Sequential Monte Carlo EM for multivariate probit models

Multivariate probit models (MPM) have the appealing feature of capturing some of the dependence structure between the components of multidimensional binary responses. The key for the dependence modelling is the covariance matrix of an underlying latent multivariate Gaussian. Most approaches to MLE in multivariate probit regression rely on MCEM algorithms to avoid computationally intensive evaluations of multivariate normal orthant probabilities. As an alternative to the much used Gibbs sampler a new SMC sampler for truncated multivariate normals is proposed. The algorithm proceeds in two stages where samples are first drawn from truncated multivariate Student $t$ distributions and then further evolved towards a Gaussian. The sampler is then embedded in a MCEM algorithm. The sequential nature of SMC methods can be exploited to design a fully sequential version of the EM, where the samples are simply updated from one iteration to the next rather than resampled from scratch. Recycling the samples in this manner significantly reduces the computational cost. An alternative view of the standard conditional maximisation step provides the basis for an iterative procedure to fully perform the maximisation needed in the EM algorithm. The identifiability of MPM is also thoroughly discussed. In particular, the likelihood invariance can be embedded in the EM algorithm to ensure that constrained and unconstrained maximisation are equivalent. A simple iterative procedure is then derived for either maximisation which takes effectively no computational time. The method is validated by applying it to the widely analysed Six Cities dataset and on a higher dimensional simulated example. Previous approaches to the Six Cities overly restrict the parameter space but, by considering the correct invariance, the maximum likelihood is quite naturally improved when treating the full unrestricted model.Comment: 26 pages, 2 figures. In press, Computational Statistics & Data Analysi

Computation of Gaussian orthant probabilities in high dimension

We study the computation of Gaussian orthant probabilities, i.e. the probability that a Gaussian falls inside a quadrant. The Geweke-Hajivassiliou-Keane (GHK) algorithm [Genz, 1992; Geweke, 1991; Hajivassiliou et al., 1996; Keane, 1993], is currently used for integrals of dimension greater than 10. In this paper we show that for Markovian covariances GHK can be interpreted as the estimator of the normalizing constant of a state space model using sequential importance sampling (SIS). We show for an AR(1) the variance of the GHK, properly normalized, diverges exponentially fast with the dimension. As an improvement we propose using a particle filter (PF). We then generalize this idea to arbitrary covariance matrices using Sequential Monte Carlo (SMC) with properly tailored MCMC moves. We show empirically that this can lead to drastic improvements on currently used algorithms. We also extend the framework to orthants of mixture of Gaussians (Student, Cauchy etc.), and to the simulation of truncated Gaussians

Conjugate Bayes for probit regression via unified skew-normal distributions

Regression models for dichotomous data are ubiquitous in statistics. Besides being useful for inference on binary responses, these methods serve also as building blocks in more complex formulations, such as density regression, nonparametric classification and graphical models. Within the Bayesian framework, inference proceeds by updating the priors for the coefficients, typically set to be Gaussians, with the likelihood induced by probit or logit regressions for the responses. In this updating, the apparent absence of a tractable posterior has motivated a variety of computational methods, including Markov Chain Monte Carlo routines and algorithms which approximate the posterior. Despite being routinely implemented, Markov Chain Monte Carlo strategies face mixing or time-inefficiency issues in large p and small n studies, whereas approximate routines fail to capture the skewness typically observed in the posterior. This article proves that the posterior distribution for the probit coefficients has a unified skew-normal kernel, under Gaussian priors. Such a novel result allows efficient Bayesian inference for a wide class of applications, especially in large p and small-to-moderate n studies where state-of-the-art computational methods face notable issues. These advances are outlined in a genetic study, and further motivate the development of a wider class of conjugate priors for probit models along with methods to obtain independent and identically distributed samples from the unified skew-normal posterior

Hierarchical Bayesian sparse image reconstruction with application to MRFM

This paper presents a hierarchical Bayesian model to reconstruct sparse images when the observations are obtained from linear transformations and corrupted by an additive white Gaussian noise. Our hierarchical Bayes model is well suited to such naturally sparse image applications as it seamlessly accounts for properties such as sparsity and positivity of the image via appropriate Bayes priors. We propose a prior that is based on a weighted mixture of a positive exponential distribution and a mass at zero. The prior has hyperparameters that are tuned automatically by marginalization over the hierarchical Bayesian model. To overcome the complexity of the posterior distribution, a Gibbs sampling strategy is proposed. The Gibbs samples can be used to estimate the image to be recovered, e.g. by maximizing the estimated posterior distribution. In our fully Bayesian approach the posteriors of all the parameters are available. Thus our algorithm provides more information than other previously proposed sparse reconstruction methods that only give a point estimate. The performance of our hierarchical Bayesian sparse reconstruction method is illustrated on synthetic and real data collected from a tobacco virus sample using a prototype MRFM instrument.Comment: v2: final version; IEEE Trans. Image Processing, 200

Efficient Gaussian Sampling for Solving Large-Scale Inverse Problems using MCMC Methods

The resolution of many large-scale inverse problems using MCMC methods requires a step of drawing samples from a high dimensional Gaussian distribution. While direct Gaussian sampling techniques, such as those based on Cholesky factorization, induce an excessive numerical complexity and memory requirement, sequential coordinate sampling methods present a low rate of convergence. Based on the reversible jump Markov chain framework, this paper proposes an efficient Gaussian sampling algorithm having a reduced computation cost and memory usage. The main feature of the algorithm is to perform an approximate resolution of a linear system with a truncation level adjusted using a self-tuning adaptive scheme allowing to achieve the minimal computation cost. The connection between this algorithm and some existing strategies is discussed and its efficiency is illustrated on a linear inverse problem of image resolution enhancement.Comment: 20 pages, 10 figures, under review for journal publicatio