Seminar 2009

Frequent Subgraph/ Substructure Mining

Lei Shi
Department of Computer Science and
Engineering
State University of New York at Buffalo

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Outline
Introduction
Apriori-based Subgrah Mining
Pattern Growth Subgraph Mining
Summary

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Graphs are everywhere

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Graph Mining Problems

Graph Pattern Mining

Frequent subgraph pattern mining

Pattern summarization
Optimal graph patterns
Graph patterns with constraints
Approximate graph patterns .

Graph Classification
Graph clustering
Important node identification
Bridge and hub identification

Other Important Topics

Graph compression
Graph model
Social network analysis.
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Subgraph pattern Mining

Frequent subgraph
A (sub)graph is frequent if its support (occurrence frequency) in a
given dataset is no less than a minimum support threshold

Application of subgraph pattern mining

Mining biochemical structures

Program control flow analysis
Mining XML structures or Web communities
Building blocks for graph classifiction, clustering,compression,
comparison and correlation analysis.

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Frequent Subgraph Example

(1)
A
A

(2)
A
C

subgraph

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C
Support

C
B

(3)

A
3

Key Challenges in Subgraph Mining

Graph isomorphism

to detect if two graphs are identical in structure

Graph representation (Canonical Labeling)

A canonical label is a unique code of a given graph.

Canonical label should be the same no matter how graphs are
represented, as long as graphs have the same topological
structure and the same labeling of edges and vertices.

Subgraph candidate generation

generate candidate frequent subgraphs from datasets

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Subgraph Mining Approaches

Apriori-based

AGM/AcGM: Inokuchi, et al. (PKDD00)

FSG: Kuramochi and Karypis (ICDM01)
M. Kuramochi and G. Karypis. Frequent subgraph discovery. In
ICDM01, pages 313-320, Nov. 2001
PATH#: Vanetik and Gudes (ICDM02, ICDM04)
FFSM: Huan, et al. (ICDM03) and SPIN: Huan et al. (KDD04)
FTOSM: Horvath et al. (KDD06)

Pattern growth based

Subdue: Holder et al. (KDD94)
MoFa: Borgelt and Berthold (ICDM02)
gSpan: Yan and Han (ICDM02)
Yan, X. and Han, J. 2002. gSpan : Graph-Based Substructure
Pattern Mining. In Proceedings of the 2002 IEEE international
Conference on Data Mining (Icdm02) (December 09-12, 2002).
ICDM. IEEE Computer Society, Washington, DC, 721
Gaston: Nijssen and Kok (KDD04)
CMTreeMiner: Chi et al. (TKDE05)
LEAP: Yan et al. (SIGMOD08)

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Outline
Introduction and Background
Apriori-based Subgrah Mining
Pattern Growth Subgraph Mining
Summary

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Apriori-based Approach

FSG : Frequent subgraph discovery. In ICDM01, Nov. 2001

M.Kuramochi and G. Karypis.
Flattened Representation as Canonical Labeling

Apriori-based method to generate subgraph candidate

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Graph Representation in FSG

Flattened Representation

0e0 00e1 00

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Graph Representation in FSG

Flatterned Representation

Lexicographic order or dictionary order

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Apriori-based method
Apriori Property

If a graph is frequent, all of its

subgraphs are frequent.

Candidate Generation
Create a set of candidate size k+1
-from given two frequent ksubgraphs
-containing the same (k-1)subgraph
-Result in several candidates size
k+1

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Apriori-based method
Graph candidate generated Example

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Apriori-based method
FlowChart

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Apriori-based method
Experiment Result
-Chemical Compound Dataset, which contains 340
compounds,24 different atoms (vertices)

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Outline
Introduction
Apriori-based Subgrah Mining
Pattern Growth Subgraph Mining
Summary

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Motivation of gSpan

Weakness of Apriori-based approach

The generation of size (k+1) subgraph candidates from size

k frequent subgraph too complicated and complex.
Pruning false positive : subgraph isomorphism is an NP
complete problem which is costly.

gSpan: Graph-Based Substructure Pattern

Mining

Change the way to represent a graph (DFS: Depth First

Search)
Using pattern growth to generate new subgraph candidate.

