Spectral Methods for Complex Networks

Richard C. Wilson Dept. of Computer Science

University of York

+ path

Outline

Part I

1. Brief recap of spectral graph theory

2. Representation

3. Spectra of graph models

4. Application to graph partitioning

Part II

1. Paths and Cycles

2. Formal Series

3. Counting paths

4. Counting cycles

Matrix Representation

A Matrix Representation X of a network is matrix with entries

representing the vertices and edges

Adjacency

00110

00100

11010

10101

00010

5

4

3

2

1

5 4 3 2 1

A1

2

3

4

5

20000

01000

00300

00030

00001

DDegree matrix

Matrix Representation

The Laplacian (L) is

Signless Laplacian

20110

01100

11310

10131

00011

ADL

ADL s

20110

01100

11310

10131

00011

Matrix Representation

Normalized Laplacian

Entries are

2

1

2

1

2

1

2

1

ˆ

LDD

ADDIL

otherwise0

),(1

1

ˆ Evudd

vu

Lvu

uv

Incidence matrix

The incidence matrix of a graph is a matrix describing the relationship

between vertices and edges

Relationship to signless Laplacian

Adjacency

Laplacian

10

11

01

2,32,1

M1

2

3

DMMA T

TMMDL 2

T

s MML

Matrix Representation

Consider the Laplacian (L) of this network

Clearly if we label the network differently, we get a different matrix

In fact

represents the same graph for any permutation matrix P of the n labels

20110

01100

11310

10131

00011

5

4

3

2

1

5 4 3 2 1

1

2

3

4

5

TPLPL '

1

2

20101

01100

11301

00011

10113

5

4

3

2

1

5 4 3 2 1

Characterisations

Are two networks the same? (Graph Isomorphism), or is there

a bijection between the vertices such that all the edges are

in correspondence?

Interesting problem in computational theory, complexity

unknown but hypothesised as separate class in NP-

hierarchy, GI-hard

Graph Automorphism: Isomorphism between a graph and

itself.

Characterisations

An equivalent statement: Two networks are isomorphic iff

there exists a permutation matrix P such that

X should contain all information about the network

– Applies to L, A etc not to D

P is a relabelling; changes the order in which we label the

vertices

Our measurements from a matrix representation should be

invariant under this transformation (similarity transform)

TPPXX 12

X is a full matrix

representation

Spectral Graph Theory

Properties of the graph from the eigenvalues (eigenvectors) of

a matrix representation of the graph

1

UUUUX

UUX

T

LR

TSymmetric (undirected)

Always has n real eigenvalues

Non-symmetric

Possibly complex eigenvalues

Perron-Frobenius Theorem

Perron-Frobenius Theorem:

If X is an irreducible square matrix with non-negative entries, then there exists an eigenpair (λ,u) such that

Applies to both left and right eigenvector

• Key theorem: if our matrix is non-negative, we can find a principal(largest) eigenvalue which is positive and has a non-negative eigenvector

• Irreducible implies associated digraph is strongly connected

0

j

i

u

i

R

Spectrum

The graph has a ordered set of eigenvalues (λ1, λ2,… λn) in

terms of size (I will use smallest first).

The (ordered) set of eigenvalues is called the spectrum of the

graph.

Theorem: The spectrum is unchanged by the relabelling

transform

Corollary: If two graphs are isomorphic, they have the same

spectrum

This does not solve the isomorphism problem, as two

different graphs may have the same spectrum

12

12

TPPXX

Undirected networks: Spectrum of A

Spectrum of A: Positive and negative eigenvalues

1

max21max 0

0)Tr(

n

n

i

dd

A

mm

T

E

n

jin

m

i

i

i

i

n

i

n

i

ii

nn

ij

n

length of cyclesdistinct ofnumber

3)Tr(

2)Tr(

Tr

length of cycles ofnumber )(Tr

and joining length of paths ofnumber gives )(

33

22

A

A

A

AA

A

Undirected networks: Spectrum of A

Bipartite graph: If λ is an eigenvalue, then so is –λ, Sp(A)

symmetric around 0

Perron-Frobenius Theorem (A non-negative matrix)

n is largest magnitude eigenvalue, corresponding eigenvector

un is non-negative

Undirected Networks: Spectrum of L

Spectrum of L: L positive semi-definite

There always exists an eigenvector 1 with eigenvalue 0,

because of zero row-sums

The number zeros in the spectrum is the number of connected

components of the network.

n

E

n

i

210

2

Spectrum of L

A spanning tree of a graph is a tree containing only edges in

the network and all the vertices

Example

Kirchhoff’s theorem

The number of spanning trees of a graph is

n

i

in 2

1

Spectrum of normalised L

Spectrum of : Positive semi-definite

As with Laplacian, the number zeros in the spectrum is the

number of disconnected components of the network.

