Learning a multivariate Gaussian mixture model with the reversible jump MCMC algorithm

This paper is a contribution to the methodology of fully Bayesian inference in a multivariate Gaussian mixture model using the reversible jump Markov chain Monte Carlo algorithm. To follow the constraints of preserving the first two moments before and after the split or combine moves, we concentrate on a simplified multivariate Gaussian mixture model, in which the covariance matrices of all components share a common eigenvector matrix. We then propose an approach to the construction of the reversible jump Markov chain Monte Carlo algorithm for this model. Experimental results on several data sets demonstrate the efficacy of our algorithm.     

Characterization of discrete scale invariant Markov sequences

ABSTRACT

Some special sampling of discrete scale invariant (DSI) processes are presented to provide a multi-dimensional self-similar process in correspondence. By imposing Markov property we show that the covariance functions of such Markov DSI sequences are characterized by variance, and covariance of adjacent samples in the first scale interval. We also provide a theoretical method for estimating spectral density matrix of corresponding multi-dimensional self-similar Markov process. Some examples such as simple Brownian motion (sBm) with drift and scale invariant autoregressive model are presented and these properties are investigated. We present two new method to estimate Hurst parameter of DSI processes and apply them to some sBm and also to the SP500 indices for some period which has DSI property. We compare our estimates with the maximum-likelihood and rescaled range (R/S) method which are applied to the corresponding multi-dimensional self-similar processes.     

Central Limit Theorem approximations for the number of runs in Markov-dependent binary sequences

We consider Markov-dependent binary sequences and study various types of success runs (overlapping, non-overlapping, exact, etc.) by examining additive functionals based on state visits and transitions in an appropriate Markov chain. We establish a multivariate Central Limit Theorem for the number of these types of runs and obtain its covariance matrix by means of the recurrent potential matrix of the Markov chain. Explicit expressions for the covariance matrix are given in the Bernoulli and a simple Markov-dependent case by expressing the recurrent potential matrix in terms of the stationary distribution and the mean transition times in the chain. We also obtain a multivariate Central Limit Theorem for the joint number of non-overlapping runs of various sizes and give its covariance matrix in explicit form for Markov dependent trials.     

Reversible jump, birth-and-death and more general continuous time Markov chain Monte Carlo samplers

Summary. Reversible jump methods are the most commonly used Markov chain Monte Carlo tool for exploring variable dimension statistical models. Recently, however, an alternative approach based on birth-and-death processes has been proposed by Stephens for mixtures of distributions. We show that the birth-and-death setting can be generalized to include other types of continuous time jumps like split-and-combine moves in the spirit of Richardson and Green. We illustrate these extensions both for mixtures of distributions and for hidden Markov models. We demonstrate the strong similarity of reversible jump and continuous time methodologies by showing that, on appropriate rescaling of time, the reversible jump chain converges to a limiting continuous time birth-and-death process. A numerical comparison in the setting of mixtures of distributions highlights this similarity.     

Covariance structure of wavelet coefficients: theory and models in a Bayesian perspective

We present theoretical results on the random wavelet coefficients covariance structure. We use simple properties of the coefficients to derive a recursive way to compute the within- and across-scale covariances. We point out a useful link between the algorithm proposed and the two-dimensional discrete wavelet transform. We then focus on Bayesian wavelet shrinkage for estimating a function from noisy data. A prior distribution is imposed on the coefficients of the unknown function. We show how our findings on the covariance structure make it possible to specify priors that take into account the full correlation between coefficients through a parsimonious number of hyperparameters. We use Markov chain Monte Carlo methods to estimate the parameters and illustrate our method on bench-mark simulated signals.     

Reference priors for linear models with general covariance structures

We develop a new class of reference priors for linear models with general covariance structures. A general Markov chain Monte Carlo algorithm is also proposed for implementing the computation. We present several examples to demonstrate the results: Bayesian penalized spline smoothing, a Bayesian approach to bivariate smoothing for a spatial model, and prior specification for structural equation models.     

Singular Gaussian graphical models: Structure learning

ABSTRACT

The goal of this article is to introduce singular Gaussian graphical models and their conditional independence properties. In fact, we extend the concept of Gaussian Markov Random Field to the case of a multivariate normally distributed vector with a singular covariance matrix. We construct, then, the associated graph’s structure from the covariance matrix’s pseudo-inverse on the basis of a characterization of the pairwise conditional independence. The proposed approach can also be used when the covariance matrix is ill-conditioned, through projecting data on a smaller subspace. In this case, our method ensures numerical stability and consistency of the constructed graph and significantly reduces the inference problem’s complexity. These aspects are illustrated using numerical experiments.     

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.     

Selection of Multivariate Stochastic Volatility Models via Bayesian Stochastic Search

We propose a Bayesian stochastic search approach to selecting restrictions on multivariate regression models where the errors exhibit deterministic or stochastic conditional volatilities. We develop a Markov chain Monte Carlo (MCMC) algorithm that generates posterior restrictions on the regression coefficients and Cholesky decompositions of the covariance matrix of the errors. Numerical simulations with artificially generated data show that the proposed method is effective in selecting the data-generating model restrictions and improving the forecasting performance of the model. Applying the method to daily foreign exchange rate data, we conduct stochastic search on a VAR model with stochastic conditional volatilities.     

