MAP segmentation in Bayesian hidden Markov models: a case study

We consider the problem of estimating the maximum posterior probability (MAP) state sequence for a finite state and finite emission alphabet hidden Markov model (HMM) in the Bayesian setup, where both emission and transition matrices have Dirichlet priors. We study a training set consisting of thousands of protein alignment pairs. The training data is used to set the prior hyperparameters for Bayesian MAP segmentation. Since the Viterbi algorithm is not applicable any more, there is no simple procedure to find the MAP path, and several iterative algorithms are considered and compared. The main goal of the paper is to test the Bayesian setup against the frequentist one, where the parameters of HMM are estimated using the training data.     

REVERSIBLE JUMP MARKOV CHAIN MONTE CARLO METHODS AND SEGMENTATION ALGORITHMS IN HIDDEN MARKOV MODELS

We consider hidden Markov models with an unknown number of regimes for the segmentation of the pixel intensities of digital images that consist of a small set of colours. New reversible jump Markov chain Monte Carlo algorithms to estimate both the dimension and the unknown parameters of the model are introduced. Parameters are updated by random walk Metropolis–Hastings moves, without updating the sequence of the hidden Markov chain. The segmentation (i.e. the estimation of the hidden regimes) is a further aim and is performed by means of a number of competing algorithms. We apply our Bayesian inference and segmentation tools to digital images, which are linearized through the Peano–Hilbert scan, and perform experiments and comparisons on both synthetic images and a real brain magnetic resonance image.     

Inference for Lévy‐Driven Stochastic Volatility Models via Adaptive Sequential Monte Carlo

Abstract. We investigate simulation methodology for Bayesian inference in Lévy‐driven stochastic volatility (SV) models. Typically, Bayesian inference from such models is performed using Markov chain Monte Carlo (MCMC); this is often a challenging task. Sequential Monte Carlo (SMC) samplers are methods that can improve over MCMC; however, there are many user‐set parameters to specify. We develop a fully automated SMC algorithm, which substantially improves over the standard MCMC methods in the literature. To illustrate our methodology, we look at a model comprised of a Heston model with an independent, additive, variance gamma process in the returns equation. The driving gamma process can capture the stylized behaviour of many financial time series and a discretized version, fit in a Bayesian manner, has been found to be very useful for modelling equity data. We demonstrate that it is possible to draw exact inference, in the sense of no time‐discretization error, from the Bayesian SV model.     

On MCMC sampling in hierarchical longitudinal models

Markov chain Monte Carlo (MCMC) algorithms have revolutionized Bayesian practice. In their simplest form (i.e., when parameters are updated one at a time) they are, however, often slow to converge when applied to high-dimensional statistical models. A remedy for this problem is to block the parameters into groups, which are then updated simultaneously using either a Gibbs or Metropolis-Hastings step. In this paper we construct several (partially and fully blocked) MCMC algorithms for minimizing the autocorrelation in MCMC samples arising from important classes of longitudinal data models. We exploit an identity used by Chib (1995) in the context of Bayes factor computation to show how the parameters in a general linear mixed model may be updated in a single block, improving convergence and producing essentially independent draws from the posterior of the parameters of interest. We also investigate the value of blocking in non-Gaussian mixed models, as well as in a class of binary response data longitudinal models. We illustrate the approaches in detail with three real-data examples.     

Nonparametric Bayesian analysis for multi-site hidden Markov model

The hidden Markov model (HMM) provides an attractive framework for modeling long-term persistence in a variety of applications including pattern recognition. Unlike typical mixture models, hidden Markov states can represent the heterogeneity in data and it can be extended to a multivariate case using a hierarchical Bayesian approach. This article provides a nonparametric Bayesian modeling approach to the multi-site HMM by considering stick-breaking priors for each row of an infinite state transition matrix. This extension has many advantages over a parametric HMM. For example, it can provide more flexible information for identifying the structure of the HMM than parametric HMM analysis, such as the number of states in HMM. We exploit a simulation example and a real dataset to evaluate the proposed approach.     

