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Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns

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Algorithms in Bioinformatics (WABI 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9289))

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Abstract

Network querying is a powerful approach to mine molecular interaction networks. Most network querying tools support queries in the form of a template sub-network, in case of topology-constrained queries, or a set of colored vertices in case of topology-free queries. A third approach is grammar-based queries, which are more flexible and expressive as they allow the addition of logic rules to the query. Previous grammar-based querying tools defined queries via string grammars and identified paths in graphs. In this paper, we extend the scope of grammar-based queries to regular tree grammar (RTG), and the scope of the identified sub-graphs from paths to trees. We introduce a new problem and propose a novel algorithm to search a given graph for the k highest scoring sub-graphs matching a tree accepted by an RTG. Our algorithm is based on dynamic programming and combines an extension to k-best parsing optimization with color coding. We implement the new algorithm and exemplify its application to mining the human-viral interaction network. Our code is available at http://www.cs.bgu.ac.il/~smolyi/RTGnet/.

These authors contributed equally to the paper.

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Acknowledgments

We thank the anonymous WABI referees for their many helpful comments.The work of Ilan Smoly, Amir Carmel and Michal Ziv-Ukelson was partially supported by the Frankel Center for Computer Science at Ben Gurion University of the Negev and by the Israel Science Foundation (ISF 179/14).

Author information

Authors and Affiliations

  1. Department of Computer Science, Ben-Gurion University of the Negev, Beer Sheva, Israel

    Ilan Smoly, Amir Carmel & Michal Ziv-Ukelson

  2. Department of Virology, Ben-Gurion University of the Negev, Beer Sheva, Israel

    Yonat Shemer-Avni

  3. Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the Negev, Beer Sheva, Israel

    Esti Yeger-Lotem

Authors
  1. Ilan Smoly
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  2. Amir Carmel
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  3. Yonat Shemer-Avni
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  4. Esti Yeger-Lotem
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  5. Michal Ziv-Ukelson
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Corresponding authors

Correspondence to Esti Yeger-Lotem or Michal Ziv-Ukelson .

Editor information

Editors and Affiliations

  1. University of Maryland, College Park, Maryland, USA

    Mihai Pop

  2. University of Lille, Lille, France

    Hélène Touzet

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Smoly, I., Carmel, A., Shemer-Avni, Y., Yeger-Lotem, E., Ziv-Ukelson, M. (2015). Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns. In: Pop, M., Touzet, H. (eds) Algorithms in Bioinformatics. WABI 2015. Lecture Notes in Computer Science(), vol 9289. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-48221-6_4

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  • DOI: https://doi.org/10.1007/978-3-662-48221-6_4

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