes University of Aveiro, Portugal
David Merodio-Codinachs ESA, France
Silja Meyer-Nieberg Universität der Bundeswehr München, Germany
Martin Middendorf University of Leipzig, Germany
Taneli Mielikainen Nokia, Finland
Kaisa Miettinen University of Jyvaskyla, Finland
Orazio Miglino University of Naples “Federico II”, Italy
Julian Miller University of York, UK
Marco Mirolli ISTC-CNR, Italy
Natasa Miskov-Zivanov University of Pittsburgh, USA
Carmen Molina-Paris University of Leeds, UK
Sara Montagna Università di Bologna, Italy
Marco Montes de Oca Clypd, Inc., USA
Sanaz Mostaghim Otto von Guericke University Magdeburg, Germany
Mohamed Nadif University of Paris Descartes, France
Hidemoto Nakada NIAIST, Japan
Amir Nakib Università Paris EST Creteil, Laboratoire LISSI, France
Mirco Nanni CNR – ISTI, Italy
Sriraam Natarajan Indiana University, USA
Chrystopher L. Nehaniv University of Hertfordshire, UK
Michael Newell Athens Consulting, LLC
Giuseppe Nicosia University of Catania, Italy
Xia Ning IUPUI, USA
Wieslaw Nowak N. Copernicus University, Poland
 Organization XIII

Eirini Ntoutsi Leibniz University of Hanover, Germany

Michal Or-Guil Humboldt University of Berlin, Germany
Mathias Pacher Goethe-Universität Frankfurt am Main, Germany
Ping-Feng Pai National Chi Nan University, Taiwan
Wei Pang University of Aberdeen, UK
George Papastefanatos IMIS/RC Athena, Greece
Luis Paquete University of Coimbra, Portugal
Panos Pardalos University of Florida, USA
Andrew J. Parkes Nottingham University, UK
Andrea Patane’ University of Oxford, UK
Joshua Payne University of Zurich, Switzerland
Jun Pei University of Florida, USA
Nikos Pelekis University of Piraeus, Greece
Dimitri Perrin Queensland University of Technology, Australia
Koumoutsakos Petros ETH, Switzerland
Juan Peypouquet Universidad Tecnica Federico Santa Maria, Chile
Andrew Philippides University of Sussex, UK
Vincenzo Piuri University of Milan, Italy
Alessio Plebe University of Messina, Italy
Silvia Poles Noesis Solutions NV
Philippe Preux Inria, France
Mikhail Prokopenko University of Sydney, Australia
Paolo Provero University of Turin, Italy
Buyue Qian IBM T. J. Watson, USA
Chao Qian University of Science and Technology of China, China
Gunther Raidl TU Wien, Austria
Helena R. Dias Lourenco Pompeu Fabra University, Spain
Palaniappan Ramaswamy University of Kent, UK
Jan Ramon Inria, France
Vitorino Ramos Technical University of Lisbon, Portugal
Shoba Ranganathan Macquarie University, Australia
Cristina Requejo Universidade de Aveiro, Portugal
John Rieffel Union College, USA
Laura Anna Ripamonti Università degli Studi di Milano, Italy
Eduardo Rodriguez-Tello Cinvestav-Tamaulipas, Mexico
Andrea Roli Università di Bologna, Italy
Vittorio Romano University of Catania, Italy
Andre Rosendo University of Cambridge, UK
Samuel Rota Bulo Fondazione Bruno Kessler, Italy
Arnab Roy Fujitsu Laboratories of America, USA
Alessandro Rozza Parthenope University of Naples, Italy
Kepa Ruiz-Mirazo University of the Basque Country, Spain
Florin Rusu University of California Merced, USA
Jakub Rydzewski N. Copernicus University, Poland
Nick Sahinidis Carnegie Mellon University, USA
Lorenza Saitta University of Piemonte Orientale, Italy
XIV Organization

Francisco C. Santos INESC-ID Instituto Superior Tecnico, Portugal

Claudio Sartori University of Bologna, Italy
Frederic Saubion Université d’Angers, France
Andrea Schaerf University of Udine, Italy
Oliver Schuetze CINVESTAV-IPN, Mexico
Luis Seabra Lopes Universidade of Aveiro, Portugal
Roberto Serra University of Modena and Reggio Emilia, Italy
Marc Sevaux Lab-STICC, Université de Bretagne-Sud, France
Ruey-Lin Sheu National Cheng Kung University, Taiwan
Hsu-Shih Shih Tamkang University, Taiwan
Patrick Siarry Université de Paris 12, France
Alkis Simitsis HP Labs, USA
Johannes Sollner Emergentec Biodevelopment GmbH, Germany
Ichoua Soumia Embry-Riddle Aeronautical University, USA
Giandomenico Spezzano CNR-ICAR, Italy
Antoine Spicher LACL University of Paris Est Creteil, France
Pasquale Stano University of Salento, Italy
Thomas Stibor GSI Helmholtz Centre for Heavy Ion Research,
Germany
Catalin Stoean University of Craiova, Romania
Reiji Suzuki Nagoya University, Japan
Domenico Talia University of Calabria, Italy
Kay Chen Tan National University of Singapore, Singapore
Letizia Tanca Politecnico di Milano, Italy
Charles Taylor UCLA, USA
Maguelonne Teisseire Cemagref – UMR Tetis, France
Tzouramanis Theodoros University of the Aegean, Greece
Jon Timmis University of York, UK
Gianna Toffolo University of Padua, UK
Joo Chuan Tong Institute of HPC, Singapore
Nickolay Trendafilov Open University, UK
Soichiro Tsuda University of Glasgow, UK
Shigeyoshi Tsutsui Hannan University, Japan
Aditya Tulsyan MIT, USA
Ali Emre Turgut IRIDIA-ULB, France
Karl Tuyls University of Liverpool, UK
Jon Umerez University of the Basque Country, Spain
Renato Umeton Harvard University, USA
Ashish Umre University of Sussex, UK
Olgierd Unold Politechnika Wroclawska, Poland
Giorgio Valentini Università degli Studi di Milano, Italy
Edgar Vallejo ITESM Campus Estado de Mexico, Mexico
Sergi Valverde Pompeu Fabra University, Spain
Werner Van Geit EPFL, Switzerland
Pascal Van Hentenryck University of Michigan, USA
Ana Lucia Varbanescu University of Amsterdam, The Netherlands
 Organization XV

Carlos Varela Rensselaer Polytechnic Institute, USA

Eleni Vasilaki University of Sheffield, UK
Richard Vaughan Simon Fraser University, Canada
Kalyan Veeramachaneni MIT, USA
Vassilios Verykios Hellenic Open University, Greece
Mario Villalobos-Arias Univesidad de Costa Rica, Costa Rica
Marco Villani University of Modena and Reggio Emilia, Italy
Katya Vladislavleva Evolved Analytics LLC, Belgium
Stefan Voss University of Hamburg, Germany
Dean Vucinic Vrije Universiteit Brussel, Belgium
Markus Wagner The University of Adelaide, Australia
Toby Walsh UNSW Sydney, Australia
Lipo Wang Nanyang Technological University, Singapore
Liqiang Wang University of Central Florida, USA
Rainer Wansch Fraunhofer IIS, Germany
Syed Waziruddin Kansas State University, USA
Janet Wiles University of Queensland, Australia
Man Leung Wong Lingnan University, Hong Kong, SAR China
Andrew Wuensche University of Sussex, UK
Petros Xanthopoulos University of Central Florida, USA
Ning Xiong Malardalen University, Sweden
Xin Xu George Washington University, USA
Gur Yaari Yale University, USA
Larry Yaeger Indiana University, USA
Shengxiang Yang De Montfort University, USA
Qi Yu Rochester Institute of Technology, USA
Zelda Zabinsky University of Washington, USA
Ras Zbyszek University of North Carolina, USA
Hector Zenil University of Oxford, UK
Guang Lan Zhang Boston University, USA
Qingfu Zhang City University of Hong Kong, Hong Kong,
SAR China
Rui Zhang IBM Research – Almaden, USA
Zhi-Hua Zhou Nanjing University, China
Tom Ziemke University of Skovde, Sweden
Antanas Zilinskas Vilnius University, Lithuania
XVI Organization

Best Paper Awards

MOD 2017 Best Paper Award
“Recipes for Translating Big Data Machine Reading to Executable Cellular Signaling
Models”
Khaled Sayed*, Cheryl Telmer**, Adam Butchy*, and Natasa Miskov-Zivanov*
*University of Pittsburgh, USA
**Carnegie Mellon University, USA
Springer sponsored the MOD 2017 Best Paper Award with a cash prize of EUR 1,000.

