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The aim of this paper is to develop a Bayesian hidden Markov model to characterize disease pathology, identify hidden states corresponding to the diagnosed stages of cognitive decline, and examine the dynamic changes of potential risk factors associated with the cognitive normal\u2013mild cognitive impairment\u2013Alzheimer\u2019s disease transition. The hidden Markov model framework consists of two major components. The first one is a state-dependent semiparametric regression for delineating the complex associations between clinical outcomes of interest and a set of prognostic biomarkers across neurodegenerative states. The second one is a parametric transition model, while accounting for potential covariate effects on the cross-state transition. The inter-individual and inter-process differences are taken into account via correlated random effects in both components. Based on the Alzheimer\u2019s Disease Neuroimaging Initiative data set, we are able to identify four states of Alzheimer\u2019s disease pathology, corresponding to common diagnosed cognitive decline stages, including cognitive normal, early mild cognitive impairment, late mild cognitive impairment, and Alzheimer\u2019s disease and examine the effects of hippocampus, age, gender, and APOE-[Formula: see text] on degeneration of cognitive function across the four cognitive states.<\/jats:p>","DOI":"10.1177\/0962280217748675","type":"journal-article","created":{"date-parts":[[2017,12,26]],"date-time":"2017-12-26T18:48:33Z","timestamp":1514314113000},"page":"2112-2124","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":29,"title":["Bayesian hidden Markov models for delineating the pathology of Alzheimer\u2019s 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