Parameterized algorithms for the Module Motif problem

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Abstract

MODULE MOTIF is a pattern matching problem that was introduced in the context of biological networks. Informally, given a multiset of colors P and a graph H in which each node is associated with a set of colors, it asks if P occurs in a module of H (i.e., in a set of nodes that have the same neighborhood outside the set). We present three parameterized algorithms for this problem, which both measure similarity between matched colors and handle deletions and insertions of colors to P. Moreover, we observe that the running times of two of them might be essentially tight, and prove that the problem is unlikely to admit a polynomial kernel.

Original languageEnglish
Pages (from-to)179-193
Number of pages15
JournalInformation and Computation
Volume251
DOIs
StatePublished - 1 Dec 2016
Externally publishedYes

Keywords

  • Computational biology
  • Kernelization
  • Module motif
  • Parameterized algorithm
  • Pattern matching

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