MOD 2016 Best Paper Award

“Machine Learning: Multi-site Evidence-Based Best Practice Discovery”
Eva Lee, Yuanbo Wang and Matthew Hagen
Eva K. Lee, Professor Director, Center for Operations Research in Medicine and
HealthCare H. Milton Stewart School of Industrial and Systems Engineering, Georgia
Institute of Technology, Atlanta, GA, USA

MOD 2015 Best Paper Award

“Learning with Discrete Least Squares on Multivariate Polynomial Spaces Using
Evaluations at Random or Low-Discrepancy Point Sets”
Giovanni Migliorati
Ecole Polytechnique Federale de Lausanne – EPFL, Lausanne, Switzerland
 Contents

Recipes for Translating Big Data Machine Reading to Executable

Cellular Signaling Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Khaled Sayed, Cheryl A. Telmer, Adam A. Butchy,
and Natasa Miskov-Zivanov

Improving Support Vector Machines Performance Using Local Search . . . . . 16

S. Consoli, J. Kustra, P. Vos, M. Hendriks, and D. Mavroeidis

Projective Approximation Based Quasi-Newton Methods . . . . . . . . . . . . . . . 29

Alexander Senov

Intra-feature Random Forest Clustering . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Michael Cohen

Dolphin Pod Optimization: A Nature-Inspired Deterministic

Algorithm for Simulation-Based Design . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Andrea Serani and Matteo Diez

Contraction Clustering (RASTER): A Big Data Algorithm

for Density-Based Clustering in Constant Memory and Linear Time . . . . . . . 63
Gregor Ulm, Emil Gustavsson, and Mats Jirstrand

Deep Statistical Comparison Applied on Quality Indicators

to Compare Multi-objective Stochastic Optimization Algorithms . . . . . . . . . . 76
Tome Eftimov, Peter Korošec, and Barbara Koroušić Seljak

On the Explicit Use of Enzyme-Substrate Reactions in Metabolic

Pathway Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Angelo Lucia, Edward Thomas, and Peter A. DiMaggio

A Comparative Study on Term Weighting Schemes

for Text Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Ahmad Mazyad, Fabien Teytaud, and Cyril Fonlupt

Dual Convergence Estimates for a Family of Greedy Algorithms

in Banach Spaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
S. P. Sidorov, S. V. Mironov, and M. G. Pleshakov

Nonlinear Methods for Design-Space Dimensionality Reduction

in Shape Optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Danny D’Agostino, Andrea Serani, Emilio F. Campana,
and Matteo Diez
XVIII Contents

A Differential Evolution Algorithm to Develop Strategies

for the Iterated Prisoner’s Dilemma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Manousos Rigakis, Dimitra Trachanatzi, Magdalene Marinaki,
and Yannis Marinakis

Automatic Creation of a Large and Polished Training Set

for Sentiment Analysis on Twitter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Stefano Cagnoni, Paolo Fornacciari, Juxhino Kavaja,
Monica Mordonini, Agostino Poggi, Alex Solimeo,
and Michele Tomaiuolo

Forecasting Natural Gas Flows in Large Networks . . . . . . . . . . . . . . . . . . . 158

Mauro Dell’Amico, Natalia Selini Hadjidimitriou,
Thorsten Koch, and Milena Petkovic

A Differential Evolution Algorithm to Semivectorial Bilevel Problems. . . . . . 172

Maria João Alves and Carlos Henggeler Antunes

Evolving Training Sets for Improved Transfer Learning

in Brain Computer Interfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Jason Adair, Alexander Brownlee, Fabio Daolio,
and Gabriela Ochoa

Hybrid Global/Local Derivative-Free Multi-objective Optimization

via Deterministic Particle Swarm with Local Linesearch. . . . . . . . . . . . . . . . 198
Riccardo Pellegrini, Andrea Serani, Giampaolo Liuzzi,
Francesco Rinaldi, Stefano Lucidi, Emilio F. Campana,
Umberto Iemma, and Matteo Diez

Artificial Bee Colony Optimization to Reallocate Personnel

to Tasks Improving Workplace Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
Beatrice Lazzerini and Francesco Pistolesi

Multi-objective Genetic Algorithm for Interior Lighting Design . . . . . . . . . . 222

Alice Plebe and Mario Pavone

An Elementary Approach to the Problem of Column Selection

in a Rectangular Matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234
Stéphane Chrétien and Sébastien Darses

A Simple and Effective Lagrangian-Based Combinatorial

Algorithm for S3 VMs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
Francesco Bagattini, Paola Cappanera, and Fabio Schoen

A Heuristic Based on Fuzzy Inference Systems for Multiobjective

IMRT Treatment Planning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Joana Dias, Humberto Rocha, Tiago Ventura, Brígida Ferreira,
and Maria do Carmo Lopes
 Contents XIX

Data-Driven Machine Learning Approach for Predicting Missing Values

in Large Data Sets: A Comparison Study . . . . . . . . . . . . . . . . . . . . . . . . . . 268
Ogerta Elezaj, Sule Yildirim, and Edlira Kalemi

Mineral: Multi-modal Network Representation Learning. . . . . . . . . . . . . . . . 286

Zekarias T. Kefato, Nasrullah Sheikh, and Alberto Montresor

Visual Perception of Mixed Homogeneous Textures in Flying Pigeons . . . . . 299

Margarita Zaleshina, Alexander Zaleshin, and Adriana Galvani

Estimating Dynamics of Honeybee Population Densities

with Machine Learning Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309
Ziad Salem, Gerald Radspieler, Karlo Griparić,
and Thomas Schmickl

SQG-Differential Evolution for Difficult Optimization Problems

under a Tight Function Evaluation Budget . . . . . . . . . . . . . . . . . . . . . . . . . 322
Ramses Sala, Niccolò Baldanzini, and Marco Pierini

Age and Gender Classification of Tweets

Using Convolutional Neural Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
Roy Khristopher Bayot and Teresa Gonçalves

Approximate Dynamic Programming with Combined Policy

Functions for Solving Multi-stage Nurse Rostering Problem . . . . . . . . . . . . . 349
Peng Shi and Dario Landa-Silva

A Data Mining Tool for Water Uses Classification

Based on Multiple Classifier Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . 362
Iván Darío López, Cristian Heidelberg Valencia,
and Juan Carlos Corrales

Parallelized Preconditioned Model Building Algorithm

for Matrix Factorization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 376
Kamer Kaya, Ş. İlker Birbil, M. Kaan Öztürk,
and Amir Gohari

A Quantitative Analysis on Required Network Bandwidth

for Large-Scale Parallel Machine Learning . . . . . . . . . . . . . . . . . . . . . . . . . 389
Mingxi Li, Yusuke Tanimura, and Hidemoto Nakada

Can Differential Evolution Be an Efficient Engine

to Optimize Neural Networks? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401
Marco Baioletti, Gabriele Di Bari, Valentina Poggioni,
and Mirco Tracolli
XX Contents

BRKGA-VNS for Parallel-Batching Scheduling on a Single Machine

with Step-Deteriorating Jobs and Release Times . . . . . . . . . . . . . . . . . . . . . 414
Chunfeng Ma, Min Kong, Jun Pei, and Panos M. Pardalos

Petersen Graph is Uniformly Most-Reliable . . . . . . . . . . . . . . . . . . . . . . . . 426

Guillermo Rela, Franco Robledo, and Pablo Romero

GRASP Heuristics for a Generalized Capacitated

Ring Tree Problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 436
Gabriel Bayá, Antonio Mauttone, Franco Robledo,
and Pablo Romero

Data-Driven Job Dispatching in HPC Systems . . . . . . . . . . . . . . . . . . . . . . 449

Cristian Galleguillos, Alina Sîrbu, Zeynep Kiziltan,
Ozalp Babaoglu, Andrea Borghesi, and Thomas Bridi

AbstractNet: A Generative Model for High Density Inputs . . . . . . . . . . . . . . 462

Boris Musarais

A Parallel Framework for Multi-Population Cultural

Algorithm and Its Applications in TSP . . . . . . . . . . . . . . . . . . . . . . . . . . . 470
Olgierd Unold and Radosław Tarnawski

