Introduction to

Graph Cluster Analysis

 Outline

• Introduction to Cluster Analysis

• Types of Graph Cluster Analysis
• Algorithms for Graph Clustering

k-Spanning Tree

Shared Nearest Neighbor

Betweenness Centrality Based

Highly Connected Components

Maximal Clique Enumeration

Kernel k-means
• Application

2
 Outline

• Introduction to Clustering
• Introduction to Graph Clustering
• Algorithms for Graph Clustering

k-Spanning Tree

Shared Nearest Neighbor

Betweenness Centrality Based

Highly Connected Components

Maximal Clique Enumeration

Kernel k-means
• Application

3
 What is Cluster Analysis?

The process of dividing a set of input data into possibly

overlapping, subsets, where elements in each subset are
considered related by some similarity measure

2 Clusters

3 Clusters

4
 Applications of Cluster Analysis

• Summarization
– Provides a macro-level view
of the data-set

Clustering precipitation
in Australia
From Tan, Steinbach, Kumar
Introduction To Data Mining,
Addison-Wesley, Edition 1

5
 Outline

• Introduction to Clustering
• Introduction to Graph Clustering
• Algorithms for Graph Clustering

k-Spanning Tree

Shared Nearest Neighbor

Betweenness Centrality Based

Highly Connected Components

Maximal Clique Enumeration

Kernel k-means
• Application

6
 What is Graph Clustering?

• Types
– Between-graph
• Clustering a set of graphs
– Within-graph
• Clustering the nodes/edges of a single graph

7
 Between-graph Clustering

Between-graph clustering methods divide a set of

graphs into different clusters

E.g., A set of graphs representing chemical compounds can

be grouped into clusters based on their structural similarity

8
 Within-graph Clustering

Within-graph clustering methods divides the nodes

of a graph into clusters

E.g., In a social networking graph, these clusters could

represent people with same/similar hobbies

Note: In this chapter we will look at different algorithms to

perform within-graph clustering

9
 Outline

• Introduction to Clustering
• Introduction to Graph Clustering
• Algorithms for Within Graph Clustering

k-Spanning Tree

Shared Nearest Neighbor

Betweenness Centrality Based

Highly Connected Components

Maximal Clique Enumeration

Kernel k-means
• Application

10
 k-Spanning Tree
2 k groups
1 3 of
k-Spanning
3 2 5 non-overlapping
Tree
4 vertices
2 4

Minimum Spanning Tree

k
STEPS:
• Obtains the Minimum Spanning Tree (MST) of input graph G
• Removes k-1 edges from the MST
• Results in k clusters

11
 What is a Spanning Tree?

A connected subgraph with no cycles that includes all

vertices in the graph
G
2 2
1 3 6 1 3 6
7 2 5 7 2 5
3 4
2 4 4 Weight = 17
5 2 4

Note: Weight can represent either distance or similarity

between two vertices or similarity of the two vertices

12
 What is a Minimum Spanning Tree
(MST)?
The spanning tree of a graph with the minimum possible sum
of edge weights, if the edge weights represent distance
G
2 Weight
2
= 11
1 3 6 1 3
7 2 5
3 4 3 2 5
2 4 4
5 2 4 4

2
1 3
Note: maximum
possible sum of edge 2 5 Weight = 13
weights, if the edge 2
1 3 2 4 4
weights represent 6 5
similarity 5
7 2
Weight = 17 13
2 4
 Algorithm to Obtain MST
Prim’s Algorithm
Given Input Graph Select Vertex Randomly Initialize Empty Graph T
G e.g., Vertex 5 with Vertex 5
2 3 6
1
T
7 2 5 5
3 4 5
2 4 4
5

Repeat until all vertices are added to T

From L select the Select a list of edges L

Add X to T edge X with from G such that at
minimum weight most ONE vertex of each
T edge is in T
5 4 6
5 4 5 3
4 4
5 4

14
 k-Spanning Tree
2
1 3
Remove k-1 edges Note: k – is the
3 2 5 number of
with highest weight clusters
2 4 4

Minimum Spanning Tree

E.g., k=3 E.g., k=3

2
1 3 1 3

5 3 2 5

2 4 2 4 4

3 Clusters 15
 k-Spanning Tree R-code
• library(GraphClusterAnalysis)
• library(RBGL)
• library(igraph)
• library(graph)
• data(MST_Example)
• G = graph.data.frame(MST_Example,directed=FALSE)
• E(G)$weight=E(G)$V3
• MST_PRIM = minimum.spanning.tree(G,weights=G$weight, algorithm = "prim")

• OutputList = k_clusterSpanningTree(MST_PRIM,3)
• Clusters = OutputList[[1]]
• outputGraph = OutputList[[2]]
• Clusters