Bayesian analysis of joint mean and covariance models for longitudinal data

Efficient estimation of the regression coefficients in longitudinal data analysis requires a correct specification of the covariance structure. If misspecification occurs, it may lead to inefficient or biased estimators of parameters in the mean. One of the most commonly used methods for handling the covariance matrix is based on simultaneous modeling of the Cholesky decomposition. Therefore, in this paper, we reparameterize covariance structures in longitudinal data analysis through the modified Cholesky decomposition of itself. Based on this modified Cholesky decomposition, the within-subject covariance matrix is decomposed into a unit lower triangular matrix involving moving average coefficients and a diagonal matrix involving innovation variances, which are modeled as linear functions of covariates. Then, we propose a fully Bayesian inference for joint mean and covariance models based on this decomposition. A computational efficient Markov chain Monte Carlo method which combines the Gibbs sampler and Metropolis–Hastings algorithm is implemented to simultaneously obtain the Bayesian estimates of unknown parameters, as well as their standard deviation estimates. Finally, several simulation studies and a real example are presented to illustrate the proposed methodology.     

A Bayesian approach to analysis of covariance in balanced randomized block experiments

Analysis of covariance in designed experiments has a long history dating back to the middle of the twentieth century. Given the popularity of Bayesian approaches to statistical modelling and inference, it is somewhat surprising that there is so little literature on the application of Bayesian methods in this context. This paper proposes methods based on a recent formulation of the problem in terms of a multivariate variance components model which allows for a conjugate Bayesian analysis of balanced randomized block experiments with concomitant information. The analysis is complicated by a linear constraint involving two covariance matrices. Two solutions are proposed and implemented using Markov chain Monte Carlo methods.     

An MCMC model search algorithm for regression problems

In this paper, we improve upon the Carlin and Chib Markov chain Monte Carlo algorithm that searches in model and parameter spaces. Our proposed algorithm attempts non-uniformly chosen ‘local’ moves in the model space and avoids some pitfalls of other existing algorithms. In a series of examples with linear and logistic regression, we report evidence that our proposed algorithm performs better than the existing algorithms.     

Bayesian covariance matrix estimation using a mixture of decomposable graphical models

We present a Bayesian approach to estimating a covariance matrix by using a prior that is a mixture over all decomposable graphs, with the probability of each graph size specified by the user and graphs of equal size assigned equal probability. Most previous approaches assume that all graphs are equally probable. We show empirically that the prior that assigns equal probability over graph sizes outperforms the prior that assigns equal probability over all graphs in more efficiently estimating the covariance matrix. The prior requires knowing the number of decomposable graphs for each graph size and we give a simulation method for estimating these counts. We also present a Markov chain Monte Carlo method for estimating the posterior distribution of the covariance matrix that is much more efficient than current methods. Both the prior and the simulation method to evaluate the prior apply generally to any decomposable graphical model.     

Phase II monitoring of binary profiles in the presence of within-profile autocorrelation based on Markov Model

This paper introduces a Markov model in Phase II profile monitoring with autocorrelated binary response variable. In the proposed approach, a logistic regression model is extended to describe the within-profile autocorrelation. The likelihood function is constructed and then a particle swarm optimization algorithm (PSO) is tuned and utilized to estimate the model parameters. Furthermore, two control charts are extended in which the covariance matrix is derived based on the Fisher information matrix. Simulation studies are conducted to evaluate the detecting capability of the proposed control charts. A numerical example is also given to illustrate the application of the proposed method.     

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.     

ON UMP INVARIANT F-TEST PROCEDURES IN A GENERAL LINEAR MODEL

A simple method of setting linear hypotheses for a split mean vector testable by F-tests in a general linear model, when the covariance matrix has a general form and is completely unknown, is provided by extending the method discussed in Ukita et al. The critical functions in these F-tests are constructed as UMP invariants, when the covariance matrix has a known structure. Further critical functions in F-tests of linear hypotheses for the other split mean vector in the model are shown to be UMP invariant if the same known structure of the covariance matrix is assumed.     

Objective Bayes Factors for Gaussian Directed Acyclic Graphical Models

Abstract. We propose an objective Bayesian method for the comparison of all Gaussian directed acyclic graphical models defined on a given set of variables. The method, which is based on the notion of fractional Bayes factor (BF), requires a single default (typically improper) prior on the space of unconstrained covariance matrices, together with a prior sample size hyper‐parameter, which can be set to its minimal value. We show that our approach produces genuine BFs. The implied prior on the concentration matrix of any complete graph is a data‐dependent Wishart distribution, and this in turn guarantees that Markov equivalent graphs are scored with the same marginal likelihood. We specialize our results to the smaller class of Gaussian decomposable undirected graphical models and show that in this case they coincide with those recently obtained using limiting versions of hyper‐inverse Wishart distributions as priors on the graph‐constrained covariance matrices.     

Ensemble preconditioning for Markov chain Monte Carlo simulation

We describe parallel Markov chain Monte Carlo methods that propagate a collective ensemble of paths, with local covariance information calculated from neighbouring replicas. The use of collective dynamics eliminates multiplicative noise and stabilizes the dynamics, thus providing a practical approach to difficult anisotropic sampling problems in high dimensions. Numerical experiments with model problems demonstrate that dramatic potential speedups, compared to various alternative schemes, are attainable.     

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.     

On inference from Markov chain macro-data using transforms

We consider data that are longitudinal, arising from n individuals over m time periods. Each individual moves according to the same homogeneous Markov chain, with s states. If the individual sample paths are observed, so that ‘micro-data’ are available, the transition probability matrix is estimated by maximum likelihood straightforwardly from the transition counts. If only the overall numbers in the various states at each time point are observed, we have ‘macro-data’, and the likelihood function is difficult to compute. In that case a variety of methods has been proposed in the literature. In this paper we propose methods based on generating functions and investigate their performance.