Thanks for your advice! I am able to train a subset of transition probabilities now!
I found something strange, first I changed my emission distributions to untrainabledistributions and the trainer didn't seem to be doing anything, all cycles have the same score. I then changed it back to SimpleDistribution (still keepting my getWeightImp in my custom distribution). this time it works and it doesn't seem to be modifying my emission probabilities. So it works for me - I am just curious if it is a bug or if I was doing something wrong? Thanks again! wendy On 3/31/06, Matthew Pocock <[EMAIL PROTECTED]> wrote: > > The DP code does some caching of probabilities, I don't think there's > > any way to turn this off without modifying the DP implementations. > > > > Thomas. > > My reccolection is that if you did turn this off, the algorithm would run > very, very much more slowly. Internally to the DP objects, the distribution > probabilities (in fact, they aren't even probabilities by this stage) are > stored in a data-structure optimized for the type of lookups performed during > the dynamic programming recursions. > > Matthew > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