Honey Yield Forecast Using Radial Basis Functions . . . . . . . . . . . . . . . . . . 483

Humberto Rocha and Joana Dias

Graph Fragmentation Problem for Natural Disaster Management . . . . . . . . . . 496

Natalia Castro, Graciela Ferreira, Franco Robledo,
and Pablo Romero

Job Sequencing with One Common and Multiple Secondary Resources:

A Problem Motivated from Particle Therapy for Cancer Treatment . . . . . . . . 506
Matthias Horn, Günther Raidl, and Christian Blum

Robust Reinforcement Learning with a Stochastic Value Function. . . . . . . . . 519

Reiji Hatsugai and Mary Inaba

Finding Smooth Graphs with Small Independence Numbers . . . . . . . . . . . . . 527

Benedikt Klocker, Herbert Fleischner, and Günther R. Raidl

BioHIPI: Biomedical Hadoop Image Processing Interface. . . . . . . . . . . . . . . 540

Francesco Calimeri, Mirco Caracciolo, Aldo Marzullo,
and Claudio Stamile

Evaluating the Dispatching Policies for a Regional Network

of Emergency Departments Exploiting Health Care Big Data . . . . . . . . . . . . 549
Roberto Aringhieri, Davide Dell’Anna, Davide Duma,
and Michele Sonnessa
 Contents XXI

Refining Partial Invalidations for Indexed Algebraic

Dynamic Programming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 562
Christopher Bacher and Günther R. Raidl

Subject Recognition Using Wrist-Worn Triaxial Accelerometer Data . . . . . . . 574

Stefano Mauceri, Louis Smith, James Sweeney, and James McDermott

Detection of Age-Related Changes in Networks of B Cells

by Multivariate Time-Series Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 586
Alberto Castellini and Giuditta Franco

Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 599

 Recipes for Translating Big Data Machine
Reading to Executable Cellular
Signaling Models

Khaled Sayed1, Cheryl A. Telmer2, Adam A. Butchy3,

and Natasa Miskov-Zivanov1,3,4(&)
1
Department of Electrical and Computer Engineering,
University of Pittsburgh, Pittsburgh, PA, USA
{k.sayed,nmzivanov}@pitt.edu
2
Department of Biological Sciences, Carnegie Mellon University,
Pittsburgh, PA, USA
ctelmer@cmu.edu
3
Department of Bioengineering, University of Pittsburgh,
Pittsburgh, PA, USA
aab133@pitt.edu
4
Department of Computational and Systems Biology,
University of Pittsburgh, Pittsburgh, PA, USA

Abstract. Biological literature is rich in mechanistic information that can be

utilized to construct executable models of complex systems to increase our
understanding of health and disease. However, the literature is vast and frag-
mented, and therefore, automation of information extraction from papers and of
model assembly from the extracted information is necessary. We describe here
our approach for translating machine reading outputs, obtained by reading
biological signaling literature, to discrete models of cellular networks. We use
outputs from three different reading engines, and demonstrate the translation of
different features using examples from cancer literature. We also outline several
issues that still arise when assembling cellular network models from
state-of-the-art reading engines. Finally, we illustrate the details of our approach
with a case study in pancreatic cancer.

Keywords: Machine reading
Big data in literature
Text mining

Cell signaling networks
Automated model generation

1 Introduction

Biological knowledge is voluminous and fragmented; it is nearly impossible to read all

scientific papers on a single topic such as cancer. When building a model of a particular
biological system, one example being cancer microenvironment, researchers usually
start by searching for existing relevant models and by looking for information about
system components and their interactions in published literature.
Although there have been attempts to automate the process of model building
[1, 2], most often modelers conduct these steps manually, with multiple iterations

© Springer International Publishing AG 2018

G. Nicosia et al. (Eds.): MOD 2017, LNCS 10710, pp. 1–15, 2018.
https://doi.org/10.1007/978-3-319-72926-8_1
2 K. Sayed et al.

between (i) information extraction, (ii) model assembly, (iii) model analysis, and
(iv) model validation through comparison with most recently published results. To
allow for rapid modeling of complex diseases like cancer, and for efficiently using
ever-increasing amount of information in published work, we need representation
standards and interfaces such that these tasks can be automated. This, in turn, will allow
researchers to ask informed, interesting questions that can improve our understanding
of health and disease.
The systems biology community has designed and proposed a standardized format
for representing biological models called the systems biology markup language
(SBML). This language allows for using different software tools, without the need for
recreating models specific for each tool, as well as for sharing the built models between
different research groups [3]. However, the SBML standard is not easily understood by
biologists who create mechanistic models, and thus requires an interface that allows
biologists to focus on modeling tasks while hiding the details of the SBML language
[4–7].
To this end, the contributions of the work presented in this paper include:
• A representation format that is straightforward to use by both machines and
humans, and allows for efficient synthesis of models from big data in literature.
• An approach to effectively use state-of-the-art machine reading output to create
executable discrete models of cellular signaling.
• A proposal for directions to further improve automation of assembly of models
from big data in literature.
In Sect. 2, we briefly describe cellular networks, our modeling approach, and our
framework that integrates machine reading, model assembly and model analysis. In
Sect. 3, we present details of our model representation format, while Sect. 4 outlines
our approach to translate reading output to the model representation format. Section 5
discusses other issues that need to be taken into account when building interface
between big data reading and model assembly in biology. Section 6 describes a case
study that uses our translation methodology. Section 7 concludes the paper.

2 Background

2.1 Cellular Networks

Intra-cellular networks include signal transduction, gene regulation, and metabolic
networks [8]. Signaling networks are characterized by protein phosphorylation and
binding events, which transduce extracellular signals across the plasma membrane and
through the cytoplasm [9]. Gene regulatory networks involve translocation of signaling
proteins from the cytoplasm to the nucleus, where the integration of these protein
signals act on the genome, resulting in changes in gene expression and cellular pro-
cesses [10]. The regulation of metabolic networks incorporates phosphorylation and
binding, as do signaling networks, and also integrates allosteric regulation, other
protein modifications, and subcellular compartmentalization [11].
 Recipes for Translating Big Data Machine Reading 3

Inter-cellular networks assume interactions between cells of the same or different

types. These interactions occur via signaling molecules such as growth factors and
cytokines, synthesized and secreted by one cell, and bound to itself or other cells in its
surroundings, or via a cell-cell contact.
At all levels of signaling, there are feedforward and feedback loops and crosstalk
between signaling pathways to either maintain homeostasis or amplify changes initi-
ated by extracellular signals [12].

2.2 Modeling Approach

When generating executable models, we use a discrete modeling approach previously
described in [13]. As illustrated in the example in Fig. 1, we represent system com-
ponents as model elements (A, B, and C in the example), where each element is defined
as having a discrete number of levels of activity. Each element has a list of regulators
called influence set. In our example, A is a positive regulator of C, B and C are positive
regulators of A, and C activates itself while B inhibits itself. Additionally, each element
has a corresponding update rule, a discrete function of its regulators. In our example, A
is a conjunction of B and C, while C is a disjunction of A and C. Although the model
structure is fixed, the simulator that we use [14] is stochastic, and thus, allows for
closely recapitulating the behavior of biological pathways and networks.

Fig. 1. Toy example illustrating our modeling approach.

2.3 Framework Overview

To automatically incorporate new reading outputs into models, we have developed a
reading-modeling-explanation framework, called DySE (Dynamic System Explana-
tion), outlined in Fig. 2. This framework allows for (i) expansion of existing models or
assembly of new models from machine reading output, (ii) analysis and explanation of
models, and (iii) generation of machine-readable feedback to reading engines. We
focus here on the front end of the framework, the translation from reading outputs to
the list of elements and their influence sets, with context information, where available.

3 Model Representation Format

To enable comprehensive translation from reading engine outputs to executable

models, the models are first represented in tabular format. It is important to note here
that the tabular representation does not include final update rules, that is, the tabular
version of the model is further translated into an executable model that can be
4 K. Sayed et al.

