[Biojava-l] Parameter Settings in BaumWelchTraining

[sacoca at MCB.McGill.CA]

Hi all. I'm trying to optimize the transition states probabilities for my
HMM. I already have set them to values which I think are pretty good.
Since I know the Baum Welch can only help with the scores and optimize
them up to a local maxima I thought of using the parameters I calculated
as a starting point. The problem is that I don't know how!
I followed the example in biojava:

....
//train the model to have uniform parameters
    ModelTrainer mt = new SimpleModelTrainer();
    //register the model to train
    mt.registerModel(hmm);

I want to use the values already set in my hmm  as the starting parameters
in the BaumWelch.  I don't want to use the uniform distribution as
indicated below!

    //as no other counts are being used the null weight will cause   
everything to be uniform
    mt.setNullModelWeight(1.0);
    mt.train();

I tried adding counts and looking up examples on the net but ended up more
confused than I started. How do I use the addCounts to make this work!

Stephane Acoca
Master's Student
McGill Center for Bioinformatics