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October 15th, 2012, 08:45 AM   #1
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Help with Hidden Markov chain

Hey All,

I've been working on this question for few hours with no success. I'd appreciate any input.

Based on the Viterbi algorithm, marginal probability of a sequences being generated by a given HMM model with the Forward algorithm, I'm trying to calculate both, the most probable path-Viterbi- as well as the marginal probability of observing the sequence “ILDE”, for the model defined below.

a. The model has two possible states: transmembrane state (TM) and non-transmembrane state (NT)

b. The state transition matrix A:

St+1
TM NT

St TM 0.8 0.2
NT 0.2 0.8

c. The emission matrix E:


Amino Acids
L I E D

State TM 0.45 0.45 0.05 0.05
NT 0.05 0.05 0.45 0.45

Assume that transition from start state to TM or NT has equal chance 0.5.
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October 15th, 2012, 10:58 PM   #2
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Re: Help with Hidden Markov chain

Hey dr_romix.

Can you reply in the thread on Math Help Forum? I posted a reply there.
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October 16th, 2012, 06:36 PM   #3
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Re: Help with Hidden Markov chain

thanks I did
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