Eigenvector exists with eigenvalue 0 and entries

‘scale invariance’ for eigenvalues

20 21

n

i V

L̂

Tnddd 21

Regular networks

• A network is regular if all vertices have the same

degree

• Spectra (eigenvalues and eigenvectors) essentially

the same

AIL

AIL

ID

k

k

k

1ˆ

Eigensystem stability and the spectral difference

• If the network changes for some reason

– Rewiring, random noise etc.

• The eigenvalues and eigenvectors will change

• Let N be a symmetric matrix representing the

change (deleted/extra edges)

• The change in an eigenvalue is bounded above by

the Frobenius norm of N

– Small perturbation, small change in eigenvalues

)()()()()( nkkkk NXNXNX

Eigensystem stability and the spectral difference

• If N is small compared to X we can apply

eigenperturbation theory

• Eigenvectors not stable if spectral difference |λk-λj|

is small

n

kjj

j

jk

k

T

kkk

k

T

kkk

,1

uNuu

uu

Nuu

NXX

References

Spectra of Graphs, Brouwer & Haemers, Springer

Graph Spectra for Complex Networks, Van Mieghem,

Cambridge University Press

Spectral Graph Theory, Fan Chung, American Mathematical

Society

Spectral Methods and Labels

So far, we have considered edges only as present or absent

{0,1}. If we have more edge information, can encode in a

variety of ways. Edges can be weighted to encode

attributes, include diagonal entries to encode vertices

00110

00100

11010

1016.02.0

0002.04.0

A0.4

0.6

0.2

Coding Attributes

• Note: When using Laplacian, add diagonal elements after

forming L

• Label attributes: Code labels into [0,1]

• Example: chemical structures

Edges

─ 0.5

═ 1.0

Aromatic 0.75

Vertices

C 0.7

N 0.8

O 0.9

Coding Attributes

Spectral theory works equally well for complex matrices

Matrix entry is x+iy so can encode two independent attributes

per entry, x and y. Symmetric matrix becomes Hermitian

matrix

Eigenvalues real, eigenvectors complex

03.01.00

2.01.003.05.0

03.05.00

†

i

ii

i

A

AA

Spectra of Network Models

• A number of famous network models give very

distinctive eigenvalue distributions

• Example: Erdos-Renyi random graph model

• Edges are chosen by connecting each pair of

vertices with fixed probability p

Erdos-Renyi Spectrum of A

-50 -40 -30 -20 -10 0 10 20 30 40 500

0.005

0.01

0.015

pq

npqnpq

p

np

1

2

1

42

1 law circle-semiWigner

of eigenvaluegiant One

Scale free

• Scale-free (Preferential attachment)

• Network grows by adding new vertices

– m new edges added each time

• Probability of connection proportional to degree

decay lawpower follow triangleof Edges

24

1on distributi Triangular

of eigenvalue large One 4/12/1

1

npqnpq

p

nm

Scale-free Spectrum of A

-10 -5 0 5 100

0.05

0.1

0.15

0.2

0.25

npqnpq

p 24

1on distributi Triangular

Small world

• Small world (Watts-Strogatz)

• Basic ring topology with m neighbours

• Reconnect edges randomly with prob. p

• When p=0, regular graph with degree m

– Degenerate spectrum with sharp peaks

• When p=1, ER random graph

– Semi-circle law

• Transitions between two for p∈[0,1]

Small world

-4 -2 0 2 4 6 8 10 120

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

p=0.0

-6 -4 -2 0 2 4 6 8 10 120

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

p=0.1

-8 -6 -4 -2 0 2 4 6 8 10 120

0.02

0.04

0.06

0.08

0.1

0.12

p=0.5

-8 -6 -4 -2 0 2 4 6 8 10 120

0.02

0.04

0.06

0.08

0.1

0.12

p=0.3

Spectral Partitioning and Cuts

• Divide a network into modules or clusters

• Minimise C

– This simple approach does not work

cut

cut),(

21 ),cut(ji

ijAPPC

Spectral Partitioning

• Should prefer equal partitions

2

21

1

21 ),cut(),cut(

P

PP

P

PPC Ratio cut

)(vol

),cut(

)(vol

),cut(

2

21

1

21

P

PP

P

PPC Normalized cut

Spectral Partitioning

• Analysis (ratio cut)

Introduce indicator vector x

Has following properties

1.

