On Thursday 01 December 2005 22:06, Todd Riley wrote: > Hello, > > I have good news! I have fixed the bug in the BaumWelchTrainer class > (hopefully the source in CVS will be updated soon).
Yay! What was it? > > Now that I am able to train my Profile HMM, I would like to feed my HMM > into a Fisher Kernel to perform SVM training in order to find the proper > scoring threshold for proper classification (ie - use SVM classification > to set a barrier for my HMM log-odds scores). Sounds like a plan... > > Has anyone implemented a Fisher Kernel (or one like it) for the BioJava > SVM classes? Any information here would be greatly appreciated. > I have not heard of one. However, I think you should be able to calcualte the needed numbers using code nearly identical to that in the BaumWelchTrainer. In fact, I have a sneeking suspicion that the ModelTrainer parameters after 1 cycle of training (before updating the model!) are the raw numbers that the SVM fischer-kernel requires. > Thanks, > Todd Matthew _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
