Viterbi algorithms for Hidden semi-Markov Models with application to DNA Analysis
RAIRO - Operations Research - Recherche Opérationnelle, Tome 49 (2015) no. 3, pp. 511-526.

In this paper we present a new Viterbi algorithm for Hidden semi-Markov models and also a second algorithm which is a generalization of the first. These algorithms can be used to decode an unobserved hidden semi-Markov process and it is the first time that the complexity is achieved to be the same as in the Viterbi for Hidden Markov models, i.e. a linear function of the number of observations and quadratic function of the number of hidden states. An example in DNA Analysis is also given.

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Accepté le :
DOI : 10.1051/ro/2014053
Classification : 68Q25, 68Q15, 60K15, 65K05
Mots clés : Viterbi algorithm, Hidden semi-Markov model, hidden Markov model, DNA Analysis
Pertsinidou, Christina-Elisavet 1, 2 ; Limnios, Nikolaos 1

1 Université de Technologie de Compiègne, Laboratoire de Mathématiques Appliquées, Centre de Recherches de Royallieu, CS 60319, 60203 Compiègne Cedex, France.
2 Aristotle University of Thessaloniki, School of Mathematics, 54124 Thessaloniki, Greece.
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     author = {Pertsinidou, Christina-Elisavet and Limnios, Nikolaos},
     title = {Viterbi algorithms for {Hidden} {semi-Markov} {Models} with application to {DNA} {Analysis}},
     journal = {RAIRO - Operations Research - Recherche Op\'erationnelle},
     pages = {511--526},
     publisher = {EDP-Sciences},
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Pertsinidou, Christina-Elisavet; Limnios, Nikolaos. Viterbi algorithms for Hidden semi-Markov Models with application to DNA Analysis. RAIRO - Operations Research - Recherche Opérationnelle, Tome 49 (2015) no. 3, pp. 511-526. doi : 10.1051/ro/2014053. http://www.numdam.org/articles/10.1051/ro/2014053/

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