2.

3. xi takes only two values

2

2

1

1

1

2

PvP

P

PvP

P

x

i

i

i

nx

0x1T

),(cut2 21 PPVT Lxx

0 subject to min x1LxxTT

𝑥 ∈ ℝ

Spectral Partitioning

• Similarly, for normalized cut

• Discretize x into two values to obtain partitions

• Solution depends on finding eigenvector

• Type of cut depends on matrix

– Equally well use another matrix, e.g. adjacency

• A measures affinity between vertices for being in

the same partition

0 subject to ˆmin),(ncut 2/1

21 xD1xLxTTPP

0 subject to max n

TTuxAxx

Modularity

• Modularity is a measure of partition quality

relative to some base graph model

• Can be summarised in modularity matrix

• Pij is the expected affinity according to base model

– Needs to be more clustered that the model

• Common to use the configuration model as the

base

ijijij PAB

||2 E

ddP

ji

ij

Modularity

• Modularity

BxxT

EQ

||2

1

xx BPP Tmax),(mcut 21

Paths

Paths

• The structure of a network can be probed by

looking at the paths

– Communicability

– Commute time

• Generally not tractable to enumerate paths – too

many

• Need to think carefully about what can be

computed in practice

– Powers of A, exp(A) etc.

TfAf UU

Path

A path is a contiguous sequence of edges in the network

The length of p, l(p) is the number of edges traversed

A simple path is a self-avoiding path, which does not repeat

any vertices (with the possible exception of i and j)

1

3

2

4

5

jiiiiiiiiiij lllwwwwwp ,,,,, 11232211

3)(

2435)5,3)(3,4)(4,2(

pl

p

Cycles

• A cycle is a closed path in a network, i.e. a path

across edges returning to the same vertex (i=j)

• Cycles are often an important structural

component of networks

1

3

2

4

5

Cycles

• A cycle is a sequence

• A simple cycle does not repeat any vertex except the

first/last

• Two cycles may be considered equivalent if they are the

same cycle with different starting points

1

3

2

4

5 121

2342~3423~4234

53435

Simple

Simple

Non-simple

iiiiiiiiiii lllwwwwwc ,,,,, 11232211

Counting paths

• Formal adjacency matrix

• Replace {0,1} with formal variables representing

edges

• Allows us to keep track of which sequences

contribute to a particular calculation

– Substitute specific values to do find actual values

00

00

00

001

100

010

31

23

12

w

w

w

WA

Counting paths

• Example

2)( with paths ofnumber 1

1,1

)2(

)2(

22

2

pl

pw

pww

ij

ij

Pp

ijij

xy

Ppk

kjikij

AW

W

1,1

!

1exp

pw

k

xy

k

kWW

Weighted sum of paths of all lengths

Walk generating function

• Can use z to control convergence, z<1/n

PpPpPp

T pppn

)3()2(

1

321

1WI1

WWWIWI

zw

w

ij

ij

converget doesn' useless, 1

Pp

plzz11

AIWI

1)(

!

1 AI z

dz

d

kP

k

kk

Example

MUTAG

Collection of 188 labelled chemical compounds.

Task is to predict whether each compound has

mutagenicity or not.

Method Dataset Accuracy

Random walk kernel

Backtrackless walk kernel

Mutag(labelled)

Mutag(labelled)

90. 0%

91.1%

Feature vector from Random walk

Feature vector from backtrackless random walk

Feature vector from Ihara coefficients

Shortest Path Kernel

COIL(unlabeled)

COIL(unlabeled)

COIL(unlabeled)

COIL(unlabeled)

94.4%

95.5%

94.4%

86.7%

Feature vector from Random walk

Feature vector from backtrackless random walk

Feature vector from Ihara coefficients

Mutag(unlabeled)

Mutag(unlabeled)

Mutag(unlabeled)

89.4%

90.5%

80.5%

Graph Kernels

• The walk generating function efficiently counts

paths

• Including backtracks

• Tottering masks interesting information

• Simple paths difficult to compute

Oriented Line Graph

• Oriented Line graph:

1 2

3 4

e21

e12

e23 e32 e42

e24

e41 e14

e43

e34

e23

e21

e12

e32

e42

e24 e41

e14

e43

e34

Oriented Line graph (OLG): no

backtracking

1. Convert edges into directed pairs

2. Each directed edge becomes a vertex

3. Join vertices where the head of one edge

meets the tail of another

4. Reverse pairs are not joined (eg. e12, e21)

Backtrackless Walks

• The adjacency of the OLG is given by T (the

Hashimoto matrix of the network)

• Paths on T are paths on A, except backtracks do

not appear

– Path of length l on T is path of length l+1 on A

• Count paths on T, but T can be big (2|E|×2|E|)

1)(

TIB zz

Efficient computation

• Complexity is a problem

• We can directly compute n×n matrix Ak, defined as

here i, j run over the vertices of G.

