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 languageAmerican English
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

Conference

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

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • General Computer Science

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