Partial information network queries

Ron Y. Pinter, Meirav Zehavi

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

7 Scopus citations

Abstract

We present a new pattern matching problem, the partial information query (PIQ) problem, which includes as special cases two problems that have important applications in bioinformatics: the alignment query (AQ) problem and the topology-free query (TFQ) problem. In both problems we have a pattern P and a graph H, and we seek a subgraph of H that resembles P. AQ requires knowing the topology of P, while TFQ ignores it. PIQ fits the scenario where partial information is available on the topology of P. Our main result is a parameterized algorithm for PIQ, which can handle inputs where P is a set of trees. It significantly improves the best known running time in solving TFQ. We also improve the best known running times in solving two special cases of AQ.

Original languageEnglish
Title of host publicationCombinatorial Algorithms - 24th International Workshop, IWOCA 2013, Revised Selected Papers
Pages362-375
Number of pages14
DOIs
StatePublished - 1 Dec 2013
Externally publishedYes
Event24th International Workshop on Combinatorial Algorithms, IWOCA 2013 - Rouen, France
Duration: 10 Jul 201312 Jul 2013

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8288 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference24th International Workshop on Combinatorial Algorithms, IWOCA 2013
Country/TerritoryFrance
CityRouen
Period10/07/1312/07/13

Keywords

  • alignment query
  • parameterized algorithm
  • partial information query
  • pattern matching
  • topology-free query

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