[Biojava-l] Partial path probs

[Schreiber, Mark]

Hi -

Is there a way to get the partial path probabilities for the viterbi
algorithm in DP (eg the path trellis)?

I suppose I could subclass it, perhaps VerboseDP :)

On a more theoretical note if one calculated the probability of the
viterbi path and compared that to the forward probability would that be
a good way of infering confidence in the predictions fit to the model?
Eg If the Viterbi path prob and the Forward prob were close you could be
confident that, according to your model, other possible paths are not
that likely. Alternatively if they are not close you might conclude that
although the viterbi path is the most parsimonious there could be other
paths that are almost as likely. Or am I barking up the wrong tree here?

- Mark
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