Generalized Baum-Welch Algorithm Based on the Similarity between Sequences
نویسندگان
چکیده
منابع مشابه
Generalized Baum-Welch Algorithm Based on the Similarity between Sequences
The profile hidden Markov model (PHMM) is widely used to assign the protein sequences to their respective families. A major limitation of a PHMM is the assumption that given states the observations (amino acids) are independent. To overcome this limitation, the dependency between amino acids in a multiple sequence alignment (MSA) which is the representative of a PHMM can be appended to the PHMM...
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A profile hidden Markov model (PHMM) is widely used in assigning protein sequences to protein families. In this model, the hidden states only depend on the previous hidden state and observations are independent given hidden states. In other words, in the PHMM, only the information of the left side of a hidden state is considered. However, it makes sense that considering the information of the b...
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This paper describes how we can use the generalized BaumWelch (GBW) algorithm to develop better extended BaumWelch (EBW) algorithms. Based on GBW, we show that the backoff term in the EBW algorithm comes from KL-divergence which is used as a regularization function. This finding allows us to develop a fast EBW algorithm, which can reduce the time of model space discriminative training by half, ...
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a profile hidden markov model (phmm) is widely used in assigning protein sequences to protein families. in this model, the hidden states only depend on the previous hidden state and observations are independent given hidden states. in other words, in the phmm, only the information of the left side of a hidden state is considered. however, it makes sense that considering the information of the b...
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The parameters of a Hidden Markov Model (HMM) are transition and emission probabilities‎. ‎Both can be estimated using the Baum-Welch algorithm‎. ‎The process of discovering the sequence of hidden states‎, ‎given the sequence of observations‎, ‎is performed by the Viterbi algorithm‎. ‎In both Baum-Welch and Viterbi algorithms‎, ‎it is assumed that...
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ژورنال
عنوان ژورنال: PLoS ONE
سال: 2013
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0080565