For viterbi training, you need to do the following:
* Create your model & initialize with random parameters
* Create a hmm training context and register the model with it
* do
o foreach training sequence
- get the viterbi aignment of the model to your sequence
- add one count to the training context for each time a state or transition is used
o call the context's train method
* while the alignments change
Good luck. I'd be interested to see what you end up with. If you need a hand with any of the APIs, send questions to the list.
Matthew
Oscar Lopes wrote:
Hi!
I'm a graduate student and I'm using biojava to implement Viterbi training algorithm.
I spent some time digging in the code, but I still can't make the relation between
TrainigAlgorithm, DistributionTrainer, etc...
What are the key classes that I can use? How does it work? I tried to look at
BaumWelchTrainer, but it didn't make sense how I would implement Viterbi Trainig.
Besides, I kept getting confused with DistributionTrainer and DistributionTrainerContext...
Can anybody help me?? It would be nice if someone explain to me how the whole thing works.
Thanks in advance
Óscar Lopes
Ps. Sorry about my english.... :)
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