Fig. 2. DySE framework.

simulated. Each row in the model table corresponds to one specific model element (i.e.,
modeled system component), and the columns are organized in several groups: (i) in-
formation about the modeled system component, (ii) information about the compo-
nent’s regulators, and (iii) information about knowledge sources. This format enables
straightforward model extension to represent both additional system components as
new rows in the table, and additional component-related features by including new
columns in the table. The addition of new columns occurs with improvements in
machine reading.
The first group of fields in our representation format includes system component-
related information. This information is either used by the executable model, or kept as
background information to provide specific details about the system component when
creating a hypothesis or explaining outcomes of wet lab experiments.
A. Name – full name of element, e.g., “Epidermal growth factor receptor”.
B. Nomenclature ID – name commonly used in the field for cellular components,
e.g., “EGFR” is used for “Epidermal growth factor receptor”.
C. Type – these are types of entities used by reading engines as listed in Table 1.
D. Unique ID – we use identifiers corresponding to elements that are listed in
databases, according to Table 1.
E. Location – we include subcellular locations and the extracellular space, as listed
in Table 2.
F. Location identifier – we use location identifiers as listed in Table 2.
G. Cell line – obtained from reading output.
H. Cell type – obtained from reading outputs.

Table 1. Element type and ID database. Table 2. The list of cellular locations and
their IDs from the Gene Ontology [15]
Element type Database name
database.
Protein UniProt [16]
Location name Location ID
Protein family Pfam [17], InterPro [18]
Protein complex Bioentities [19] Cytoplasm GO:0005737
Chemical PubChem [20] Cytosol GO:0005829
Gene HGNC [21] Plasma membrane GO:0005886
Biological process GO [15], MeSH [22] Nucleus GO:0005634
Mitochondria GO:0005739
Extracellular GO:0005576
Endoplasmic reticulum GO:0005783
 Recipes for Translating Big Data Machine Reading 5

I. Tissue type – obtained from reading output.

J. Organism – obtained from reading output.
K. Executable model variable – variable names currently include above
described fields B, C, E, and H.
The second group of fields in our representation includes component regulators-
related information that is mainly used by executable models, with a few fields used
for bookkeeping, similar to the first group of fields.
L. Positive regulator nomenclature IDs – list of positive regulators of the
element.
M. Negative regulator nomenclature IDs – list of negative regulators of
the element.
N. Interaction type – for each listed regulator, in case it is known whether
interaction is direct or indirect.
O. Interaction mechanism – for each known direct interaction, if the mecha-
nism of interaction is known. Mechanisms that can be obtained from reading
engines are listed in Table 3.
P. Interaction score – for each interaction, a confidence score obtained from
reading.
The third group of fields in our representation includes interaction-related
provenance information.
Q. Reference paper IDs – for each interaction, we list IDs of published papers
that mention the interaction. This information is obtained directly from reading
output.
R. Sentences – for each interaction, we list sentences describing the interaction.
This information is obtained directly from reading output.
It is worth mentioning that this representation format can be converted into the
SBML format to be used by different software tools and shared between different
working groups. Additionally, the tabular format provides an interface that can be
easily created or read by biologists, and generated or parsed by a machine.

4 From Reading to Model

We obtain outputs from three types of reading engines, namely REACH [2], RUBI-
CON [24], and Leidos table reading (LTR) [25]. These reading engines provide output
files with similar but not exactly the same format. In Table 3, we list the interaction
mechanisms that can be obtained from these three reading engines, and in the following
sub-sections we outline their differences and the advantages of each reading engine.
6 K. Sayed et al.

Table 3. Intracellular interactions (mechanisms) recognized by the three reading engines.

Reading Recognized mechanisms
engine
REACH Activation, Inhibition, Binding, Phosphorylation, Dephosphorylation,
[23] Ubiquitination, Acetylation, Methylation, Increase or Decrease Amount,
Transcription, Translocation
RUBICON Activation, Inhibition, Promotes, Signaling, Reduce, Induce, Supports,
[24] Attenuates, Stimulate, Antagonize, Synergize, Increase and Decrease
Amount, Abrogates
LTR [25] Binding, Phosphorylation, Dephosphorylation, Isomerizations

4.1 Simple Interaction Translation

The first type of reading engine, REACH [2], can extract both direct and indirect
interactions, as well as interaction mechanisms, where available. The simplest and most
common reading outputs are those that include only a regulated element and a single
regulator, each of them having one of the entity types listed in Table 1, with the
interaction mechanism being one of the mechanisms described in Table 3. Such
interactions have straightforward translation to our representation format, that is, they
are translated into a single table row with some or all of the fields described in Sect. 3.
Given that our modeling formalism accounts for positive and negative regulators, while
reading engines can also output specific mechanisms where available in text, we
assume in the translation that Phosphorylation, Acetylation, Increase Amount, and
Methylation represent positive regulations, and Dephosphorylation, Ubiquitination,
Decrease Amount, and Demethylation represent negative regulations. Additionally, we
treat Transcription events as positive regulation.

4.2 Translation of Translocation Interaction

We translate translocation events (moving components from one cellular location to
another) using the formalism described in [26]. This formalism requires including two

Fig. 3. Schematic representation of a situation common to many biological signaling pathways

where the regulation of complex formation, A binding to B, is regulated by a third protein, C, so
that the A/B complex can activate D and inhibit E. F can regulate A that is able to regulate G
without forming a complex.
 Recipes for Translating Big Data Machine Reading 7

separate model elements for the translocated component, one at the original and one at
the new location. Additionally, in the translocation type of interaction, translocation
regulators can be listed.

4.3 Translation of Complexes

Binding interaction mechanism represents formation of protein complexes in most
cases. However, in order to include both individual proteins and complexes in which
they participate within a single model, we defined rules for incorporating complexes
listed in reading outputs into our model representation format.
A generic example is shown in Fig. 3. If an element in the reading output file is a
complex, we incorporate that output into our model representation format by creating a
separate table row for each component of the protein complex, and change the regu-
lation set as described in the example outlined in Fig. 3. If the formation of complex
AB is regulated by C, then we create two rows; one for element A, which is also
positively regulated by F, and one for element B. The positive regulation rule for
element A becomes (C AND B) OR F, while the positive regulation rule for element B
becomes (C AND A). Additionally, if an element is regulated by a complex, we list all
components of that complex as positive regulators for the element. In the example in
Fig. 3, the positive regulation rule for element D is (A AND B) because D is regulated by
the complex AB. An example of how complexes are translated from reading output into
our representation format is shown in Table 4.

Table 4. Converting REACH output for complexes into our modeling representation format.
Column name Element Positive regulator Mech. Paper Evidence
Name Type ID Name ID type ID
REACH output {FAK, {Protein, {Q05397, PIN1 Q13526 Binding PMC PIN1
PTP-PEST} Protein} Q05209} 3272802 stimulates
DySE Comp. 1 FAK Protein Q05397 PIN1 AND (Q13526, PMC the
format PTP-PEST Q05209) 3272802 binding of
Comp. 2 PTP-PEST Protein Q05209 PIN1 AND (Q13526, PMC FAK to
FAK Q05397) 3272802 PTP-PEST

4.4 Translation of Nested Interactions

REACH reading engine can also detect nested interactions, where some of the par-
ticipants are interactions themselves. The following sub-sections show several exam-
ples of these interactions.
Positive Regulation of Activation. As shown in Fig. 4(a), REACH can find and
output interactions where element A is activating element B, while element C is
positively regulating the interaction between A and B. We also include in this and the
following examples element D. In this case, we assume that D is a negative regulator of
B. This means that C will activate B only when A is active. If A is inactive, only D will
inhibit B, while C will not have any effect on B. The following is an example of the
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The people are a fine race; but, since the days when they were ejected from
Spain and returned to Morocco to be subject to the rule of Sultans who are Pope-
Kings, they have degenerated gradually and become a degraded people.
I am described by Mr. Allen as being all-powerful. If so, the inference naturally
is that I have neglected to do my duty in requiring the Sultan and his Government
to introduce reforms and improvements.
I have never ceased for nearly forty years to preach and pray, to urge and beg.
My archives are full of notes addressed to Ministers of the Moorish Government,
with suggestions and propositions for improving commerce, introducing railways,
roads, telegraphs, mining operations, removal of restrictions on commerce, &c.,
&c. All this, however, to little purpose, for the venal advisers of the Sultan have no
interest in reforms or improvements when they do not see a direct means of filling
their own pockets. Promises are frequently made to me, but rarely fulfilled. I have
lately received promises that the prohibition on the exportation of barley and
wheat, now lying rotting in granaries, will be removed, and yet they hesitate and
delay; and so it is with everything.
Yet I may conscientiously declare that the few improvements which have been
effected in this country have been brought about through my representations and
acts.
I have worked hard of late to obtain the revision of the Treaty of Commerce (of
1856), which has been agreed to by the Sultan; but still the old story of promise,
pause, postpone, and then leave the matter alone.
I have frequently pointed out to my masters at home that if we consider it
desirable that the independence and integrity of a neutral Sovereign like the Sultan
should be upheld, so that the passage of our shipping through the Straits should
remain free in time of peace or war, it is our duty, it is the duty of all those Powers
who desire to maintain the status quo, to take a more active and decided part than
they have done hitherto in requiring the Sultan and his Ministers to introduce
reforms and improvements, and that the people of this country, who can be almost
seen from the shores of Europe, should not be allowed to remain in their present
degraded state—a disgrace to civilisation. But this is a totally different view of the
question from that of allowing France to become the mistress of the great gut of
commerce, where all our shipping must pass when bound for the East or for India,
and to say to us Ne plus ultra.

