PeakSeg: Constrained optimal segmentation and supervised penalty learning for peak detection in count data

Toby Dylan Hocking, Guillem Rigaill, Guillaume Bourque

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

8 Scopus citations

Abstract

Peak detection is a central problem in genomic data analysis, and current algorithms for this task are unsupervised and mostly effective for a single data type and pattern (e.g. H3K4me3 data with a sharp peak pattern). We propose PeakSeg, a new constrained maximum likelihood segmentation model for peak detection with an efficient inference algorithm: constrained dynamic programming. We investigate unsupervised and supervised learning of penalties for the critical model selection problem. We show that the supervised method has state-of-the-art peak detection across all data sets in a benchmark that includes both sharp H3K4me3 and broad H3K36me3 patterns.

Original languageEnglish (US)
Title of host publication32nd International Conference on Machine Learning, ICML 2015
EditorsFrancis Bach, David Blei
PublisherInternational Machine Learning Society (IMLS)
Pages324-332
Number of pages9
ISBN (Electronic)9781510810587
StatePublished - 2015
Externally publishedYes
Event32nd International Conference on Machine Learning, ICML 2015 - Lile, France
Duration: Jul 6 2015Jul 11 2015

Publication series

Name32nd International Conference on Machine Learning, ICML 2015
Volume1

Conference

Conference32nd International Conference on Machine Learning, ICML 2015
Country/TerritoryFrance
CityLile
Period7/6/157/11/15

ASJC Scopus subject areas

  • Human-Computer Interaction
  • Computer Science Applications

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