• Recursions for the matrices Ak – Let A be the adjacency matrix of a simple graph G and Q be a n×n

diagonal matrix whose ith diagonal entry is the degree of the ith node minus 1. Then

ji

kGA

jikat ending and at starting

ngbacktracki no with length of in paths ofnumber ,

3 if

2 if

1 if

21-k

2

k

k

k

k

k

QAAA

IQA

A

A

42 || || nEnV

[Stark and Terras 1996,

Aziz et al 2013]

Cycles

• It is easy to count short simple cycles in a network

• As we noted earlier, (number of

2-cycles)

• (number of simple 3-cycles)

• which is the number of 4-cycles,

most of which are not simple

1

4

2

3

cycle-4 a also is 12141

cycle-4 simple a is

141 ,121 ,12341

32

1

321

cc

c

ccc

123Tr 33 TA

102Tr 22 EA

50Tr 44 A

Cycles

• A cycle in OLG(G) induces a cycle in G

• Since backtracks are not allowed, certain cycles do not

appear

– Cycles of length 2

– Cycles with tails

• Let T be the adjacency of the OLG

– Called the Hashimoto matrix of G

• Still get repeats at larger size, eg c12, c1c2

2

exactly 5length toup cycles simple counts Tr nnn

TT

Cycles

• What about other matrix functions?

• Structural measures should be invariant to

permutation similarity transform

• det and perm seem obvious choices

– Counts hikes of length n, collections of disjoint cycles

• perm hard to compute

nn

i

S

m

S

n

i

i cccw

21

1

, sgnsgndet W

nn

i

S

m

S

n

i

i cccw

21

1

,perm W

Ihara Zeta Function

• Ihara (1966), Sunada (1986)

• Prime cycle of a graph:

– A cycle which has no backtracking and is not a multiple of another

cycle

Prime Not Prime

(backtracking)

Not Prime (twice

round a single

cycle)

Prime Cycles

– Similar trick to walk generating function

– Sum over hikes of any length

• Use T to eliminate backtracks in the hikes and let

wij → z to get a generating function

• Ihara zeta function of network

– Effectively series over Ihara prime cycles

• Efficient evaluation using (large) eigenvalues of T

Hh

h1

det WI

HCc

pl

G zzz 1)(1)1(det)( TI

Application: Social Balance

• Some social interactions can be characterised by a

positive/negative interaction

– Friend/enemy, for/against

• Social theory suggests that networks should evolve

into a balanced state to decrease tension

– Does this happen in practice?

Alice

Bob

Carol

+

+

-

Balance in Networks

• Early work focussed on triangles

– Easy to count

unbalanced 1

balanced 1

enemies 1

friends 1

c

wij

3

33

33

33

Tr2

TrTr

A

AA s

NN

NR

Cycles

• Problem with counting balanced squares:

• There is no simple way of counting simple cycles of

arbitrary length in a graph

• A Hamiltonian cycle is a simple cycle which visits all

vertices of the graph

• Determining whether such a cycle existing is known to be

NP-complete

– No polynomial-time algorithm likely for general simple cycle

counting

Cycles

• Can count Ihara cycles instead

– Simple up to length 5

– No cycle powers ck

ld

d

slld

l

lNN

|

)(1

TTr

ld

d

lld

l

lNN

|

)(1

TTr

Simple cycles

• Generating function for simple cycles

– S all simple cycles

• There is a trace formula for this function [Giscard

et al 2016]

• Naturally this is NP-hard to compute

– Can get efficient approximations for shorter cycles

using Monte Carlo sampling, particularly on sparse

graphs

Ss

slzzP )()(

dzzzz

zPGH

HN

H

H

H

)|(||| )()(Tr1

)( AIA

Balance in real networks

• WikiElections network represents the votes of

wikipedia users during the elections of other users

to adminship.

– Directed, 8,297 vertices, 12915 edges

Balance in real networks

• The Epinions network is a large directed graph on 131,828

vertices representing relations between the users of the

consumer review website Epinions.com.

– Directed with 841,372 edges