Mod/Resc parsimony inference

Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, Olivier Duron, Marie France Sagot

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

4 Scopus citations

Abstract

We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by Mod/Resc Parsimony Inference, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the Bipartite Biclique Edge Cover problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the Bipartite Biclique Edge Cover. Finally, we present experimental results where we applied some of our techniques to a real-life data set.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 21st Annual Symposium, CPM 2010, Proceedings
Pages202-213
Number of pages12
DOIs
StatePublished - 1 Dec 2010
Externally publishedYes
Event21st Annual Symposium on Combinatorial Pattern Matching, CPM 2010 - New York, NY, United States
Duration: 21 Jun 201023 Jun 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6129 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference21st Annual Symposium on Combinatorial Pattern Matching, CPM 2010
Country/TerritoryUnited States
CityNew York, NY
Period21/06/1023/06/10

Keywords

  • Biclique edge covering
  • Bipartite graph
  • Boolean matrix
  • Computational biology
  • Fixed-parameter tractability
  • Graph theory
  • Kernelization
  • NP-completeness

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science

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