Hidden Markov Model Induction by Bayesian Model Merging

Hidden Markov Models (HMMs) are a well-studied approach to the modelling of sequence data. HMMs can be viewed as a stochastic generalization of finite-state automata, where both the transitions between states and the generation of output symbols are governed by probability distributions. HMMs have been important in speech recognition (Rabiner & Juang, 1986), cryptography, and more recently in other areas such as protein classification and alignment (Haussler, Krogh, Mian & SjOlander, 1992; Baldi, Chauvin, Hunkapiller & McClure, 1993). Practitioners have typically chosen the HMM topology by hand, so that learning the HMM from sample data means estimating only a fixed number of model parameters. The standard approach is to find a maximum likelihood (ML) or maximum a posteriori probability (MAP) estimate of the HMM parameters.