An EM-Based Viterbi Approximation Algorithm for Mixed-State Latent Factor Models

In this article, a state-space model based on an underlying hidden Markov chain model (HMM) with factor analysis observation process is introduced. The HMM generates a piece-wise constant state evolution process and the observations are produced from the state vectors by a conditionally heteroscedastic factor analysis observation process. More specifically, we concentrate on situations where the factor variances are modeled by univariate Generalized Quadratic Autoregressive Conditionally Heteroscedastic processes (GQARCH). An expectation maximization (EM) algorithm combined with a mixed-state version of the Viterbi algorithm is derived for maximum likelihood estimation. The various regimes, common factors, and their volatilities are supposed unobservable and the inference must be carried out from the observable process. Extensive Monte Carlo simulations show promising results of the algorithms, especially for segmentation and tracking tasks.     

Multivariate Stochastic Volatility Models: Bayesian Estimation and Model Comparison

In this paper we show that fully likelihood-based estimation and comparison of multivariate stochastic volatility (SV) models can be easily performed via a freely available Bayesian software called WinBUGS. Moreover, we introduce to the literature several new specifications that are natural extensions to certain existing models, one of which allows for time-varying correlation coefficients. Ideas are illustrated by fitting, to a bivariate time series data of weekly exchange rates, nine multivariate SV models, including the specifications with Granger causality in volatility, time-varying correlations, heavy-tailed error distributions, additive factor structure, and multiplicative factor structure. Empirical results suggest that the best specifications are those that allow for time-varying correlation coefficients.     

Multivariate Stochastic Volatility Models: Bayesian Estimation and Model Comparison

In this paper we show that fully likelihood-based estimation and comparison of multivariate stochastic volatility (SV) models can be easily performed via a freely available Bayesian software called WinBUGS. Moreover, we introduce to the literature several new specifications that are natural extensions to certain existing models, one of which allows for time-varying correlation coefficients. Ideas are illustrated by fitting, to a bivariate time series data of weekly exchange rates, nine multivariate SV models, including the specifications with Granger causality in volatility, time-varying correlations, heavy-tailed error distributions, additive factor structure, and multiplicative factor structure. Empirical results suggest that the best specifications are those that allow for time-varying correlation coefficients.     

Classical and Bayesian Analysis of Univariate and Multivariate Stochastic Volatility Models

In this paper, efficient importance sampling (EIS) is used to perform a classical and Bayesian analysis of univariate and multivariate stochastic volatility (SV) models for financial return series. EIS provides a highly generic and very accurate procedure for the Monte Carlo (MC) evaluation of high-dimensional interdependent integrals. It can be used to carry out ML-estimation of SV models as well as simulation smoothing where the latent volatilities are sampled at once. Based on this EIS simulation smoother, a Bayesian Markov chain Monte Carlo (MCMC) posterior analysis of the parameters of SV models can be performed.     

Classical and Bayesian Analysis of Univariate and Multivariate Stochastic Volatility Models

In this paper, efficient importance sampling (EIS) is used to perform a classical and Bayesian analysis of univariate and multivariate stochastic volatility (SV) models for financial return series. EIS provides a highly generic and very accurate procedure for the Monte Carlo (MC) evaluation of high-dimensional interdependent integrals. It can be used to carry out ML-estimation of SV models as well as simulation smoothing where the latent volatilities are sampled at once. Based on this EIS simulation smoother, a Bayesian Markov chain Monte Carlo (MCMC) posterior analysis of the parameters of SV models can be performed.     

