The Index-Based Subgraph Matching Algorithm (ISMA): Fast Subgraph Enumeration in Large Networks Using Optimized Search Trees |
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| Authors: | Sofie Demeyer Tom Michoel Jan Fostier Pieter Audenaert Mario Pickavet Piet Demeester |
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| Affiliation: | 1. Department of Information Technology, Ghent University, Ghent, Belgium.; 2. School of Life Sciences - LifeNet, Freiburg Institute of Advanced Studies, Freiburg, Germany.; 3. Division of Genetics and Genomics, The Roslin Institute - University of Edinburgh, Midlothian, Scotland, United Kingdom.; King Abdullah University of Science and Technology, Saudi Arabia, |
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| Abstract: | Subgraph matching algorithms are designed to find all instances of predefined subgraphs in a large graph or network and play an important role in the discovery and analysis of so-called network motifs, subgraph patterns which occur more often than expected by chance. We present the index-based subgraph matching algorithm (ISMA), a novel tree-based algorithm. ISMA realizes a speedup compared to existing algorithms by carefully selecting the order in which the nodes of a query subgraph are investigated. In order to achieve this, we developed a number of data structures and maximally exploited symmetry characteristics of the subgraph. We compared ISMA to a naive recursive tree-based algorithm and to a number of well-known subgraph matching algorithms. Our algorithm outperforms the other algorithms, especially on large networks and with large query subgraphs. An implementation of ISMA in Java is freely available at http://sourceforge.net/projects/isma/. |
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