[Biojava-l] Generalized HMM in biojava?

[wendy wong]

Thanks!
Now I have two questions about the SimpleEmissionState class:

1. advance: I am not entirely sure what it does. So if my state emits
4 symbols at a time do I set it to {4}?

2. Each of my sites can emit up to more than 100 alphabets and if 
each state emits 4 symbols at a time the number of alphabet for each
state is 100^4. I am a bit concerned about setting up the
distributions (too much memory consumption?). Is there a function that
I can overload so that the probability of each emission alphabet can
be calculated on the run?

Thanks for your help!

wendy


On 1/11/06, Matthew Pocock <matthew.pocock at ncl.ac.uk> wrote:
> If each state emits a fixed number of symbols then you can just do an HMM
> where the emissions are over alpha^length. If you want the symbols to overlap
> then use an order-n distribution.
>
> Matthew
>
> On Wednesday 11 January 2006 09:37, wendy wong wrote:
> > what I mean by Generalized HMM is that each state emits a sequence of
> > symbols (fixed length though), which doesn't seen very straight
> > forward in biojava?
> >
> > thanks,
> > wendy
> >
> > On 1/11/06, mark.schreiber at novartis.com <mark.schreiber at novartis.com> wrote:
> > > Depending on what you mean by generalized....
> > >
> > > You can create lots of custom HMM architechtures using the DP packages of
> > > biojava.
> > >
> > > - Mark
> > >
> > >
> > >
> > >
> > >
> > > wendy wong <wendy.wong at gmail.com>
> > > Sent by: biojava-l-bounces at portal.open-bio.org
> > > 01/11/2006 05:00 AM
> > > Please respond to sww8
> > >
> > >
> > >         To:     biojava-l at biojava.org
> > >         cc:     (bcc: Mark Schreiber/GP/Novartis)
> > >         Subject:        [Biojava-l] Generalized HMM in biojava?
> > >
> > >
> > > Hi,
> > >
> > > I was wondering if it is possible to use the biojava library to
> > > construct a generalized HMM?
> > >
> > > thanks,
> > > Wendy
> > >
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