Applications of continuous time hidden Markov models to the study of misclassified disease outcomes

Alexandre Bureau, Stephen Shiboski, James P. Hughes

Research output: Contribution to journalArticlepeer-review

40 Scopus citations


Disease progression in prospective clinical and epidemiological studies is often conceptualized in terms of transitions between disease states. Analysis of data from such studies can be complicated by a number of factors, including the presence of individuals in various prevalent disease states and with unknown prior disease history, interval censored observations of state transitions and misclassified measurements of disease states. We present an approach where the disease states are modelled as the hidden states of a continuous time hidden Markov model using the imperfect measurements of the disease state as observations. Covariate effects on transitions between disease states are incorporated using a generalized regression framework. Parameter estimation and inference are based on maximum likelihood methods and rely on an EM algorithm. In addition, techniques for model assessment are proposed. Applications to two binary disease outcomes are presented: the oral lesion hairy leukoplakia in a cohort of HIV infected men and cervical human papillomavirus (HPV) infection in a cohort of young women. Estimated transition rates and misclassification probabilities for the hairy leukoplakia data agree well with clinical observations on the persistence and diagnosis of this lesion, lending credibility to the interpretation of hidden states as representing the actual disease states. By contrast, interpretation of the results for the HPV data are more problematic, illustrating that successful application of the hidden Markov model may be highly dependent on the degree to which the assumptions of the model are satisfied.

Original languageEnglish (US)
Pages (from-to)441-462
Number of pages22
JournalStatistics in Medicine
Issue number3
StatePublished - Feb 15 2003
Externally publishedYes


  • Hidden Markov models
  • Infectious diseases
  • Longitudinal data
  • Misclassification

ASJC Scopus subject areas

  • Epidemiology
  • Statistics and Probability


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