Again on June 13, 1884, Sir John returns to the subject of French
designs and British apathy:—

Papers will tell you much of passing events here, some correct, others,
especially French, full of mis-statements. Did you see the Standard of June 3?
It contains an admirable article and a letter from ‘One who Knows.’
John Bull ought to know what our insidious neighbours are about, though
singing to our Government ‘Lullaby, lullaby,’ whilst preparing the mine which will
explode when it suits their purpose to make themselves masters of the Straits and
Southern coast of the Mediterranean from Spartel to Tripoli!
You will have seen in the papers that Ordega returned in an ironclad and
demanded that the fort should salute the French flag with twenty-one guns before
his landing, and that the acting Minister for Foreign Affairs and all the authorities
should come down to the pier to meet him. ‘To hear is to obey,’ with the heavy
guns of the ‘Redoutable’ pointed at this wretched town; and all asked for was
conceded.
Yesterday a squadron of eight ships (!) arrived here; they remain, I am told, at
the disposition of Ordega.
P.S.—Just as I closed my letter the French squadron left, and I got a note to
say some arrangement has been made about protection to the Sheríf, and that the
question of frontier is deferred. It will come on, however, before long.

For the time the danger, as the following letter shows, was
averted:—

I said to a colleague the other day that man was prone to attribute to the
machinations of the devil anything that was adverse, whereas the poor devil is the
victim of his traducers; thus, I said, it is with me. Whatever goes wrong in Morocco
is attributed to that bête noire—Drummond Hay.
I know not whether you have seen another clever letter of ‘One who Knows’ in
the Standard of 30th ult.
 With reference to the last paragraph, I have to say that a great change has
come over Ordega since the hurried departure of the French squadron (ordered by
telegraph). He has altered his tone with the Moorish Government and the local
authorities, and has told the Sheríf he cannot support the tribes who seek for his
protection against the authority of the Sultan. The question of rectifying the frontier
has also been abandoned, and the most solemn assurances are given to Italy,
Spain, and England that France will not disturb the status quo, unless a state of
anarchy takes place in Morocco compelling her to interfere. That is, however, the
question. Insurrection has been prevented, and the Sultan has given orders for the
chastisement of the disaffected tribes. This system of ‘eating up’ rebels, which you
can remember in the time of the old Sultan, renders of course the Sovereign most
unpopular with his unfortunate subjects.

With reference to the calumnious article in the Gaulois to which he

had called Lord Granville’s attention, he writes from London on
October 18, 1884:—

I have just received a courteous private letter from Lord Granville, saying he
had delayed replying to my letter as he has been in communication with
Waddington; he asks to see me on Monday.

The result of the interview is given in a letter three days later:—

Lord Granville was very civil and kind.

Ferry shirked getting justice done by publishing a disclaimer. His Lordship
agreed that a question should be put in the House of Lords. He only asked that
Zouche should give him notice, and promised to reply in a manner that would be
satisfactory to me. I gave him a full dose; outpouring all that was in my heart, both
about abuse and my having been passed over in the course of my career by
juniors—being told my ‘services were too useful in Morocco to be dispensed
with’—and now, I said, ‘the public press declares that I am useless and stop the
way,’ &c.
Lord Granville looked blandly at me, now and then making encouraging
remarks, such as, ‘Your character stands too high to be affected by the attacks of
men like Monsieur Ordega, and that bankrupt fellow,’ meaning ———.

Before the subject was mentioned in the House of Lords, Her

Majesty’s Government had given proof that they did not underrate
Sir John’s integrity and good service, thereby affording him sincere
satisfaction.

‘I think you will be glad to hear,’ he writes from Ravensrock in November, 1884,
‘that I have just received a note from Lord Granville announcing that Her Majesty
has been pleased to confer upon me the G.C.M.G., “in recognition of my long and
good service.” I confess I care little to add some letters of the alphabet after my
name, but I am pleased at the discomfiture of enemies who have been plotting
against me. My French colleague will have an attack of the English malady,
“spleen.” He is now treating with these unfortunate Moors at the cannon’s mouth.
‘An ironclad is in the bay to support his demands. He seeks for revenge, on
account of the humiliation suffered by his protégé and dupe the Sheríf, who is now
treated almost as an outcast by the Moors of Tangier, and is called the Sheríf
“francés.”’

The question to which Sir John referred in his interview with Lord
Granville was asked by a personal friend in the House of Lords. It
elicited replies which completely exonerated him from all the blame
which had been cast upon him, and was made the occasion for the
strongest expressions of satisfaction with his long and arduous
services. The following passages are taken from the Times of
November 22, 1884:—

Lord Zouche asked Her Majesty’s Government whether any official denial had
been published by the French Government to an article which appeared in the
Gaulois newspaper in the spring of this year wherein the editor accused several of
the Foreign Representatives at Tangier of corrupt practices, and among them the
British Minister, Sir John Drummond Hay, stating that he (the editor) had obtained
this information from the French Minister at Tangier, M. Ordega, who was at that
time in Paris on leave of absence; and, as it would appear that, owing to the fact of
no denial having been given to those grave charges, other accusations were made
by French journals which were referred to in English journals to the effect that Sir
J. D. Hay had obstructed British enterprise and commerce, and had encouraged
the Sultan of Morocco in his policy of resistance to all reform and improvement,
whether there were any grounds for such grave charges having been put forward.
Sir John Hay had been passed over by many of his juniors, and had now been
upwards of forty years in his present post, and he and his friends thought it
incumbent upon them to have some sort of public contradiction of these most
unfounded charges and some sort of public vindication of his character.
 Earl Granville.—My Lords, I think the noble lord has correctly stated the facts of
the case. The editor of the Gaulois, it appears, accused Sir John Hay and his
colleagues of most intolerable practices, and gave M. Ordega as his authority.
Now, I am not sure that if I read such an article as this concerning myself I should
not treat it with contempt and trust to whatever character I had. But it is a different
thing when men serving their country in distant countries are thus unjustly
attacked, for, as in this case, the extract from the French paper is copied not only
into other foreign newspapers, but into English newspapers. However, after what
has occurred I thought it necessary, at the request of Sir J. D. Hay, to make an
application to M. Ferry, in courteous terms, that M. Ordega should be called upon
either to substantiate, or retract, or to say that he had not communicated the article
to the Gaulois. M. Ferry, in the first instance, said the Gaulois was perfectly wrong,
that no such report had been circulated by Ordega himself, and that he thought
that it was hardly worth while to contradict a statement made in a newspaper
which was well known to be so strongly opposed to the existing French
Government. M. Ordega was, however, applied to, and he telegraphed to Paris
entirely denying that he had communicated or inspired any such article in the
Gaulois. M. Ferry took the view that a great deal of time had elapsed, and that it
was really better not to call attention to the matter now. I have been in
correspondence with Sir J. D. Hay, and the last letter I received from him, only a
day or two ago, was to the effect that he was perfectly satisfied and that he should
trouble his head no more in the matter. I am glad to be able to add that I believe
there is no man in the diplomatic service more honourable or more energetic in the
discharge of his duties than Sir J. D. Hay. The noble lord says that Sir J. D. Hay
has been passed over for promotion; but I remember instances where persons
employed in the diplomatic service have been, to use a homely phrase, kicked
upstairs to get them out of a place where they were doing mischief instead of
good. I believe it to be exactly the contrary in the case of Sir John Drummond Hay.
He is most fit for the post he has held, and for that reason he has lost some
chances of personal advancement. I really can only repeat in the strongest way
that Sir Drummond Hay was quite justified in dismissing from his mind any
imputation made against him, and I have great pleasure in adding that a short time
ago the Queen granted him the Grand Cross of St. Michael and St. George.
The Marquis of Salisbury.—As the youngest and most recent of the foreign
secretaries the noble earl has referred to, I have very great pleasure in joining with
him in expressing the high estimation which was always entertained for Sir
Drummond Hay by his superiors. Not only was the charge against him ridiculous,
as it would have been against any representative of the Crown, but he is a man of
singular integrity and patriotism, and a more able, progressive, and intelligent
adviser does not exist in the diplomatic service. I always thought it a weak point in
our diplomatic arrangements that a class of men like Sir Drummond Hay, of whom
there are several in the service, who have special qualities for the particular post
they occupy, cannot be rewarded as they should be rewarded without detriment to
the public service, because by the rules of the service their rank cannot be
increased where they are, and because they cannot be removed from the post
they occupy without doing harm to the public service. I think Sir Drummond Hay
has been more than repaid by the universal confidence with which he is looked up
to and the very high esteem in which he has always been held. I think it is
unnecessary to vindicate any English statesman against foreign newspapers,
because their statements are, as a rule, absolutely phenomenal. I remember one
statement in a foreign newspaper which informed us that the noble duke for whose
eloquence we are waiting to-night was about to go abroad to spend the winter in
the South of France with his well-known greyhounds; and I remember another
such statement which informed us that a well-known statesman, and English Lord
Chancellor, was about to receive some high honour from the Crown for his
services as President of the Berlin Congress.
The Earl of Malmesbury and Lord Napier of Magdala also bore their testimony
to the high integrity and character of Sir Drummond Hay, and,
The Earl of Derby said that he did not know any person in any branch of the
public service more utterly incapable of such conduct as that imputed to him than
Sir Drummond Hay. He had always known him as an active and able public
servant.
RAVENSROCK
 CHAPTER XXV.

