- Lawrence R. Rabiner (February 1989). "A tutorial on Hidden Markov Models and selected applications in speech recognition". Proceedings of the IEEE 77 (2): 257–286. doi:10.1109/5.18626. http://www.ece.ucsb.edu/Faculty/Rabiner/ece259/Reprints/tutorial%20on%20hmm%20and%20applications.pdf. [1]
- Xuedong Huang, M. Jack, and Y. Ariki (1990). Hidden Markov Models for Speech Recognition. Edinburgh University Press. ISBN 0748601627.
- Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison (1999). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press. ISBN 0-521-62971-3.
- Xuedong Huang, Alex Acero, and Hsiao-Wuen Hon (2001). Spoken Language Processing. Prentice Hall. ISBN 0-13-022616-5.
- Lior Pachter and Bernd Sturmfels (2005). Algebraic Statistics for Computational Biology. Cambridge University Press. ISBN 0-521-85700-7.
- Olivier Cappé, Eric Moulines, Tobias Rydén (2005). Inference in Hidden Markov Models. Springer. ISBN 0-387-40264-0.
- Kristie Seymore, Andrew McCallum, and Roni Rosenfeld. Learning Hidden Markov Model Structure for Information Extraction. AAAI 99 Workshop on Machine Learning for Information Extraction, 1999 (also at CiteSeer: [2]).
- Li J, Najmi A, Gray RM (February 2000). "Image classification by a two dimensional hidden Markov model". IEEE Transactions on Signal Processing 48 (2): 517–533. doi:10.1109/78.823977. http://www.stat.psu.edu/~jiali.
- Ephraim Y, Merhav N (June 2002). "Hidden Markov processes". IEEE Trans. Inform. Theory 48: 1518–1569. doi:10.1109/TIT.2002.1003838.
- Newberg LA (July 2009). "Error statistics of hidden Markov model and hidden Boltzmann model results". BMC Bioinformatics 10: article 212. doi:10.1186/1471-2105-10-212. PMID 19589158. PMC 2722652. http://www.biomedcentral.com/1471-2105/10/212.
- B. Pardo and W. Birmingham. Modeling Form for On-line Following of Musical Performances. AAAI-05 Proc., July 2005.
- Thad Starner, Alex Pentland. Visual Recognition of American Sign Language Using Hidden Markov. Master's Thesis, MIT, Feb 1995, Program in Media Arts
- Satish L, Gururaj BI (April 2003). "Use of hidden Markov models for partial discharge pattern classification". IEEE Transactions on Dielectrics and Electrical Insulation.
The path-counting algorithm, an alternative to the Baum-Welch algorithm:
- Davis RIA, Lovell BC (2000). "Comparing and evaluating HMM ensemble training algorithms using train and test and condition number criteria". Journal of Pattern Analysis and Applications 0 (0): 1–7. http://citeseer.ist.psu.edu/677948.html.
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