Algorithms for regular tree grammar network search and their application to mining human-viral infection patterns

Ilan Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger-Lotem, Michal Ziv-Ukelson

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

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/.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 15th International Workshop, WABI 2015, Proceedings
EditorsMihai Pop, Hélène Touzet
PublisherSpringer Verlag
Pages53-65
Number of pages13
ISBN (Print)9783662482209
DOIs
StatePublished - 1 Jan 2015
Event15th International Workshop on Algorithms in Bioinformatics, WABI 2015 - Atlanta, United States
Duration: 10 Sep 201512 Sep 2015

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9289
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference15th International Workshop on Algorithms in Bioinformatics, WABI 2015
Country/TerritoryUnited States
CityAtlanta
Period10/09/1512/09/15

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science

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