Literature DB >> 8891955

A learning method of hidden Markov models for sequence discrimination.

H Mamitsuka1.   

Abstract

We propose a learning method for hidden Markov models (HMM) for sequence discrimination. When given an HMM, our method sets a function that corresponds to the product of a difference between the observed and the desired likelihoods for each training sequence, and using a gradient descent algorithm, trains the HMM parameters so that the function should be minimized. This method allows us to use not only the examples belonging to a class that should be represented by the HMM, but also the examples not belonging to the class, i.e., negative examples. We evaluated our method in a series of experiments based on a type of cross-validation, and compared the results with those of two existing methods. Experimental results show that our method greatly reduces the discrimination errors made by the other two methods. We conclude that both the use of negative examples and our method of using negative examples are useful for training HMMs in discriminating unknown sequences.

Mesh:

Year:  1996        PMID: 8891955     DOI: 10.1089/cmb.1996.3.361

Source DB:  PubMed          Journal:  J Comput Biol        ISSN: 1066-5277            Impact factor:   1.479


  4 in total

1.  Prediction of MHC class I binding peptides by a query learning algorithm based on hidden markov models.

Authors:  Keiko Udaka; Hiroshi Mamitsuka; Yukinobu Nakaseko; Naoki Abe
Journal:  J Biol Phys       Date:  2002-06       Impact factor: 1.365

2.  Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum.

Authors:  Nicolas Terrapon; Olivier Gascuel; Eric Maréchal; Laurent Bréhélin
Journal:  BMC Bioinformatics       Date:  2012-05-01       Impact factor: 3.169

3.  HMM-ModE--improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences.

Authors:  Prashant K Srivastava; Dhwani K Desai; Soumyadeep Nandi; Andrew M Lynn
Journal:  BMC Bioinformatics       Date:  2007-03-27       Impact factor: 3.169

4.  HMM-ModE: implementation, benchmarking and validation with HMMER3.

Authors:  Swati Sinha; Andrew Michael Lynn
Journal:  BMC Res Notes       Date:  2014-07-30
  4 in total

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