部分状态可见的隐马尔可夫模型状态序列的估计方法

本文考虑了部分状态可见的隐马尔可夫模型的状态序列估计问题,在分析了现有算法无法合理估计状态路径之后,以状态转移概率、观测概率和可见状态作为先验信息,通过贝叶斯分析计算可见状态前后向状态的后验概率,并给出初始条件和递推公式,运用动态规划递推得到每个观测值对应的最可能状态以及最可能的状态路径。最后,本文给出一个系统故障识别的应用例子,验证了所设计算法的可行性。     

Hierarchical Bayesian Approach to a Multi-Site Hidden Markov Model

Multivariate data with a sequential or temporal structure occur in various fields of study. The hidden Markov model (HMM) provides an attractive framework for modeling long-term persistence in areas of pattern recognition through the extension of independent and identically distributed mixture models. Unlike in typical mixture models, the heterogeneity of data is represented by hidden Markov states. This article extends the HMM to a multi-site or multivariate case by taking a hierarchical Bayesian approach. This extension has many advantages over a single-site HMM. For example, it can provide more information for identifying the structure of the HMM than a single-site analysis. We evaluate the proposed approach by exploiting a spatial correlation that depends on the distance between sites.     

Modelling stochastic volatility using generalized t distribution

In modelling financial return time series and time-varying volatility, the Gaussian and the Student-t distributions are widely used in stochastic volatility (SV) models. However, other distributions such as the Laplace distribution and generalized error distribution (GED) are also common in SV modelling. Therefore, this paper proposes the use of the generalized t (GT) distribution whose special cases are the Gaussian distribution, Student-t distribution, Laplace distribution and GED. Since the GT distribution is a member of the scale mixture of uniform (SMU) family of distribution, we handle the GT distribution via its SMU representation. We show this SMU form can substantially simplify the Gibbs sampler for Bayesian simulation-based computation and can provide a mean of identifying outliers. In an empirical study, we adopt a GT–SV model to fit the daily return of the exchange rate of Australian dollar to three other currencies and use the exchange rate to US dollar as a covariate. Model implementation relies on Bayesian Markov chain Monte Carlo algorithms using the WinBUGS package.     

Variable dimension via stochastic volatility model using FX rates

In this paper, changepoint analysis is applied to stochastic volatility (SV) models which aim to understand the locations and movements of high frequency FX financial time series. Bayesian inference using the Markov Chain Monte Carlo method is performed using a process called variable dimension for SV parameters. Interesting results are that FX series have locations where one or more positions of the sequence correspond to systemic changes, and overall non-stationarity, in the returns process. Furthermore, we found that the changepoint locations provide an informative estimate for all FX series. Importantly in most cases, the detected changepoints can be identified with economic factors relevant to the country concerned. This helps support the fact that macroeconomics news and the movement in financial price are positively related.     

Parallel algorithms for Markov chain Monte Carlo methods in latent spatial Gaussian models

Markov chain Monte Carlo (MCMC) implementations of Bayesian inference for latent spatial Gaussian models are very computationally intensive, and restrictions on storage and computation time are limiting their application to large problems. Here we propose various parallel MCMC algorithms for such models. The algorithms' performance is discussed with respect to a simulation study, which demonstrates the increase in speed with which the algorithms explore the posterior distribution as a function of the number of processors. We also discuss how feasible problem size is increased by use of these algorithms.     

A Bayesian HMM with random effects and an unknown number of states for DNA copy number analysis

Hidden Markov models (HMMs) have been shown to be a flexible tool for modelling complex biological processes. However, choosing the number of hidden states remains an open question and the inclusion of random effects also deserves more research, as it is a recent addition to the fixed-effect HMM in many application fields. We present a Bayesian mixed HMM with an unknown number of hidden states and fixed covariates. The model is fitted using reversible-jump Markov chain Monte Carlo, avoiding the need to select the number of hidden states. We show through simulations that the estimations produced are more precise than those from a fixed-effect HMM and illustrate its practical application to the analysis of DNA copy number data, a field where HMMs are widely used.     

