Further results on message-passing algorithms for motif finding

Sang Hyun Lee, Haris Vikalo, Sriram Vishwanath

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

A new class of message-passing algorithms for motif finding is presented. Motif finding is the problem of identifying a collection of common subsequences within a given set of DNA sequences. It can be cast as an integer linear program (ILP). Message-passing techniques are a computationally efficient alternative to the often infeasible combinatorial solutions to the ILP. We introduce a new graphical representation of the ILP formulation of the problem, and use it to develop new message-passing algorithms for motif finding. Simulation results demonstrate that the new algorithms have better performance and convergence properties than the previously proposed solutions.

Original languageEnglish
Title of host publication2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010 - Proceedings
Pages534-537
Number of pages4
DOIs
Publication statusPublished - 2010
Externally publishedYes
Event2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010 - Dallas, TX, United States
Duration: 2010 Mar 142010 Mar 19

Publication series

NameICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
ISSN (Print)1520-6149

Other

Other2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010
CountryUnited States
CityDallas, TX
Period10/3/1410/3/19

Keywords

  • Message passing
  • Motif finding

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Electrical and Electronic Engineering

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