LAST YEAR OF OFFICIAL LIFE. 1885.

Early in 1885 Monsieur Ordega was recalled by the French

Government and succeeded by Monsieur Féraud. Of the new French
Minister Sir John writes on March 30:—

Féraud has arrived, and is all that he has been described—very friendly and
desirous to please, liked by every one.
I gave him a dinner, and we have had many chats. He disapproves entirely of
Ordega’s proceedings, especially of his conduct towards me and of his
contributing venomous articles to journals regarding me and my acts.
He is a first-rate Arabic scholar and even poet, a good artist, a great
archæologist, and is writing a work on Tripoli. In two affairs I have tested his
assurances of good-will, and have good grounds for being satisfied.
I told him positively that there was no reason why there should not always be a
perfect ‘accord’ between us, except on one point, viz. if either of our Governments
desired to take possession of Morocco. ‘Kick it out,’ I said, ‘into the Atlantic a
hundred miles, and then the sooner Morocco was colonised by a civilised people
the better.’

Subsequent intercourse confirmed the favourable impression. In a

later letter Sir John writes again of M. Féraud:—

I think I told you that Féraud complained the other day of inaccurate and
malevolent reports, about his doings, in local papers, and said he hoped I did not
believe them. I told him I was the last man to put any faith in newspapers; that I
had been the butt of their shafts, which, at first, had stung; but I had grown so
accustomed to abuse that now, when not held up as the author of evil, I feel it and
wonder whether I have ceased to be of any importance in the eyes of my revilers.
‘You,’ I said, ‘will soon be accustomed to this also, and find it pleasant.’ ‘Charmes,’
the contributor of Débats, who has been with Féraud to Fas, was in the room, and
had been introduced to me. Last year he wrote virulent articles against me,
inspired, I think, by Ordega. He was sitting on my right, a little behind me, so I took
an opportunity of letting go my shaft, and added, ‘Why, even leading papers in
France chose last year to publish virulent and untruthful articles about me; but, far
from my having any rancorous feeling against the writers, I am grateful to them.
They drew public attention to me and my conduct in such a manner that it was
taken up in our Senate, and my conduct and character were vindicated by the
Ministers of all parties, and a mark of Her Majesty’s approval conferred upon me. I
am grateful to my revilers in England and France.’
When leaving, I gave C. my hand, and my eye, I dare say, twinkled. C. has
lately written an article in the Débats on the policy of keeping the status quo in
Morocco and disapproving of all the late policy. Féraud evidently inspired it.

In June, 1885, he writes:—

Now I am an old man, having entered my seventieth year. How time glides by.
Next year, if I live till then, we shall be quitting this for good. . . .
Féraud is still at the Court. He has made a good name by rejecting the
trumped-up and usurious claims of protected Jews. He denounced them to the
Sultan, and complained of public notaries who, in league with claimants, had
drawn up false documents.
Though he told me and other colleagues he had no affair of importance at Fas,
we know better. He aims at obtaining what France wants by cajolery and presents.
He eschews menace and force. He is more dangerous and far more able than his
predecessor. I shall, I think, get on well with him; I cannot blame him for playing
the game which suits his country. If England had been as contiguous to Morocco
as is France, I think ere this we should have annexed this misgoverned country;
but it would never do for us that France should hold the Straits—the gut of
commerce, the passage to India and the East. It is far more likely to be injurious
than if she held the Canal. As a sentinel of the Straits, I fire my gun, as a warning,
when I know of a move to obtain that object.
An article in Débats says, with some reason, that England, in consequence of
her failures in the East, is no longer looked up to by the Moorish Government as
before, and Italy is the rising sun. There is some truth in this. . . .
Oh! I shall be so glad to be at rest next year, if I live. I am sick of this
Government and its stupid, blind policy. As I said to Torras[63], ‘What is the use of
a fair lady saying she loves you better than any one in the world, and yet, while
refusing to allow you to embrace her, she showers kisses on the man whom she
declares she detests?’ Moor shut up by the sillygism.
 His letters become at this time to an increasing degree full of
expressions showing that he was weary of the hopelessness of his
task. Thus he writes:—

Every day as the time draws nearer I sing, ‘Oh be joyful!’ I am sick of the
bother, and the dirty work of British subjects that I have to attend to. I am tired also
of writing and talking to this fossil Government, who cannot, or will not, understand
their true interests.

The same note is struck in a letter written from Ravensrock on

July 3, and September 7, 1885:—

We are well. Air here delightful, only 78° up till now, in the shade. Cholera
striding fast in a deadly march on the other continent.
Weber[64] just left. This time next year I shall have gone also, and go without a
pang, except to leave this lovely spot and the kindly peasantry who always
welcome me with bright faces and affectionate words. Civilised men are getting too
independent to be demonstrative of good-will and gratitude.

Sept. 7.
The Sultan has sent orders for the settlement of various long-pending affairs,
but nothing about the Convention of Commerce. Their last mot on this is, ‘How is it
possible that the Sultan’s treasury can be benefited by a reduction of duties on
exports?’ and, ‘If we export all that the English Minister suggests, in the revised
Tariff, the price of food will rise and the Moslem will be starved!’ These Moors are a
parcel of children; but we can hardly be surprised at their holding these absurd
views when a restrictive policy is pursued in commerce by the greatest nation in
the world.
As to the cable between this and Gibraltar, the Sultan’s advisers tell him that,
once it is laid, ‘Every day some Representative will telegraph for a ship of war!’
One does not know whether to laugh or to cry at such tomfoolery. I think, however,
jealous folk drop poison in the ear of the Sultan, and din in His Sherifian Majesty’s
ears that England has fallen from her high estate, and that she barks but can no
longer bite. The French papers in Arabic from Algeria sing this loudly.

The existence of slavery in Morocco called forth now and again

articles or letters which appeared in British journals, and in this and
the previous year the subject was much discussed in the
newspapers. At Sir John’s suggestion, all natives,—who as
employés of the officials attached to the Legation or Consulates
enjoyed British protection,—were required to liberate their slaves. He
believed, however, the form of slavery in that country to be lenient,
and though always urging on the Moorish Government the
desirability of abolishing an institution so obnoxious to modern ideas,
he foresaw difficulties that might, and did, prove insuperable in his
day. The following extracts from his letters on this topic, written at
different times, will show the attitude which he adopted towards the
question:—

We have no Slave Treaty with Morocco.