Bayesian bridge-randomized penalized quantile regression estimation for linear regression model with AP(q) perturbation

Bridge penalized regression has many desirable statistical properties such as unbiasedness, sparseness as well as ‘oracle’. In Bayesian framework, bridge regularized penalty can be implemented based on generalized Gaussian distribution (GGD) prior. In this paper, we incorporate Bayesian bridge-randomized penalty and its adaptive version into the quantile regression (QR) models with autoregressive perturbations to conduct Bayesian penalization estimation. Employing the working likelihood of the asymmetric Laplace distribution (ALD) perturbations, the Bayesian joint hierarchical models are established. Based on the mixture representations of the ALD and generalized Gaussian distribution (GGD) priors of coefficients, the hybrid algorithms based on Gibbs sampler and Metropolis-Hasting sampler are provided to conduct fully Bayesian posterior estimation. Finally, the proposed Bayesian procedures are illustrated by some simulation examples and applied to a real data application of the electricity consumption.     

An efficient Monte Carlo EM algorithm for Bayesian lasso

The lasso is a popular technique of simultaneous estimation and variable selection in many research areas. The marginal posterior mode of the regression coefficients is equivalent to estimates given by the non-Bayesian lasso when the regression coefficients have independent Laplace priors. Because of its flexibility of statistical inferences, the Bayesian approach is attracting a growing body of research in recent years. Current approaches are primarily to either do a fully Bayesian analysis using Markov chain Monte Carlo (MCMC) algorithm or use Monte Carlo expectation maximization (MCEM) methods with an MCMC algorithm in each E-step. However, MCMC-based Bayesian method has much computational burden and slow convergence. Tan et al. [An efficient MCEM algorithm for fitting generalized linear mixed models for correlated binary data. J Stat Comput Simul. 2007;77:929–943] proposed a non-iterative sampling approach, the inverse Bayes formula (IBF) sampler, for computing posteriors of a hierarchical model in the structure of MCEM. Motivated by their paper, we develop this IBF sampler in the structure of MCEM to give the marginal posterior mode of the regression coefficients for the Bayesian lasso, by adjusting the weights of importance sampling, when the full conditional distribution is not explicit. Simulation experiments show that the computational time is much reduced with our method based on the expectation maximization algorithm and our algorithms and our methods behave comparably with other Bayesian lasso methods not only in prediction accuracy but also in variable selection accuracy and even better especially when the sample size is relatively large.     

Model selection in finite mixture of regression models: a Bayesian approach with innovative weighted g priors and reversible jump Markov chain Monte Carlo implementation

Finite mixture of regression (FMR) models are aimed at characterizing subpopulation heterogeneity stemming from different sets of covariates that impact different groups in a population. We address the contemporary problem of simultaneously conducting covariate selection and determining the number of mixture components from a Bayesian perspective that can incorporate prior information. We propose a Gibbs sampling algorithm with reversible jump Markov chain Monte Carlo implementation to accomplish concurrent covariate selection and mixture component determination in FMR models. Our Bayesian approach contains innovative features compared to previously developed reversible jump algorithms. In addition, we introduce component-adaptive weighted g priors for regression coefficients, and illustrate their improved performance in covariate selection. Numerical studies show that the Gibbs sampler with reversible jump implementation performs well, and that the proposed weighted priors can be superior to non-adaptive unweighted priors.     

Estimation of parameters in incomplete data models defined by dynamical systems

Parametric incomplete data models defined by ordinary differential equations (ODEs) are widely used in biostatistics to describe biological processes accurately. Their parameters are estimated on approximate models, whose regression functions are evaluated by a numerical integration method. Accurate and efficient estimations of these parameters are critical issues. This paper proposes parameter estimation methods involving either a stochastic approximation EM algorithm (SAEM) in the maximum likelihood estimation, or a Gibbs sampler in the Bayesian approach. Both algorithms involve the simulation of non-observed data with conditional distributions using Hastings–Metropolis (H–M) algorithms. A modified H–M algorithm, including an original local linearization scheme to solve the ODEs, is proposed to reduce the computational time significantly. The convergence on the approximate model of all these algorithms is proved. The errors induced by the numerical solving method on the conditional distribution, the likelihood and the posterior distribution are bounded. The Bayesian and maximum likelihood estimation methods are illustrated on a simulated pharmacokinetic nonlinear mixed-effects model defined by an ODE. Simulation results illustrate the ability of these algorithms to provide accurate estimates.