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 Nov 8
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

Fingerprint

Message passing
DNA sequences

Keywords

  • Message passing
  • Motif finding

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Electrical and Electronic Engineering

Cite this

Lee, S. H., Vikalo, H., & Vishwanath, S. (2010). Further results on message-passing algorithms for motif finding. In 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010 - Proceedings (pp. 534-537). [5495623] (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings). https://doi.org/10.1109/ICASSP.2010.5495623

Further results on message-passing algorithms for motif finding. / Lee, Sang Hyun; Vikalo, Haris; Vishwanath, Sriram.

2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010 - Proceedings. 2010. p. 534-537 5495623 (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings).

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

Lee, SH, Vikalo, H & Vishwanath, S 2010, Further results on message-passing algorithms for motif finding. in 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010 - Proceedings., 5495623, ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings, pp. 534-537, 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010, Dallas, TX, United States, 10/3/14. https://doi.org/10.1109/ICASSP.2010.5495623
Lee SH, Vikalo H, Vishwanath S. Further results on message-passing algorithms for motif finding. In 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010 - Proceedings. 2010. p. 534-537. 5495623. (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings). https://doi.org/10.1109/ICASSP.2010.5495623
Lee, Sang Hyun ; Vikalo, Haris ; Vishwanath, Sriram. / Further results on message-passing algorithms for motif finding. 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010 - Proceedings. 2010. pp. 534-537 (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings).
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