16
 Outline

• Introduction to Clustering
• Introduction to Graph Clustering
• Algorithms for Within Graph Clustering

k-Spanning Tree

Shared Nearest Neighbor Clustering

Betweenness Centrality Based

Highly Connected Components

Maximal Clique Enumeration

Kernel k-means
• Application

17
 Shared Nearest Neighbor Clustering

Shared Nearest Neighbor Graph (SNN)

0
2 2 Groups
1 of
Shared
2 2 2 3 4 Nearest non-overlapping
1 Neighbor vertices
1 3 Clustering
2

STEPS:
τ
• Obtains the Shared Nearest Neighbor Graph (SNN) of input graph G
• Removes edges from the SNN with weight less than τ

18
 What is Shared Nearest Neighbor?
(Refresher from Proximity Chapter)
Shared Nearest Neighbor is a proximity measure and denotes the
number of neighbor nodes common between any given pair of nodes

u v

19

 
 
 Shared Nearest Neighbor (SNN)
Graph
Given input graph G, weight each edge (u,v) with the number of shared
nearest neighbors between u and v
G SNN
0 2
0
2 2 1
4
2 2 2 3 4
1 3
1 3 1
1
Node 0 and Node 1 have 2 neighbors
in common: Node 2 and Node 3

20
 Shared Nearest Neighbor Clustering
Jarvis-Patrick Algorithm
SNN graph of input graph G
0
2 2 If u and v share more than τ
1
neighbors
2 2 2 3 4 Place them in the same
1 3 1 cluster

2
E.g., τ =3
0 2
4
1 3
21
 SNN-Clustering R code
• library(GraphClusterAnalysis)
• library(RBGL)
• library(igraph)
• library(graph)
• data(SNN_Example)
• G = graph.data.frame(SNN_Example,directed=FALSE)
• tkplot(G)

• Output = SNN_Clustering(G,3)
• Output

22
 Outline

• Introduction to Clustering
• Introduction to Graph Clustering
• Algorithms for Within Graph Clustering

k-Spanning Tree

Shared Nearest Neighbor Clustering

Betweenness Centrality Based

Highly Connected Components

Maximal Clique Enumeration

Kernel k-means
• Application

23
 What is Betweenness Centrality?
(Refresher from Proximity Chapter)
Betweenness centrality quantifies the degree to which a vertex
(or edge) occurs on the shortest path between all the other
pairs of nodes

Two types:
– Vertex Betweenness
– Edge Betweenness

24
 Vertex Betweenness
The number of shortest paths in the graph G that
pass through a given node S
G

E.g., Sharon is likely a liaison between NCSU and DUKE and

hence many connections between DUKE and NCSU pass
through Sharon
25
 Edge Betweenness
The number of shortest paths in the graph G that
pass through given edge (S, B)
E.g., Sharon and
Bob both study at
NCSU NCSU and they are
the only link
between NY
DANCE and CISCO
groups

Vertices and Edges with high Betweenness

form good starting points to identify
clusters
26
 Vertex Betweenness Clustering
Given Input graph G Betweenness for each vertex

1. Disconnect graph at
Repeat until Select vertex v with
selected vertex (e.g.,
highest vertex the highest
vertex 3 )
betweenness ≤ µ betweenness
2. Copy vertex to both
Components E.g., Vertex 3 with
value 0.67

27
 Vertex Betweenness Clustering
R code
• library(GraphClusterAnalysis)
• library(RBGL)
• library(igraph)
• library(graph)
• data(Betweenness_Vertex_Example)
• G = graph.data.frame(Betweenness_Vertex_Example,directed=FALSE)
• betweennessBasedClustering(G,mode="vertex",threshold=0.2)

28
 Edge-Betweenness Clustering
Girvan and Newman Algorithm
Given Input Graph G Betweenness for each edge

Disconnect graph at
Repeat until Select edge with
selected edge
highest edge Highest
(E.g., (3,4 ))
betweenness ≤ µ Betweenness
E.g., edge (3,4) with
value 0.571

29
 Edge Betweenness Clustering
R code
• library(GraphClusterAnalysis)
• library(RBGL)
• library(igraph)
• library(graph)
• data(Betweenness_Edge_Example)
• G = graph.data.frame(Betweenness_Edge_Example,directed=FALSE)
• betweennessBasedClustering(G,mode="edge",threshold=0.2)

30
 Outline

• Introduction to Clustering
• Introduction to Graph Clustering
• Algorithms for Within Graph Clustering

k-Spanning Tree

Shared Nearest Neighbor Clustering

Betweenness Centrality Based

Highly Connected Components

Maximal Clique Enumeration

Kernel k-means
• Application

31
 What is a Highly Connected Subgraph?

• Requires the following definitions

– Cut
– Minimum Edge Cut (MinCut)
– Edge Connectivity (EC)