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gSpan: Graph-Based Substructure Pattern Mining

DFS (Depth First Search) Code
First Step: DFS the graph and use edges on the path to
represent the graph.
Second Step: DFS Lexicographic Order

Pattern Growth subgraph generation

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DFS code

An edge is
presented
by 5 tuples.

(i, j , li , l( i , j ) , l j )
(0,1, X , a, Y )

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DFS code
Second Step: DFS Lexicographic Order

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Pattern Growth Approach

Pattern Growth (free extension)

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Pattern Growth Approach

Duplicate Graphs

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Pattern Growth Approach

Free extension

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Pattern Growth Approach

Right most extension

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Pattern Growth Approach

Exmaples (cont.)

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gSpan

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gSpan

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Pattern Growth Approach

Experimental result using Chemical data
340 molecules
66 atom types and
4 bond types as labels
On average only 27
vertices with 28 edges

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Summary
Graph representation
Flattern representation vs. DFS code

Generation of Candidate Patterns

apriori vs. pattern growth

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Pattern-Growth Approach

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Frequent Graph Pattern

Given a graph dataset D, find subgraph g, s.t.

freq(g )
Where
freq(g ) is the percentage of graphs in D
that contain g.

Problem 1 : Exponential Pattern Set

Problem 2 : Threshold Setting

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Difference between frequent itemset and frequent

subgraph discovery

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Frequent itemset discovery

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subgraph Mining Algorithms

Apriori-based approach
AGM/AcGM: Inokuchi, et al. (PKDD00)
FSG: Kuramochi and Karypis (ICDM01)
PATH#: Vanetik and Gudes (ICDM02, ICDM04)
FFSM: Huan, et al. (ICDM03) and SPIN: Huan et al. (KDD04)
FTOSM: Horvath et al. (KDD06)

Pattern growth approach

Subdue: Holder et al. (KDD94)
MoFa: Borgelt and Berthold (ICDM02)
gSpan: Yan and Han (ICDM02)
Gaston: Nijssen and Kok (KDD04)
CMTreeMiner: Chi et al. (TKDE05)
LEAP: Yan et al. (SIGMOD08)

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Framework of subraph Mining Algorithms

Search Order
breadth vs. depth
complete vs. incomplete
Generation of Candidate Patterns
apriori vs. pattern growth
Discovery Order of Patterns
DFS order
path tree graph
Elimination of Duplicate Subgraphs
passive vs. active
Support Calculation
embedding store or not

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Frequent Subgraph
Examples:

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Example (cont.)

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Subgraph Mining Approaches

Apriori-based approach

AGM/AcGM: Inokuchi, et al. (PKDD00)

FSG: Kuramochi and Karypis (ICDM01)
M. Kuramochi and G. Karypis. Frequent subgraph discovery. In
ICDM01, pages 313-320, Nov. 2001
PATH#: Vanetik and Gudes (ICDM02, ICDM04)
FFSM: Huan, et al. (ICDM03) and SPIN: Huan et al. (KDD04)
FTOSM: Horvath et al. (KDD06)

Pattern growth approach

Subdue: Holder et al. (KDD94)
MoFa: Borgelt and Berthold (ICDM02)
gSpan: Yan and Han (ICDM02)
Yan, X. and Han, J. 2002. gSpan : Graph-Based Substructure
Pattern Mining. In Proceedings of the 2002 IEEE international
Conference on Data Mining (Icdm02) (December 09-12, 2002).
ICDM. IEEE Computer Society, Washington, DC, 721
Gaston: Nijssen and Kok (KDD04)
CMTreeMiner: Chi et al. (TKDE05)
LEAP: Yan et al. (SIGMOD08)

University at BuffaloThe State University of New York

Outline
Introduction and Background

Apriori-based Subgrah Mining

Pattern Growth Subgraph Mining
Summary

DFS code
Yan, X. and Han, J. 2002. gSpan : Graph-Based Substructure
Pattern Mining. In Proceedings of the 2002 IEEE international
Conference on Data Mining (Icdm02) (December 09-12, 2002).
ICDM. IEEE Computer Society, Washington, DC, 721

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Pattern Growth Approach

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