mikeizbicki / hmm Goto Github PK

Hello,
let be these functions:

smm = simpleMM ("ABCD" :: String) 2
smmBW = baumWelch smm (listToArray ("ABCDABCDABCDABCD" :: [Char])) 100
viterbi' hmm d = viterbi hmm (listToArray d)
listToArray d = listArray (1, fromIntegral $ length d) d

Some Tests:
(viterbi' smmBW "A") == ["B"]
True

(viterbi' smmBW "B") == ["C"]
False

(viterbi' smmBW "C") == ["D"]
False

(viterbi' smmBW "D") == ["A"]
False

I think, there is something I do not understand.

May you indicate me where is my mistake please ?

I found you library while searching for code that would calculate the entropy of a hidden Markov model for me. The library does not provide it directly, it seems, but I was wondering if this is something you’d plan to add?

Given the states:
["AT","NP","NN","JJ","VBD","NR","IN"]
And the events:
["The","Fulton","County","Grand","Jury","said","Friday","an","investigation","of"]
Training a simpleHMM with baumWelch on the same list of events,result in
Data.Number.LogFloat.(/): argument out of range

I think that problem was reported first at http://izbicki.me/blog/using-hmms-in-haskell-for-bioinformatics#comment-798 , is there a more recent library to use for hidden markov models? I don't mind having a go at trying to fix this, but some guidance would be appreciated!

Thanks!

See http://hydra.cryp.to/build/574131/log/raw for a complete build log.