Bayesian clustering for continuous-time hidden Markov models

We develop clustering procedures for longitudinal trajectories based on a continuous-time hidden Markov model (CTHMM) and a generalized linear observation model. Specifically, in this article we carry out finite and infinite mixture model-based clustering for a CTHMM and achieve inference using Markov chain Monte Carlo (MCMC). For a finite mixture model with a prior on the number of components, we implement reversible-jump MCMC to facilitate the trans-dimensional move between models with different numbers of clusters. For a Dirichlet process mixture model, we utilize restricted Gibbs sampling split–merge proposals to improve the performance of the MCMC algorithm. We apply our proposed algorithms to simulated data as well as a real-data example, and the results demonstrate the desired performance of the new sampler.     

Forecasting with non-homogeneous hidden Markov models

We present a Bayesian forecasting methodology of discrete-time finite state-space hidden Markov models with non-constant transition matrix that depends on a set of exogenous covariates. We describe an MCMC reversible jump algorithm for predictive inference, allowing for model uncertainty regarding the set of covariates that affect the transition matrix. We apply our models to interest rates and we show that our general model formulation improves the predictive ability of standard homogeneous hidden Markov models.     

Testing for two states in a hidden Markov model

The authors consider hidden Markov models (HMMs) whose latent process has m ≥ 2 states and whose state‐dependent distributions arise from a general one‐parameter family. They propose a test of the hypothesis m = 2. Their procedure is an extension to HMMs of the modified likelihood ratio statistic proposed by Chen, Chen & Kalbfleisch (2004) for testing two states in a finite mixture. The authors determine the asymptotic distribution of their test under the hypothesis m = 2 and investigate its finite‐sample properties in a simulation study. Their test is based on inference for the marginal mixture distribution of the HMM. In order to illustrate the additional difficulties due to the dependence structure of the HMM, they show how to test general regular hypotheses on the marginal mixture of HMMs via a quasi‐modified likelihood ratio. They also discuss two applications.     

Penalized maximum likelihood estimation for Gaussian hidden Markov models

ABSTRACT

The likelihood function of a Gaussian hidden Markov model is unbounded, which is why the maximum likelihood estimator (MLE) is not consistent. A penalized MLE is introduced along with a rigorous consistency proof.     

On-line inference for hidden Markov models via particle filters

Summary.  We consider the on-line Bayesian analysis of data by using a hidden Markov model, where inference is tractable conditional on the history of the state of the hidden component. A new particle filter algorithm is introduced and shown to produce promising results when analysing data of this type. The algorithm is similar to the mixture Kalman filter but uses a different resampling algorithm. We prove that this resampling algorithm is computationally efficient and optimal, among unbiased resampling algorithms, in terms of minimizing a squared error loss function. In a practical example, that of estimating break points from well-log data, our new particle filter outperforms two other particle filters, one of which is the mixture Kalman filter, by between one and two orders of magnitude.     

Spatial hidden Markov models and species distributions

A spatial hidden Markov model (SHMM) is introduced to analyse the distribution of a species on an atlas, taking into account that false observations and false non-detections of the species can occur during the survey, blurring the true map of presence and absence of the species. The reconstruction of the true map is tackled as the restoration of a degraded pixel image, where the true map is an autologistic model, hidden behind the observed map, whose normalizing constant is efficiently computed by simulating an auxiliary map. The distribution of the species is explained under the Bayesian paradigm and Markov chain Monte Carlo (MCMC) algorithms are developed. We are interested in the spatial distribution of the bird species Greywing Francolin in the south of Africa. Many climatic and land-use explanatory variables are also available: they are included in the SHMM and a subset of them is selected by the mutation operators within the MCMC algorithm.     

Quantifying uncertainty in transdimensional Markov chain Monte Carlo using discrete Markov models

Bayesian analysis often concerns an evaluation of models with different dimensionality as is necessary in, for example, model selection or mixture models. To facilitate this evaluation, transdimensional Markov chain Monte Carlo (MCMC) relies on sampling a discrete indexing variable to estimate the posterior model probabilities. However, little attention has been paid to the precision of these estimates. If only few switches occur between the models in the transdimensional MCMC output, precision may be low and assessment based on the assumption of independent samples misleading. Here, we propose a new method to estimate the precision based on the observed transition matrix of the model-indexing variable. Assuming a first-order Markov model, the method samples from the posterior of the stationary distribution. This allows assessment of the uncertainty in the estimated posterior model probabilities, model ranks, and Bayes factors. Moreover, the method provides an estimate for the effective sample size of the MCMC output. In two model selection examples, we show that the proposed approach provides a good assessment of the uncertainty associated with the estimated posterior model probabilities.

