paper presentation april 10, 2006 rui min topic in bioinformatics, dr. charles yan - training hmm...
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Paper Presentation
April 10, 2006
Rui Min
Topic in Bioinformatics, Dr. Charles Yan
- Training HMM structure with genetic algorithm for biological sequence analysis
Overview
• An automatic means of optimizing the structure of HMMs
• Genetic algorithm (GA) for optimizing the HMM structure
• Experiments on two models– Promoter model of C.jejuni
– Coding region model of C.jejuni
• Conclusion
Train HMM structure by GA
Problems• Biologically interpretable structure• Controllable complexity
Method• Combine Baum-Wetch training with
GA, called GA for hidden Markov models (GA-HMM).
Flowchart
Genetic Operations (I)
• Selection– Roulette wheel selection– Stochastic universal sampling
Genetic Operations (II)
• Mutation
Genetic Operations (III)
• Crossover
Selective Baum-Welch
• The Log-likelihood of model k
Fitness value
• Fitness
Experiment I: promoter model of C.jejuni
• Parameters
Structure
Comparison
Experiment II: coding region model of C.jejuni
Experiment II: coding region model of C.jejuni
Conclusion
• Drawbacks– Biologically interpretable structure– No novel types of architecture– No large HMM structures– Those may be the future works
• Merit– Capability of dealing with substructures– GA has an application on bioinformatics
Unstated Aspects
• Too many constant parameters– Probability of population for Baum-Welch
training– Percentage of training/validation– Iteration times– Are they best?
• Unclear parameters– Terminal condition– The distribution of results, t-test?– The specific way to crossover, single?
Questions &
Discussion