Geometric Ergodicity and Scanning Strategies for Two-Component Gibbs Samplers

In Markov chain Monte Carlo analysis, rapid convergence of the chain to its target distribution is crucial. A chain that converges geometrically quickly is geometrically ergodic. We explore geometric ergodicity for two-component Gibbs samplers (GS) that, under a chosen scanning strategy, evolve through one-at-a-time component-wise updates. We consider three such strategies: composition, random sequence, and random scans. We show that if any one of these scans produces a geometrically ergodic GS, so too do the others. Further, we provide a simple set of sufficient conditions for the geometric ergodicity of the GS. We illustrate our results using two examples.     

Efficiency and Convergence Properties of Slice Samplers

The slice sampler (SS) is a method of constructing a reversible Markov chain with a specified invariant distribution. Given an independence MetropolisHastings algorithm (IMHA) it is always possible to construct a SS that dominates it in the Peskun sense. This means that the resulting SS produces estimates with a smaller asymptotic variance than the IMHA. Furthermore the SS has a smaller second-largest eigenvalue. This ensures faster convergence to the target distribution. A sufficient condition for uniform ergodicity of the SS is given and an upper bound for the rate of convergence to stationarity is provided.     

Improving Convergence of the HastingsMetropolis Algorithm with an Adaptive Proposal

The HastingsMetropolis algorithm is a general MCMC method for sampling from a density known up to a constant. Geometric convergence of this algorithm has been proved under conditions relative to the instrumental (or proposal) distribution. We present an inhomogeneous HastingsMetropolis algorithm for which the proposal density approximates the target density, as the number of iterations increases. The proposal density at the n th step is a non-parametric estimate of the density of the algorithm, and uses an increasing number of i.i.d. copies of the Markov chain. The resulting algorithm converges (in n ) geometrically faster than a HastingsMetropolis algorithm with any fixed proposal distribution. The case of a strictly positive density with compact support is presented first, then an extension to more general densities is given. We conclude by proposing a practical way of implementation for the algorithm, and illustrate it over simulated examples.     

Adaptive Step Size Selection for Hessian‐Based Manifold Langevin Samplers

In this paper, I explore the usage of positive definite metric tensors derived from the second derivative information in the context of the simplified manifold Metropolis adjusted Langevin algorithm. I propose a new adaptive step size procedure that resolves the shortcomings of such metric tensors in regions where the log‐target has near zero curvature in some direction. The adaptive step size selection also appears to alleviate the need for different tuning parameters in transient and stationary regimes that is typical of Metropolis adjusted Langevin algorithm. The combination of metric tensors derived from the second derivative information and the adaptive step size selection constitute a large step towards developing reliable manifold Markov chain Monte Carlo methods that can be implemented automatically for models with unknown or intractable Fisher information, and even for target distributions that do not admit factorization into prior and likelihood. Through examples of low to moderate dimension, I show that the proposed methodology performs very well relative to alternative Markov chain Monte Carlo methods.     

A joint modeling approach for spatial earthquake risk variations

Modeling spatial patterns and processes to assess the spatial variations of data over a study region is an important issue in many fields. In this paper, we focus on investigating the spatial variations of earthquake risks after a main shock. Although earthquake risks have been extensively studied in the literatures, to our knowledge, there does not exist a suitable spatial model for assessing the problem. Therefore, we propose a joint modeling approach based on spatial hierarchical Bayesian models and spatial conditional autoregressive models to describe the spatial variations in earthquake risks over the study region during two periods. A family of stochastic algorithms based on a Markov chain Monte Carlo technique is then performed for posterior computations. The probabilistic issue for the changes of earthquake risks after a main shock is also discussed. Finally, the proposed method is applied to the earthquake records for Taiwan before and after the Chi-Chi earthquake.     

Bayes and MCMC for Undergraduates

Students of statistics should be taught the ideas and methods that are widely used in practice and that will help them understand the world of statistics. Today, this means teaching them about Bayesian methods. In this article, I present ideas on teaching an undergraduate Bayesian course that uses Markov chain Monte Carlo and that can be a second course or, for strong students, a first course in statistics.     

Generalized multiple-point Metropolis algorithms for approximate Bayesian computation

It is well known that the approximate Bayesian computation algorithm based on Markov chain Monte Carlo methods suffers from the sensitivity to the choice of starting values, inefficiency and a low acceptance rate. To overcome these problems, this study proposes a generalization of the multiple-point Metropolis algorithm, which proceeds by generating multiple-dependent proposals and then by selecting a candidate among the set of proposals on the basis of weights that can be chosen arbitrarily. The performance of the proposed algorithm is illustrated by using both simulated and real data.     