     

A semiparametric approach to hidden Markov models under longitudinal observations

We propose a hidden Markov model for longitudinal count data where sources of unobserved heterogeneity arise, making data overdispersed. The observed process, conditionally on the hidden states, is assumed to follow an inhomogeneous Poisson kernel, where the unobserved heterogeneity is modeled in a generalized linear model (GLM) framework by adding individual-specific random effects in the link function. Due to the complexity of the likelihood within the GLM framework, model parameters may be estimated by numerical maximization of the log-likelihood function or by simulation methods; we propose a more flexible approach based on the Expectation Maximization (EM) algorithm. Parameter estimation is carried out using a non-parametric maximum likelihood (NPML) approach in a finite mixture context. Simulation results and two empirical examples are provided.     

An extension on INAR models with discrete Laplace marginal distributions

The main theme considered in this article is an integer-valued thinning operator with both positive and negative values, its properties, and a new time series with skew discrete Laplace marginals. Some properties of this model are discussed, as well as estimators of unknown parameters, similarities and differences with some other existing models, applications in real-life situations, and identification and approximation of latent processes affecting the concerning process.     

The strong laws of large numbers for countable non homogeneous hidden Markov models

In this article, we are going to study the strong laws of large numbers for countable non homogeneous hidden Markov models. First, we introduce the notion of countable non homogeneous hidden Markov models. Then, we obtain some properties for those Markov models. Finally, we establish two strong laws of large numbers for countable non homogeneous hidden Markov models. As corollaries, we obtain some known results of strong laws of large numbers for finite non homogeneous Markov chains.     

Dynamic latent trait models with mixed hidden Markov structure for mixed longitudinal outcomes

We propose a general Bayesian joint modeling approach to model mixed longitudinal outcomes from the exponential family for taking into account any differential misclassification that may exist among categorical outcomes. Under this framework, outcomes observed without measurement error are related to latent trait variables through generalized linear mixed effect models. The misclassified outcomes are related to the latent class variables, which represent unobserved real states, using mixed hidden Markov models (MHMMs). In addition to enabling the estimation of parameters in prevalence, transition and misclassification probabilities, MHMMs capture cluster level heterogeneity. A transition modeling structure allows the latent trait and latent class variables to depend on observed predictors at the same time period and also on latent trait and latent class variables at previous time periods for each individual. Simulation studies are conducted to make comparisons with traditional models in order to illustrate the gains from the proposed approach. The new approach is applied to data from the Southern California Children Health Study to jointly model questionnaire-based asthma state and multiple lung function measurements in order to gain better insight about the underlying biological mechanism that governs the inter-relationship between asthma state and lung function development.     

Reparameterization strategies for hidden Markov models and Bayesian approaches to maximum likelihood estimation

This paper synthesizes a global approach to both Bayesian and likelihood treatments of the estimation of the parameters of a hidden Markov model in the cases of normal and Poisson distributions. The first step of this global method is to construct a non-informative prior based on a reparameterization of the model; this prior is to be considered as a penalizing and bounding factor from a likelihood point of view. The second step takes advantage of the special structure of the posterior distribution to build up a simple Gibbs algorithm. The maximum likelihood estimator is then obtained by an iterative procedure replicating the original sample until the corresponding Bayes posterior expectation stabilizes on a local maximum of the original likelihood function.     

Robust estimation for order of hidden Markov models based on density power divergences

In this paper, we study the robust estimation for the order of hidden Markov model (HMM) based on a penalized minimum density power divergence estimator, which is obtained by utilizing the finite mixture marginal distribution of HMM. For this task, we adopt the locally conic parametrization method used in [D. Dacunha-Castelle and E. Gassiate, Testing in locally conic models and application to mixture models. ESAIM Probab. Stat. (1997), pp. 285–317; D. Dacunha-Castelle and E. Gassiate, Testing the order of a model using locally conic parametrization: population mixtures and stationary arma processes, Ann. Statist. 27 (1999), pp. 1178–1209; T. Lee and S. Lee, Robust and consistent estimation of the order of finite mixture models based on the minimizing a density power divergence estimator, Metrika 68 (2008), pp. 365–390] to avoid the difficulties that arise in handling mixture marginal models, such as the non-identifiability of the parameter space and the singularity problem with the asymptotic variance. We verify that the estimated order is consistent and simulation results are provided for illustration.     

