[Biojava-l] Re: Looking for a Fisher(like) Kernel
matthew.pocock at ncl.ac.uk
Fri Dec 2 06:11:15 EST 2005
On Thursday 01 December 2005 22:06, Todd Riley wrote:
> 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.
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