On population-based simulation for static inference

In this paper we present a review of population-based simulation for static inference problems. Such methods can be described as generating a collection of random variables {X _n } _n=1,…,N in parallel in order to simulate from some target density π (or potentially sequence of target densities). Population-based simulation is important as many challenging sampling problems in applied statistics cannot be dealt with successfully by conventional Markov chain Monte Carlo (MCMC) methods. We summarize population-based MCMC (Geyer, Computing Science and Statistics: The 23rd Symposium on the Interface, pp. 156–163, 1991; Liang and Wong, J. Am. Stat. Assoc. 96, 653–666, 2001) and sequential Monte Carlo samplers (SMC) (Del Moral, Doucet and Jasra, J. Roy. Stat. Soc. Ser. B 68, 411–436, 2006a), providing a comparison of the approaches. We give numerical examples from Bayesian mixture modelling (Richardson and Green, J. Roy. Stat. Soc. Ser. B 59, 731–792, 1997).     

Metropolis–Hastings algorithms with adaptive proposals

Different strategies have been proposed to improve mixing and convergence properties of Markov Chain Monte Carlo algorithms. These are mainly concerned with customizing the proposal density in the Metropolis–Hastings algorithm to the specific target density and require a detailed exploratory analysis of the stationary distribution and/or some preliminary experiments to determine an efficient proposal. Various Metropolis–Hastings algorithms have been suggested that make use of previously sampled states in defining an adaptive proposal density. Here we propose a general class of adaptive Metropolis–Hastings algorithms based on Metropolis–Hastings-within-Gibbs sampling. For the case of a one-dimensional target distribution, we present two novel algorithms using mixtures of triangular and trapezoidal densities. These can also be seen as improved versions of the all-purpose adaptive rejection Metropolis sampling (ARMS) algorithm to sample from non-logconcave univariate densities. Using various different examples, we demonstrate their properties and efficiencies and point out their advantages over ARMS and other adaptive alternatives such as the Normal Kernel Coupler.     

Riemann manifold Langevin methods on stochastic volatility estimation

In this article, we perform Bayesian estimation of stochastic volatility models with heavy tail distributions using Metropolis adjusted Langevin (MALA) and Riemman manifold Langevin (MMALA) methods. We provide analytical expressions for the application of these methods, assess the performance of these methodologies in simulated data, and illustrate their use on two financial time series datasets.     

A geometric approach to transdimensional markov chain monte carlo

The authors present theoretical results that show how one can simulate a mixture distribution whose components live in subspaces of different dimension by reformulating the problem in such a way that observations may be drawn from an auxiliary continuous distribution on the largest subspace and then transformed in an appropriate fashion. Motivated by the importance of enlarging the set of available Markov chain Monte Carlo (MCMC) techniques, the authors show how their results can be fruitfully employed in problems such as model selection (or averaging) of nested models, or regeneration of Markov chains for evaluating standard deviations of estimated expectations derived from MCMC simulations.     

Bayesian inference for generalized extreme value distributions via Hamiltonian Monte Carlo

In this article, we propose to evaluate and compare Markov chain Monte Carlo (MCMC) methods to estimate the parameters in a generalized extreme value model. We employed the Bayesian approach using traditional Metropolis-Hastings methods, Hamiltonian Monte Carlo (HMC), and Riemann manifold HMC (RMHMC) methods to obtain the approximations to the posterior marginal distributions of interest. Applications to real datasets and simulation studies provide evidence that the extra analytical work involved in Hamiltonian Monte Carlo algorithms is compensated by a more efficient exploration of the parameter space.     

Bayesian Truncated Poisson Regression with Application to Dutch Illegal Immigrant Data

This article presents a Bayesian approach to the regression analysis of truncated data, with a focus on zero-truncated counts from the Poisson distribution. The approach provides inference not only on the regression coefficients but also on the total sample size and the parameters of the covariate distribution. The theory is applied to some illegal immigrant data from The Netherlands. Several models are fitted with the aid of Markov chain Monte Carlo methods and assessed via posterior predictive p-values. Inferences are compared with those obtained elsewhere using other approaches.     

Relabelling algorithms for mixture models with applications for large data sets

Mixture models are flexible tools in density estimation and classification problems. Bayesian estimation of such models typically relies on sampling from the posterior distribution using Markov chain Monte Carlo. Label switching arises because the posterior is invariant to permutations of the component parameters. Methods for dealing with label switching have been studied fairly extensively in the literature, with the most popular approaches being those based on loss functions. However, many of these algorithms turn out to be too slow in practice, and can be infeasible as the size and/or dimension of the data grow. We propose a new, computationally efficient algorithm based on a loss function interpretation, and show that it can scale up well in large data set scenarios. Then, we review earlier solutions which can scale up well for large data set, and compare their performances on simulated and real data sets. We conclude with some discussions and recommendations of all the methods studied.     

