Bioinformatics Advance Access originally published online on August 5, 2004
Bioinformatics 2004 20(18):3613-3619; doi:10.1093/bioinformatics/bth454
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.
Training HMM structure with genetic algorithm for biological sequence analysis
1 ISIS Group, ECS, University of Southampton, SO17 1BJ, UK and 2 Bioinformatics Centre, University of Copenhagen, DK-2100 Copenhagen, Denmark
Received on October 23, 2004; revised on July 11, 2004; accepted on July 23, 2004
Advance Access Publication August 5, 2004
Summary: Hidden Markov models (HMMs) are widely used for biological sequence analysis because of their ability to incorporate biological information in their structure. An automatic means of optimizing the structure of HMMs would be highly desirable. However, this raises two important issues; first, the new HMMs should be biologically interpretable, and second, we need to control the complexity of the HMM so that it has good generalization performance on unseen sequences. In this paper, we explore the possibility of using a genetic algorithm (GA) for optimizing the HMM structure. GAs are sufficiently flexible to allow incorporation of other techniques such as Baum–Welch training within their evolutionary cycle. Furthermore, operators that alter the structure of HMMs can be designed to favour interpretable and simple structures.
In this paper, a training strategy using GAs is proposed, and it is tested on finding HMM structures for the promoter and coding region of the bacterium Campylobacter jejuni. The proposed GA for hidden Markov models (GA-HMM) allows, HMMs with different numbers of states to evolve. To prevent over-fitting, a separate dataset is used for comparing the performance of the HMMs to that used for the Baum–Welch training. The GA-HMM was capable of finding an HMM comparable to a hand-coded HMM designed for the same task, which has been published previously.
Contact: j.won{at}ecs.soton.ac.uk
* To whom correspondence should be addressed.
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