The British Government has at times called upon me for reports upon slavery. It
is of the mildest description. There is no slave trade by sea; five or six hundred
slaves are brought yearly by land, I believe. The men are bought for servants in
the houses of wealthy Moors, and the women as handmaids or servants. They are
very kindly treated, and when their masters die are given their liberty and a portion
of the estate.
With one exception, the only cases where I have been appealed to, to
intervene in behalf of slaves, have been to beg that the masters should not give
their slaves liberty! They preferred, they said, a comfortable home! Of course it is
desirable that slavery should be abolished even in Morocco; but it would be a
hopeless task to urge upon the Moorish Government the abolition of a domestic
institution, admitted by the laws of the Prophet, unless England had an opportunity
of rendering Morocco some great service, such as preventing her being attacked
by a stronger Power. Hitherto we have given her no aid but much advice in the
hour of need, and then deserted her.
When England has done as much for Morocco as she has done for Turkey and
Egypt, by preventing unjust aggressions, &c., &c., then she may hope to persuade
the Sultan to abolish slavery. Do you remember the long correspondence between
our dear father and the Sultan on the subject, which finished by His Sherifian
Majesty quoting Scripture in favour of slavery? I also have had a fling on the
subject. But slavery in Morocco exists in the mildest form. Slaves are not used for
agricultural purposes—not transported, like pigs, in vessels—and are generally the
spoilt children of the house.
I am not going to tell all this to the world, and thus appear to be defending
slavery.
 However, I hammer away at the Moors on the subject, and in my last note
hinted that if they do not seek to satisfy public opinion by abolishing the
objectionable institution, they may be finally abolished—or something to that effect.
...
The Anti-Slavery Commissioners came to me to say good-bye, thanked me for
courtesy to them, and volunteered to say, ‘You are much belied, Sir John, but we
have taken care to sift for truth and shall make it known.’
The story about the Jewess who was flogged last year by the Governor of Dar-
el-Baida, in the presence of the native employed as British Interpreter, is most
exaggerated. I dismissed the Interpreter as soon as I heard he had been present
at the flogging of a woman.
Esther is a pretty girl of a dissolute character. The sons of the Interpreter had
been wasting their father’s patrimony on her, and when the old father remonstrated
with his sons, caught with Esther, one of them fired a pistol at him, so the
Interpreter rushed off to the Governor to demand the arrest and punishment of the
woman and of his sons. The Governor arrested and flogged all three, in
accordance with the law of this country, but there was no brutal punishment of the
girl. What nonsense to talk about the Interpreter having left without giving
compensation! Who was to give it, and who receive it? The Governor did his duty
according to their tyrannical law. The Interpreter did not punish the woman or his
sons; it was the Governor; and the Interpreter got dismissed by me from his
employment, a very severe mode of showing my disapproval of his being present
at the flogging of a woman. Subsequently I got the Sultan to abolish the flogging of
women by Governors for immorality, and to ordain that it shall be inflicted by a
Kadi only. Now a Kadi cannot order a woman to be flogged for adultery unless six
honourable men of spotless character declare they witnessed her misdeed! So no
woman will henceforward be flogged in Morocco. This I obtained in black and
white, and Esther got a warming with a beneficial result to all females of her class.
Féraud is to join the German Minister and me in negotiation. He is one of the
best Frenchmen I ever had to deal with. I expect the Sultan will kick hard against
the reduction of the Tariff.

Another subject with which Sir John was much occupied during
the closing years of his residence at Tangier was a scheme of prison
reform and the restriction of the period of incarceration for debt.
Writing on this point in March, 1886, he says:—

As to prisons, they are no doubt very bad; and so, Mrs. Fry tells us, were ours
fifty years ago. I obtained an order from the Sultan for cleaning them, and for
bread for those who have no means to buy food; but such orders, though given, if
they entail any expense, are soon disregarded. At Tangier I send a soldier of this
Legation now and then to inspect the bread. The quality and quantity diminish, and
the profits go into the pocket of the person in charge, so I have a constant battle
with the authorities.
Unless the whole administration of the Government were reformed, it is a
hopeless task trying to sweep this Augean stable.
English humanitarians are shocked to find no beds provided for prisoners. They
do not bear in mind that the poorer classes can always take up their bed and walk
—their bed, i.e. a rug, or piece of mat. They say how horrid it is that the prisoners
should have fetters. At Tetuan the fetters were removed; one hundred and fifty
prisoners rushed to the door, knocked over the guards, and fled into the
mountains. This has often occurred when prisoners are free of fetters.
I have taken steps to put a stop to the arrest and imprisonment of debtors of
British subjects without trial. Great cruelties have been practised upon debtors at
the demand of the Foreign Representatives, often for claims that are either
fraudulent or unjust. There is an outcry against me by British creditors because I
do not back the Government in extorting money from wretched debtors, too often
the victims of usurious Christians and Jews. I have just sent in a report to the
Government on this subject.
The Jews are certainly an oppressed race, but many of those who have
obtained protection conduct themselves in such an arrogant manner, and are guilty
of such infamous proceedings in forging false documents about debts of Moors, or
in putting forward preposterous claims based upon the grossest usury, that the
Mohammedans are exasperated, and some day, when a revolution takes place or
the Sultan dies, there will be a massacre and pillage of Jews in the interior.
When the chief Jews of Fas requested Féraud, during his mission, to obtain for
them a grant of ground to add to the Mellah[65], they especially requested that
protected Jews should not be allowed to inhabit the new quarter, as they said they
expected some day an onslaught of the Mohammedans on these persons, and
they wished to be separated from them. Féraud told me this.

The revision of the Commercial Treaty of 1856 might, perhaps,

have been forced upon the Moorish Government by the united
Representatives of the Foreign Powers. But, though on this point the
various Ministers joined hands, the hope entertained by Sir John that
a Convention might be framed which would abolish the system of
irregular protection was not realised. Under the terms of the
Convention of 1882, protection is still afforded to the numerous
agents of European traders and agriculturists, who therefore are not
immediately amenable to the jurisdiction of the Moorish authorities.
On this point Sir John had been defeated by the action of his
colleagues. But the wisdom of his proposals was abundantly justified
by the course which was taken by the negotiations for a new
Commercial Treaty in 1886. On the advantages of revising the
Commercial Code of 1856 all the Representatives of Foreign Powers
were agreed, and made common cause together. But their efforts
resulted in failure, and this failure was principally due to their
previous refusal to surrender or restrict their privileges of protection.
The Moorish Government showed a natural reluctance to encourage
European trade by an improved treaty, fearing that a greater influx of
European merchants and agriculturists would only multiply the
number of irregularly protected Moorish subjects as agents, and
remove more natives from the direct control of the Moorish
authorities.
Though Sir John might reasonably derive some satisfaction from
this practical proof of the wisdom of his advice to his colleagues, his
failure to obtain a revision of the Commercial Treaty deepened his
sense of the impossibility of reforming the Moorish Government. He
was weary of the hopeless struggle which he had carried on for more
than forty years. In spite of his personal regret at severing his
connection with Morocco, he longed to throw off the official harness
under which he had so often chafed. His letters in the summer of
1886 are filled with expressions of his delight at his freedom:—

July 2, 1886. Eve of departure. The Jews have sent a deputation and address.
Moors pour in with lamentations. Torras weeps in a letter. Even British subjects join
in the wail, whilst I continue to sing, ‘O be joyful.’
Alas! dinners and lunches are the disorder of the day; and speeches, which
being pathetic about our departure, choke me and prevent a fitting response.
July 4, 1886. Here I am, with my harness off, kicking my heels like an old horse
turned out to grass. So glad to send dispatches and letters to my address to the
Chargé d’Affaires.
 I had a very flattering letter from Lord Rosebery’s private secretary, Villiers, to
say that his Lordship, in ‘recognition of my long and distinguished services,’ will
meet my wishes, &c., &c. . . .
We have been fêted successively by the diplomats here, and speeches were
made laudatory of me. In a circular, each vied in saying flattering things, such as
that I had been looked up to for my experience and clear-headedness as the
guide, &c. of the Diplomatic Corps.
We are on the look out for the s.s. Mogador. I think I told you the Forwood
Company have placed her at my disposal. . . .