Bayesian inference in hidden Markov models through the reversible jump Markov chain Monte Carlo method

Hidden Markov models form an extension of mixture models which provides a flexible class of models exhibiting dependence and a possibly large degree of variability. We show how reversible jump Markov chain Monte Carlo techniques can be used to estimate the parameters as well as the number of components of a hidden Markov model in a Bayesian framework. We employ a mixture of zero-mean normal distributions as our main example and apply this model to three sets of data from finance, meteorology and geomagnetism.     

Estimation for hidden Markov random fields

A finite state Markov random field is noisily observed via a second finite state process. The parameters of the model are estimated, as well as the most likely signal given the observations.     

Reversible jump and the label switching problem in hidden Markov models

Reversible jump Markov chain Monte Carlo (RJMCMC) algorithms can be efficiently applied in Bayesian inference for hidden Markov models (HMMs), when the number of latent regimes is unknown. As for finite mixture models, when priors are invariant to the relabelling of the regimes, HMMs are unidentifiable in data fitting, because multiple ways to label the regimes can alternate during the MCMC iterations; this is the so-called label switching problem. HMMs with an unknown number of regimes are considered here and the goal of this paper is the comparison, both applied and theoretical, of five methods used for tackling label switching within a RJMCMC algorithm; they are: post-processing, partial reordering, permutation sampling, sampling from a Markov prior and rejection sampling. The five strategies we compare have been proposed mostly in the literature of finite mixture models and only two of them, i.e. rejection sampling and partial reordering, have been presented in RJMCMC algorithms for HMMs. We consider RJMCMC algorithms in which the parameters are updated by Gibbs sampling and the dimension of the model changes in split-and-merge and birth-and-death moves. Finally, an example illustrates and compares the five different methodologies.     

Robust fitting of hidden Markov regression models under a longitudinal setting

We propose a robust estimation procedure for the analysis of longitudinal data including a hidden process to account for unobserved heterogeneity between subjects in a dynamic fashion. We show how to perform estimation by an expectation–maximization-type algorithm in the hidden Markov regression literature. We show that the proposed robust approaches work comparably to the maximum-likelihood estimator when there are no outliers and the error is normal and outperform it when there are outliers or the error is heavy tailed. A real data application is used to illustrate our proposal. We also provide details on a simple criterion to choose the number of hidden states.     

A stationarity test on Markov chain models based on marginal distribution

A stationarity test on Markov chain models is proposed in this paper. Most of the previous test procedures for the Markov chain models have been done based on the conditional probabilities of a transition matrix. The likelihood ratio and Pearson type chi-square tests have been used for testing stationarity and order of Markov chains. This paper uses the efficient score test, an extension of the test developed by Tsiatis (1980) [18], for testing the stationarity of Markov chain models based on the marginal distribution as obtained by Azzalini (1994) [2]. For testing the suitability of the proposed method, a numerical example of real life data and simulation studies for comparison with an alternative test procedure are given.     

Detecting homogeneous segments in DNA sequences by using hidden Markov models

In recent years there has been a rapid growth in the amount of DNA being sequenced and in its availability through genetic databases. Statistical techniques which identify structure within these sequences can be of considerable assistance to molecular biologists particularly when they incorporate the discrete nature of changes caused by evolutionary processes. This paper focuses on the detection of homogeneous segments within heterogeneous DNA sequences. In particular, we study an intron from the chimpanzee α-fetoprotein gene; this protein plays an important role in the embryonic development of mammals. We present a Bayesian solution to this segmentation problem using a hidden Markov model implemented by Markov chain Monte Carlo methods. We consider the important practical problem of specifying informative prior knowledge about sequences of this type. Two Gibbs sampling algorithms are contrasted and the sensitivity of the analysis to the prior specification is investigated. Model selection and possible ways to overcome the label switching problem are also addressed. Our analysis of intron 7 identifies three distinct homogeneous segment types, two of which occur in more than one region, and one of which is reversible.