32
 Cut

• The set of edges whose removal disconnects a graph

6 7
Cut = {(3,5),(4,2)} 8
6 7
8
0
0 5
1
5
1
4
3 2
4 6 7
2 8
3
0
5
1
Cut = {(0,1),(1,2),(1,3}
4
3 2 33
 Minimum Cut

The minimum set of edges whose removal disconnects

a graph
MinCut = {(3,5),(4,2)}

6 7
8
6 7
8
0
0 5
1
5
1
4
3 2
4
3 2

34
 Edge Connectivity (EC)

• Minimum NUMBER of edges that will disconnect

a graph

MinCut = {(3,5),(4,2)} Edge Connectivity

6 7
8
EC = | MinCut|
0 = | {(3,5),(4,2)}|
5 =2
1

4
3 2

35
 Highly Connected Subgraph (HCS)

A graph G =(V,E) is highly connected if EC(G)>V/2

G
6 7
8

0
5
EC(G) > V/2
1 2 > 9/2
4
3 2

G is NOT a highly connected subgraph

36
 HCS Clustering
Return G
Given Input graph G
Find the YES
6 7 8 Minimum Cut
MinCut (G)
0
(3,5),(4,2)} Is EC(G)> V/2
5
1

4 Process Graph G1
3 2
Process Graph G2 NO

Divide G
using MinCut

G1 G2

37
 HCS Clustering R code

• library(GraphClusterAnalysis)
• library(RBGL)
• library(igraph)
• library(graph)
• data(HCS_Example)
• G = graph.data.frame(HCS_Example,directed=FALSE)
• HCSClustering(G,kappa=2)

38
 Outline

• Introduction to Clustering
• Introduction to Graph Clustering
• Algorithms for Within Graph Clustering

k-Spanning Tree

Shared Nearest Neighbor Clustering

Betweenness Centrality Based

Highly Connected Components

Maximal Clique Enumeration

Kernel k-means
• Application

39
 What is a Clique?

A subgraph C of graph G with edges between

all pairs of nodes

G C
7 7
6 6

8
5
5 Clique

40
 What is a Maximal Clique?

A maximal clique is a clique that is not part

of a larger clique.
Clique
6 7
7
6
8

5 5

7
4 6

Maximal Clique 8

5 41
 Maximal Clique Enumeration
Bron and Kerbosch Algorithm
Input Graph G
BK(C,P,N)
C - vertices in current clique
P – vertices that can be added to C
N – vertices that cannot be added to C

Condition:
If both P and N are empty – output C as
maximal clique

42
 Maximal Clique R code
• library(GraphClusterAnalysis)
• library(RBGL)
• library(igraph)
• library(graph)
• data(CliqueData)
• G = graph.data.frame(CliqueData,directed=FALSE)
• tkplot(G)
• maximalCliqueEnumerator (G)

43
 Outline

• Introduction to Clustering
• Introduction to Graph Clustering
• Algorithms for Within Graph Clustering

k-Spanning Tree

Shared Nearest Neighbor Clustering

Betweenness Centrality Based

Highly Connected Components

Maximal Clique Enumeration

Kernel k-means
• Application

44
 What is k-means?

• k-means is a clustering algorithm applied to vector

data points
• k-means recap:
– Select k data points from input as centroids
1. Assign other data points to the nearest centroid
2. Recompute centroid for each cluster
3. Repeat Steps 1 and 2 until centroids don’t change

45
 k-means on Graphs
Kernel K-means
• Basic algorithm is the same as k-means on Vector data
• We utilize the “kernel trick” (recall Kernel Chapter)
• “kernel trick” recap
– We know that we can use within-graph kernel functions to
calculate the inner product of a pair of vertices in a user-
defined feature space.
– We replace the standard distance/proximity measures used in
k-means with this within-graph kernel function

46
 Outline

• Introduction to Clustering
• Introduction to Graph Clustering
• Algorithms for Within Graph Clustering

k-Spanning Tree

Shared Nearest Neighbor Clustering

Betweenness Centrality Based

Highly Connected Components

Maximal Clique Enumeration

Kernel k-means
• Application

47
 Application
• Functional modules in protein-protein interaction
networks
• Subgraphs with pair-wise interacting nodes => Maximal
cliques
R-code
• library(GraphClusterAnalysis)
• library(RBGL)
• library(igraph)
• library(graph)
• data(YeasPPI)
• G = graph.data.frame(YeasPPI,directed=FALSE)
• Potential_Protein_Complexes = maximalCliqueEnumerator (G)
• Potential_Protein_Complexes

48