3 4

32
1 14
4 2
1
3 2

and 2

Other Applications of
Graphs and Networks

Jo Ellis-Monaghan
St. Michaels College
Colchester, VT 05439
e-mail: jellis-monaghan@smcvt.edu
website: http://academics.smcvt.edu/jellis-monaghan
 Graphs and Networks
A Graph or Network is a set of vertices (dots) with edges (lines)
connecting them.

A A
A B B
B

A multiple edge

C D C
D D C

A loop

Two vertices are adjacent if there is a line between them. The vertices A and
B above are adjacent because the edge AB is between them. An edge is
incident to each of the vertices which are its end points.

The degree of a vertex is the number of edges sticking out from it.
 The Kevin Bacon Game
or
6 Degrees of separation
Bacon # of Connery # of
Number People Number people
0 1 0 1
1 1766 1 2216
2 141840 2 204269
3 385670 3 330591
4 93598 4 32857
5 7304 5 2948
6 920 6 409
http://www.spub.ksu.edu/issues/v100/FA/n069/fea- 7 115 7 46
making-bacon-fuqua.html
8 61 8 8
Total number of linkable
Kevin Bacon is not even actors: 631275
Average Connery
Number: 2.706
among the top 1000 most Weighted total of linkable
actors: 1860181
connected actors in Hollywood Average Bacon number: Data from The Oracle of
Bacon at UVA
(1222th). 2.947
 The small world phenomenon
http://mathforum.org/mam/04/poster.html
Stanley Milgram sent a
series of traceable letters
from people in the
Midwest to one of two
destinations in Boston.
The letters could be sent
only to someone whom
the current holder knew
by first name. Milgram
kept track of the letters
and found a median
chain length of about six,
thus supporting the
notion of "six degrees of
separation."
Social Networks
•Stock Ownership (2001 NY
Stock Exchange)
•Children’s Social Network
•Social Network of Sexual
Contacts

http://mathforum.org/mam/04/poster.html
Infrastructure and Robustness
Scale Free

Number of vertices
Vertex degree
JetBlue

Distributed

Number of vertices

Vertex degree
MapQuest
Maximal Matchings in Bipartite Graphs

A Bipartite Graph

Start with any matching

Start at an
unmatched
vertex on the left End at an unmatched
vertex on the right

Find an alternating path

A maximal Switch matching to

matching! nonmatching and vice
versa
 Conflict Scheduling

A A

E B E B

D C D C
Draw edges between classes Color so that adjacent vertices have different colors.
with conflicting times Minimum number of colors = minimum required
classrooms.
 Conflict Scheduling
Frequency Assignment
Assign frequencies to mobile radios and
other users of the electromagnetic
spectrum. Two customers that are
sufficiently close must be assigned
different frequencies, while those that
are distant can share frequencies.
Minimize the number of frequencies.
 Vertices: users of mobile radios
 Edges: between users whose
frequencies might interfere
 Colors: assignments of different
frequencies
Need at least as many frequencies as the
minimum number of colors required!
Register Allocation
Assign variables to hardware registers
during program execution. Variables
conflict with each other if one is used both
before and after the other within a short
period of time (for instance, within a
subroutine). Minimize the use of non-
register memory.
Vertices: the different variables
Edges: between variables which conflict
with each other
Colors: assignment of registers
Need at least as many registers as the
minimum number of colors required!
 Rectilinear pattern recognition
joint work with J. Cohn (IBM), R. Snapp and D. Nardi (UVM)
IBM’s objective is to check a chip’s design and find all occurrences of a
simple pattern to:
– Find possible error spots
– Check for already patented segments
– Locate particular devices for updating

The Haystack

The Needle…
 Pre-Processing
BEGIN /* GULP2A CALLED ON THU FEB 21 15:08:23 2002 */
EQUIV 1 1000 MICRON +X,+Y
MSGPER -1000000 -1000000 1000000 1000000 0 0
HEADER GYMGL1 'OUTPUT 2002/02/21/14/47/12/cohn'
LEVEL PC
LEVEL RX
(Raw data format)
CNAME ULTCB8AD

CELL ULTCB8AD PRIME

PGON N RX 1467923 780300 1468180 780300 1468180 780600 +
1469020 780600 1469020 780300 1469181 780300 1469181 +
781710 1469020 781710 1469020 781400 1468180 781400 +
1468180 781710 1467923 781710
PGON N PC 1468500 782100 1468300 782100 1468300 781700 +
1468260 781700 1468260 780300 1468500 780300 1468500 +
780500 1468380 780500 1468380 781500 1468500 781500
RECT N PC 1467800 780345 1503 298
ENDMSG

Two different layers/rectangles

are combined into one
layer that contains three shapes;
one rectangle (purple)
and two polygons (red and blue)

Algorithm is cutting edge, and not currently used for this application in industry.
 Linear time subgraph search for
target

Both target pattern and entire chip are encoded like this, with the vertices
also holding geometric information about the shape they represent. Then
we do a depth-first search for the target subgraph. The addition information
in the vertices reduces the search to linear time, while the entire chip
encoding is theoretically N2 in the number of faces, but practically NlogN.
 Netlist Layout
How do we convert this…

… into this?
 Netlist
A set S of vertices ( the pins) hundreds of thousands.
A partition P1 of the pins (the gates) 2 to 1000 pins per gate, average of
about 3.5.
A partition P2 of the pins (the wires) again 2 to 1000 pins per wire,
average of about 3.5.
A maximum permitted delay between pairs of pins.