Disgusted at the last proof of Moorish apathy and obstinacy, Sir

John declined to pay a formal visit of farewell to the Moorish Court,
and the Sultan’s Prime Minister addressed him a valedictory letter on
behalf of himself and his colleagues in office, a translation of which is
subjoined as a curious specimen of Oriental phraseology:—

Praise be to God!
The beloved and judicious Counsellor, who strives to promote good relations
between the two friendly Sovereigns, the Minister of the exalted Queen of Great
Britain and Empress of India, in the dominions of Morocco.
We continue to make inquiries regarding you and regarding your condition, and
we trust that you may always be prosperous.
Which premised, we have received your letter in which you inform us that, your
term of office having expired, you are about to quit this country, and you express
your regret that you are unable to have an audience of His Majesty, exalted by
God, in order to take leave of His Sherifian Majesty, and express your gratitude for
the marks of good-will, confidence, and friendship that His Majesty has shown
towards you, and you observe that you have served for forty years in these happy
dominions, and that our Lord and Master, the grandsire of our present Lord and
Master (assisted by God), and our Master the sire of His Majesty (may God
sanctify them both), bestowed on you their confidence, friendship, and trust, and
that our Lord and Master (may God assist him) has likewise held you in the same
regard, and that the friendship between the two Governments has remained in the
same state as formerly, it has neither altered nor been disturbed; and that you will
never grow weak in your devotion to the welfare of His Majesty and of his subjects,
for you are convinced of the friendship of His Majesty and of his subjects towards
you: you request us also to bid farewell in your name to the Uzirs and chief officers
of the Sherifian Court, whom you name, and you further state that, should God
prolong your life, you will return to this country after the lapse of a year, and will
reside here for a time during the winter months, and that, should it meet with Her
Majesty’s approval and your Government grant its consent, you would then visit
the Court in a private capacity with the view of taking leave in person of His
Majesty, exalted by God.
I have laid your letter before our Lord the Sultan, and His Majesty has taken
into consideration all you state in it, and (may God render him powerful) has
commanded me to reply to it and to state that your departure from these blessed
dominions causes great grief and sorrow, as it was sure to do, for you are one of
the wise and judicious persons of your illustrious Government, who have from
ancient times mediated between them and the Sherifian Government with
friendship, sincerity, and consideration, as is known to all, and about which there
can be no dispute, and which at all times has been continuously renewed, proved,
and confirmed by the strength and power of God. And the fact that your exalted
Queen selected a sagacious person like yourself, of excellent social qualities,
pleasant to have relations with, and seeking to do good, for service in this country
for so long a time, is a proof of her sincere friendship and of her desire to promote
good feeling and to strengthen the bonds of union between the two friendly
Sovereigns, and is a sign whereby is known Her Majesty’s extreme judiciousness,
wisdom, and judgment; for a person gives proof of his judgment and condition by
one of these things, viz. his envoy, his letter, or his present. His Sherifian Majesty
(may God render him powerful) has commanded me to convey the expression of
his sincere thanks and best acknowledgments to your beloved Queen, and to
yourself also, O friend, and invoked on Her Majesty an increase of power,
greatness, dignity, and grandeur; and on you, blessings on yourself, on your family,
children, relatives, and posterity.
I am to add that what you state regarding the confidence that was reposed in
you by our Lord and Master, His Sherifian Majesty’s sire (may God sanctify him), is
true and well known to every one, and His Sherifian Majesty (may God render him
powerful) likewise reposes confidence in you and regards you as a sincere friend,
and that your remark that the friendship between the two Governments has
undergone no change during the term of your office is also true, for the friendship
between the two Governments is the result of your services, verifying the opinion
held of you by your illustrious Government, the soundness of their judgment and
the accuracy of their discernment regarding yourself, and it (the friendship) has
through your assistance increased in purity, constancy and growth, in love and
affection, in word and deed. And as to what you say that you will not grow weak in
your devotion to His Sherifian Majesty and to his subjects, this is in accordance
with the opinion formed of you, and is what is confidently expected of you, for such
is the disposition of persons of a friendly and affectionate character, whether they
be near or far.
 I have taken leave in your name of the Uzirs and officers of the Sherifian Court
whom you mentioned, and they all reciprocated your affection and gave
expression to it, and praised you, and invoked blessings on you, and were not
sparing in their expressions of sorrow and grief at your departure, and recited the
lines of the ancient poet:—
‘Though severed in body we suffer no hurt; for our hearts are united, welded by
pure love.’
With regard to your statement that if God prolongs your life, and it is agreeable
to His Sherifian Majesty, you will visit the Sherifian Court (exalted by God), and
that, should your Government approve, you would come with the object you
mention, our Lord (may God make him glorious) has commanded me to reply that
he prays your life may be prolonged by the power of God, and that you may
continue in happiness and health, leading an agreeable life; and if your
Government sanction your coming with this object, you are welcome, and such
sanction will be agreeable to His Sherifian Majesty (may God assist him), for it
(your Government) desires for you and for His Sherifian Majesty only what is good,
and you seek only to promote the welfare of them both, and how indeed could your
Government refuse to grant its sanction for what is beneficial? Our friendship for
you is everlasting, and its freshness will never fade day or night. May God be
gracious on the leave-taking, and not forbid the meeting.
Finished the last day of Ramadan, 1303 (July 3, 1886).
Mohammed Mefadal Ben Mohammed Gharrit.

On his retirement, Her Majesty was pleased to make Sir John a

Privy Councillor, and, though no longer holding a responsible post,
he was constantly appealed to on Morocco affairs by the British
Government.

‘The Foreign Office,’ he writes, in December, 1886, to his daughter, Mrs.

Brooks, ‘continue to send me dispatches about Morocco to be reported on, and,
when I make suggestions as to actions, they are adopted. This is pleasing to me,
and Government, though they rather bother me with their consultations, flatter me
by their continued confidence in my counsels.’

The Emperor of Austria sent Sir John his portrait set in brilliants
on the lid of a golden casket or snuff-box, and by special permission
of Her Majesty he was allowed to accept the order of the Grand
Cross of the Danebrog from the King of Denmark—for whom as for
Austria he had so long acted as Agent in Morocco. The Danish order
was the only one he was permitted to accept of the many foreign
decorations bestowed on him during his long career.

Until the end of Sir John’s life, it may be added, his name and
personal influence retained their ascendency over the natives, as will
be seen from such passages as the three following extracts from
some of his letters, written from Ravensrock in 1891 and 1892:—

The Basha, Hadj Mohammed Ben Abd-el-Sadek, called to make known to me

an order he had received from the Sultan to tell me that His Sherifian Majesty
looked upon me as a true friend of himself and of the people of this country, and
the Basha said he was directed, should any serious question arise, to ask for my
advice, as His Sherifian Majesty felt persuaded that I would always be actuated by
feelings of justice and friendship in giving counsels, as in the time of his sire and
grandsire.
I informed the Basha that I had withdrawn from intervention in official affairs,
and that some of the Foreign Representatives might be disposed to resent such
interference, even if my counsels happened to be beneficial to them in bringing
about settlements of vexatious questions.
The Spaniards are making lime at the caves of Ashkar, and live there. The
caves are Government property, and the stone has been used for making mill-
stones for two thousand years. The poor villagers of Medióna and Jebíla
complained to me, saying that they are afraid some day that mountaineers who
visit Ashkar to buy mill-stones may kill or rob these Spaniards, and then an
indemnity will be demanded by the Spanish Government, and they (the villagers)
will be thrown into prison. (I told the villagers to complain to the Basha.) . . .

Or again, in January, 1892:—

The ‘Thunderer’ remains here, as the mountaineers belonging to the Tangier

province have revolted against the Basha, and troubles are expected. I think the
Sultan will remove the Basha, who is unfit to govern. Happen what may, I and
mine are quite safe, for the Moors on mountains and plains look upon me as their
friend; and so indeed have I been. I remained during the Spanish war, when every
Christian and Jew bolted, and no barbarian harmed me or mine. . . .

Or, once more, the following written in February, 1892:—

 When you arrive, all will be settled with the tribes. The Fahs are coming in with
presents of oxen, &c. Jebála follow. The new Basha, a good fellow, has written me
a letter, received yesterday, to say he is coming up here to pay me a visit as soon
as all the tribes have come in (and looks upon me as Baba[66]). The fact is, I was
appealed to by the tribes, &c. whether they should accept him, as he is a relative
of the late Basha. I said certainly—and told them to come. Ships of war are
leaving. All’s well that ends well.
CHAPTER XXVI.

OUT OF HARNESS.