[Biojava-l] viterbi training in biojava

[Richard Holland]

I just got a bounce response for this message. So I'm trying again in
case you didn't get it the first time...

cheers,
Richard

On Wed, 2006-05-31 at 09:49 +0100, Richard Holland wrote:
> I've modified BaumWelchSampler in CVS so that it accepts alternative
> score types as an additional parameter to singleSequenceIterator().
> 
> cheers,
> Richard.
> 
> 
> On Tue, 2006-05-30 at 16:43 +0100, wendy wong wrote:
> > thanks! i only need one head so BaumWelchSampler works fine with me.
> > The default SCORETYPE is probability and when I tried it the score
> > goes back and forth, like + for one time and - for the next time. I
> > then changed it to LOGODDS  and recompiled biojava and now that the
> > score is steadily increasing. I was wondering if the SCORETYPE could
> > be passed in as an argument in the next version of biojava?
> > 
> > thanks,
> > wendy
> > 
> > 
> > On 30 May 2006 12:19:15 +0100, David Huen <smh1008 at cam.ac.uk> wrote:
> > > On May 30 2006, wendy wong wrote:
> > >
> > > >Hi,
> > > >
> > > >I was wondering if viterbi training is implemented in biojava, or if
> > > >there's any open source version implemented using biojava?
> > > >
> > > There is one-head viterbi training already I think. The training framework
> > > doesn't work for two-head - I wrote a viterbi training API that works for
> > > two head but it is not fully compatible with the existing API so I never
> > > put it into CVS, plus it doesn't have Baum-Welch implemented either.
> > >
> > > If it is any use to you you can have it.
> > >
> > > Regards,
> > > David
> > >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416