Example

Gate Pin Wire

The Wires
 The Wiring Space

Placement layer- Vias (vertical

gates/pins go here connectors)

Horizontal wiring Vertical wiring

layer
Up to 12 or so layers
layer
The general idea
Place the pins so that pins are in
their gates on the placement
layer with non-overlapping
gates.

Place the wires in the wiring

space so that the delay
constrains on pairs of pins
are met, where delay is
proportional to minimum
distance within the wiring,
and via delay is negligible
 Lots of ProbLems….
Identify Congestion
B D G
 Identify dense substructures from the netlist
 Develop a congestion ‘metric’ A F

C E H
Congested area Congested
area

What often happens What would be good

Automate Wiring Small Configurations

Some are easy to place and route

Simple left to right logic
No / few loops (circuits)
Uniform, low fan-out
Statistical models work

Some are very difficult

E.g. ‘Crossbar Switches’
Many loops (circuits)
Non-uniform fan-out
Statistical models don’t work
 Biomolecular constructions

Nano-Origami: Scientists At
Scripps Research Create
Single, Clonable Strand Of
DNA That Folds Into An
Octahedron
A group of scientists at The Scripps
Research Institute has designed,
constructed, and imaged a single
strand of DNA that spontaneously
folds into a highly rigid, nanoscale
octahedron that is several million
times smaller than the length of a
standard ruler and about the size of
several other common biological
structures, such as a small virus or
a cellular ribosome.

http://www.sciencedaily.com/releases/2004/02/040
212082529.htm
 Assuring cohesion
A problem from biomolecular computing—physically constructing
graphs by ‘zipping together’ single strands of DNA

(not allowed)
N. Jonoska, N.
Saito, ’02
 DNA sequencing

It is very hard in
general to “read
off’ the sequence of
a long strand of
DNA. Instead,
researchers probe
AGGCTC
AGGCT for “snippets” of a
GGCTC
fixed length, and
read those.
CTACT
TCTAC
The problem then
becomes
reconstructing the
original long strand
of DNA from the
CTCTA TTCTA
set of snippets.
 Enumerating the reconstructions

This leads to a directed graph with the same number of in-arrows as out
arrows at each vertex.

The number of reconstructions is then equal to the number of paths

through the graph that traverse all the edges in the direction of their
arrows.
 Conquering the crazy cubes

The cubes from my puzzle are represented below.

B R

G W R G G W G B

W B
2
1

G R

R W R B R W B G

R 3 W 4
 Build the Model

We will model each cube with a multigraph.

The vertices will correspond to the four colors and we connect the
corresponding vertices u and v if there is a pair of opposite faces colored u
and v.

1 2

3 4
 Build the Model

Now construct a single multigraph with 4 vertices and the 12 edges,

labeling each edge by the cube associated with it.

3 4
R W
3
2
1
1 4
1 2 4 2

1
3
B 2 G

2
3 4
 Characterize a Solution

Suppose the puzzle has a

3 4
solution. How would it be
represented on the final 3
multigraph? 2
1
1 4
4 2

1
3
2

One subgraph will represent the front and back of the tower 2
and a second subgraph will represent the sides of the tower.

Using an edge in a subgraph corresponds to a positioning of the

cube (either front/back or sides).
 Characterize Front/Back and Left/Right
subgraphs

What are the restrictions on the subgraphs and how do they

relate to the solution?

1. Uses all four vertices. (all four colors)

2. Must contain four edges, one from each cube. (orient each cube)

3. No edge can be used more than once. (can’t use same

orientation twice)

4. Each vertex must be of degree 2. (use that color twice,

one front & one back,
or one left & one right)
 Two Subgraphs satisfying the conditions

4
Here are two such subgraphs: 3
3
21
2 14
4
1
3 2

2 3 2

4 1 2 4
3 1

Front/Back Sides

Now, stack the cubes using these faces as the front/back and sides.
Since each edge represents an orientation, label the edges to determine the
orientation.
 Build the solution stack

4
Now, stack the cubes using these faces as the front/back 3
3
and sides. 21
2 14
4
1
3 2

b b r 2
f f 3
2 l r l
4 1 2 4
b 3 f b r r
l
f l 1

Front/Back Sides
? Is there another solution?
? Is it possible to find a set of subgraphs that use the loops ?
 All subgraphs with 4 edges and
4 vertices of degree 2
Only six types of subgraphs meet the solution requirements:

“square cycle” “crossed cycle” “loop and triangle”

“four loops” “two loops and a C2” “two C2’s”

 “Same”
Crossed Cycles

Loop and a Triangle

“Same” Arrangements
Two double loops

Three loops
So, look for these types of subgraphs

“square cycle” “crossed cycle” “loop and triangle”

“four loops” “two loops and a C2” “two C2’s”

Crazy Cubes/Instant Insanity slides modified from:

Sarah Graham--http://academics.smcvt.edu/jellis-monaghan/combo2/special_topics_presentations.htm
Judy Lalani-- http://math.hope.edu/lalani/ScienceDay.ppt