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Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics

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Interdisciplinary Sciences: Computational Life Sciences Aims and scope Submit manuscript

Abstract

Many scientific applications entail solving the subgraph isomorphism problem, i.e., given an input pattern graph, find all the subgraphs of a (usually much larger) target graph that are structurally equivalent to that input. Because subgraph isomorphism is NP-complete, methods to solve it have to use heuristics. This work evaluates subgraph isomorphism methods to assess their computational behavior on a wide range of synthetic and real graphs. Surprisingly, our experiments show that, among the leading algorithms, certain heuristics based only on pattern graphs are the most efficient.

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Notes

  1. http://www.internationalgenome.org/.

  2. http://www.encodeproject.org.

  3. https://cancergenome.nih.gov/.

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Acknowledgements

We would like to thank the authors of algorithm VF3 to have provided the software and for all your support on testing it. R. G., V. B., and A. A. would like to acknowledge the support of the Italian Ministry of Education, Universities and Research (MIUR) “Dipartimenti di Eccellenza 2018-2022”, and Regione del Veneto, Regione del Veneto (IT) (Grants 2016-JPVR16FNCL, 2017-B33C17000440003, GNCS-INDAM). A. P., G. M., and A. F. acknowledge the support of Italian Ministry of Education, Universities and Research (Ministero dell’Istruzione, dell’Università e della Ricerca, MIUR) Grant SCN_00451. D. S. would like to acknowledge the support of the U.S. National Science Foundation Grants MCB-1158273, IOS-1339362, and MCB-1412232.

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Authors and Affiliations

  1. Department of Computer Science, University of Verona, Verona, Italy

    Antonino Aparo, Vincenzo Bonnici & Rosalba Giugno

  2. Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy

    Giovanni Micale, Alfredo Ferro & Alfredo Pulvirenti

  3. Computer Science Department, Courant Institute, New York University, New York, USA

    Dennis Shasha

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  1. Antonino Aparo
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  2. Vincenzo Bonnici
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  7. Rosalba Giugno
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Correspondence to Rosalba Giugno.

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Aparo, A., Bonnici, V., Micale, G. et al. Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics. Interdiscip Sci Comput Life Sci 11, 21–32 (2019). https://doi.org/10.1007/s12539-019-00323-0

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  • DOI: https://doi.org/10.1007/s12539-019-00323-0

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