We derive a tight perturbation bound for hidden Markov models.
Using this bound, we show that, in many cases, the distribution of
a hidden Markov model is considerably more sensitive to
perturbations in the emission probabilities than to perturbations
in the transition probability matrix and the initial distribution
of the underlying Markov chain. Our approach can also be used to
assess the sensitivity of other stochastic models, such as mixture
processes and semi-Markov processes.
References
Archer, G. E. B. and Titterington, D. M. (2002). Parameter estimation for hidden Markov chains. J. Statist. Planning Infer. 108, 365--390.
Ball, F., Milne, R. K. and Yeo, G. F. (1991). Aggregated semi-Markov processes incorporating time interval omission. Adv. Appl. Prob. 23, 772--797.
Baum, L. E. and Petrie, T. (1966). Statistical inference for probabilistic functions of finite Markov chains. Ann. Math. Statist. 37, 1554--1563.
Mathematical Reviews (MathSciNet):
MR202264
Baum, L. E., Petrie, T., Soules, G. and Weiss, N. (1970). A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann. Math. Statist. 41, 164--171.
Mathematical Reviews (MathSciNet):
MR287613
Besemer, J. and Borodovsky, M. (1999). Heuristic approach to deriving models for gene finding. Nucleic Acids Res. 27, 3911--3920.
Besemer, J., Lomsadze, A. and Borodovsky, M. (2001). GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 29, 2607--2618.
Bickel, P. G., Ritov, Y. and Rydén, T. (1998). Asymptotic normality of the maximum-likelihood estimator for general hidden Markov models. Ann. Statist. 26, 1614--1635.
Cho, G. E. and Meyer, C. D. (2001). Comparison of perturbation bounds for the stationary distribution of a Markov chain. Linear Algebra Appl. 335, 137--150.
Cohen, J. E., Kemperman, J. H. B. and Zbăganu, Gh. (1998). Comparisons of Stochastic Matrices. Birkhäuser, Boston, MA.
Ephraim, Y. and Merhav, N. (2002). Hidden Markov processes. IEEE Trans. Inf. Theory 48, 1518--1569.
Granovsky, B. L. and Zeifman, A. I. (2000). Nonstationary Markovian queues. J. Math. Sci. (New York) 99, 1415--1438.
Jensen, J. L. and Petersen, N. V. (1999). Asymptotic normality of the maximum likelihood estimator in state space models. Ann. Statist. 27, 514--535.
Juang, B.-H. and Rabiner, L. R. (1985). A probabilistic distance measure for hidden Markov models. AT&T Tech. J. 64, 391--408.
Kartashov, N. V. (1996). Strong Stable Markov Chains. VSP, Utrecht.
Koski, T. (2001). Hidden Markov Models for Bioinformatics. Kluwer, Dordrecht.
Leroux, B. G. (1992). Maximum likelihood estimation for hidden Markov models. Stoch. Process. Appl. 40, 127--143.
Lukashin, A. L. and Borodovsky, M. (1998). GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26, 1107--1115.
McDonald, I. and Zucchini, W. (1997). Hidden Markov and Other Models for Discrete-Valued Time Series. Chapman and Hall, London.
Mitrophanov, A. Yu. (2003). Stability and exponential convergence of continuous-time Markov chains. J. Appl. Prob. 40, 970--979.
Mitrophanov, A. Yu. (2004). The spectral gap and perturbation bounds for reversible continuous-time Markov chains. J. Appl. Prob. 41, 1219--1222.
Mitrophanov, A. Yu. (2005). Ergodicity coefficient and perturbation bounds for continuous-time Markov chains. Math. Ineq. Appl. 8, 159--168.
Mitrophanov, A. Yu. (2005). Estimates of sensitivity to perturbations for finite homogeneous continuous-time Markov chains. Teor. Veroyat. Primen. 50, 371--379 (in Russian). English translation to appear in Theory Prob. Appl.
Mitrophanov, A. Yu. (2005). Sensitivity and convergence of uniformly ergodic Markov chains. To appear in J. Appl. Prob.
Peshkin, L. and Gelfand, M. S. (1999). Segmentation of yeast DNA using hidden Markov models. Bioinformatics 15, 980--986.
Petrie, T. (1969). Probabilistic functions of finite state Markov chains. Ann. Math. Statist. 40, 97--115.
Mathematical Reviews (MathSciNet):
MR239662
Pyke, R. (1961). Markov renewal processes: definitions and preliminary properties. Ann. Math. Statist. 32, 1231--1242.
Mathematical Reviews (MathSciNet):
MR133888
Qin, F., Auerbach, A. and Sachs, F. (2000). A direct optimization approach for hidden Markov modelling for single channel kinetics. Biophys. J. 79, 1915--1927.
Rabiner, L. R. (1989). A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77, 257--284.
Rosales, R., Stark, J. A., Fitzgerald, W. J. and Hladky, S. B. (2001). Bayesian restoration of ion channel recordings using hidden Markov models. Biophys. J. 80, 1088--1103.
Seneta, E. (1981). Nonnegative Matrices and Markov Chains. Springer, New York.
Mathematical Reviews (MathSciNet):
MR719544
Seneta, E. (1984). Explicit forms for ergodicity coefficients and spectrum localization. Linear Algebra Appl. 60, 187--197.
Mathematical Reviews (MathSciNet):
MR749184
Zeifman, A. I. (1995). Upper and lower bounds on the rate of convergence for nonhomogeneous birth and death processes. Stoch. Process. Appl. 59, 157--173.
Zeifman, A. I. and Isaacson, D. L. (1994). On strong ergodicity for nonhomogeneous continuous-time Markov chains. Stoch. Process. Appl. 50, 263--273.