Discriminatively trained markov model for sequence classification

Oksana Yakhnenko, Adrian Silvescu, Vasant Honavar

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

44 Scopus citations

Abstract

In this paper, we propose a discriminative counterpart of the directed Markov Models of order k - 1, or MM (k - 1) for sequence classification. MM(k - 1) models capture dependencies among neighboring elements of a sequence. The parameters of the classifiers are initialized to based on the maximum likelihood estimates for their generative counterparts. We derive gradient based update equations for the parameters of the sequence classifiers in order to maximize the conditional likelihood function. Results of our experiments with data sets drawn from biological sequence classification (specifically protein function and subcellular localization) and text classification applications show that the discriminatively trained sequence classifiers outperform their generative counterparts, confirming the benefits of discriminative training when the primary objective is classification. Our experiments also show that the discriminatively trained MM(k - 1) sequence classifiers are competitive with the computationally much more expensive Support Vector Machines trained using k-gram representations of sequences.

Original languageEnglish (US)
Title of host publicationProceedings - Fifth IEEE International Conference on Data Mining, ICDM 2005
Pages498-505
Number of pages8
DOIs
StatePublished - Dec 1 2005
Event5th IEEE International Conference on Data Mining, ICDM 2005 - Houston, TX, United States
Duration: Nov 27 2005Nov 30 2005

Publication series

NameProceedings - IEEE International Conference on Data Mining, ICDM
ISSN (Print)1550-4786

Other

Other5th IEEE International Conference on Data Mining, ICDM 2005
CountryUnited States
CityHouston, TX
Period11/27/0511/30/05

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All Science Journal Classification (ASJC) codes

  • Engineering(all)

Cite this

Yakhnenko, O., Silvescu, A., & Honavar, V. (2005). Discriminatively trained markov model for sequence classification. In Proceedings - Fifth IEEE International Conference on Data Mining, ICDM 2005 (pp. 498-505). [1565717] (Proceedings - IEEE International Conference on Data Mining, ICDM). https://doi.org/10.1109/ICDM.2005.52