Bayesian image analysis with Markov chain Monte Carlo and coloured continuum triangulation models

It is now possible to carry out Bayesian image segmentation from a continuum parametric model with an unknown number of regions. However, few suitable parametric models exist. We set out to model processes which have realizations that are naturally described by coloured planar triangulations. Triangulations are already used, to represent image structure in machine vision, and in finite element analysis, for domain decomposition. However, no normalizable parametric model, with realizations that are coloured triangulations, has been specified to date. We show how this must be done, and in particular we prove that a normalizable measure on the space of triangulations in the interior of a fixed simple polygon derives from a Poisson point process of vertices. We show how such models may be analysed by using Markov chain Monte Carlo methods and we present two case-studies, including convergence analysis.     

Understanding the Hastings Algorithm

The Hastings algorithm is a key tool in computational science. While mathematically justified by detailed balance, it can be conceptually difficult to grasp. Here, we present two complementary and intuitive ways to derive and understand the algorithm. In our framework, it is straightforward to see that the celebrated Metropolis–Hastings algorithm has the highest acceptance probability of all Hastings algorithms.     

Stochastic search variable selection for log-linear models

We develop a Markov chain Monte Carlo algorithm, based on ‘stochastic search variable selection’ (George and McCuUoch, 1993), for identifying promising log-linear models. The method may be used in the analysis of multi-way contingency tables where the set of plausible models is very large.     

Adaptive multiple importance sampling for Gaussian processes

In applications of Gaussian processes (GPs) where quantification of uncertainty is a strict requirement, it is necessary to accurately characterize the posterior distribution over Gaussian process covariance parameters. This is normally done by means of standard Markov chain Monte Carlo (MCMC) algorithms, which require repeated expensive calculations involving the marginal likelihood. Motivated by the desire to avoid the inefficiencies of MCMC algorithms rejecting a considerable amount of expensive proposals, this paper develops an alternative inference framework based on adaptive multiple importance sampling (AMIS). In particular, this paper studies the application of AMIS for GPs in the case of a Gaussian likelihood, and proposes a novel pseudo-marginal-based AMIS algorithm for non-Gaussian likelihoods, where the marginal likelihood is unbiasedly estimated. The results suggest that the proposed framework outperforms MCMC-based inference of covariance parameters in a wide range of scenarios.     

Parallelizing MCMC for Bayesian spatiotemporal geostatistical models

When MCMC methods for Bayesian spatiotemporal modeling are applied to large geostatistical problems, challenges arise as a consequence of memory requirements, computing costs, and convergence monitoring. This article describes the parallelization of a reparametrized and marginalized posterior sampling (RAMPS) algorithm, which is carefully designed to generate posterior samples efficiently. The algorithm is implemented using the Parallel Linear Algebra Package (PLAPACK). The scalability of the algorithm is investigated via simulation experiments that are implemented using a cluster with 25 processors. The usefulness of the method is illustrated with an application to sulfur dioxide concentration data from the Air Quality System database of the U.S. Environmental Protection Agency.     

Note on posterior inference for the Bingham distribution

The properties of high-dimensional Bingham distributions have been studied by Kume and Walker (2014 Kume, A., and S. G. Walker. 2014. On the Bingham distribution with large dimension. Journal of Multivariate Analysis 124:345–52.[Crossref], [Web of Science ®] , [Google Scholar]). Fallaize and Kypraios (2016 Fallaize, C. J., and T. Kypraios. 2016. Exact Bayesian inference for the Bingham distribution. Statistics and Computing 26:349–60.[Crossref], [Web of Science ®] , [Google Scholar]) propose the Bayesian inference for the Bingham distribution and they use developments in Bayesian computation for distributions with doubly intractable normalizing constants (Møller et al. 2006 Møller, J., A. N. Pettitt, R. Reeves, and K. K. Berthelsen. 2006. An efficient Markov chain Monte Carlo method for distributions with intractable normalising constants. Biometrika 93 (2):451–458.[Crossref], [Web of Science ®] , [Google Scholar]; Murray, Ghahramani, and MacKay 2006 Murray, I., Z. Ghahramani, and D. J. C. MacKay. 2006. MCMC for doubly intractable distributions. In Proceedings of the 22nd annual conference on uncertainty in artificial intelligence (UAI-06), 359–66. AUAI Press. [Google Scholar]). However, they rely heavily on two Metropolis updates that they need to tune. In this article, we propose instead a model selection with the marginal likelihood.