Yves F. Atchadé

Towards optimal scaling of metropolis-coupled Markov chain Monte Carlo

We consider optimal temperature spacings for Metropolis-coupled Markov chain Monte Carlo (MCMCMC) and Simulated Tempering algorithms. We prove that, under certain conditions, it is optimal (in terms of maximising the expected squared jumping distance) to space the temperatures so that the proportion of temperature swaps which are accepted is approximately 0.234. This generalises related work by physicists, and is consistent with previous work about optimal scaling of random-walk Metropolis algorithms.

Bayesian Time Series Models: Adaptive Markov chain Monte Carlo: theory and methods

In general, the transition probability P of the Markov chain depends on some tuning parameter θ defined on some space Θ which can be either finite dimensional or infinite dimensional. The success of the MCMC procedure depends crucially upon a proper choice of θ. To illustrate, consider the standard Metropolis-Hastings (MH) algorithm. For simplicity, we assume that π has a density also denoted by π with respect to the Lebesgue measure on X = R endowed with its Borel σ-field X . Given that the chain is at x, a candidate y is sampled from a proposal transition density q(x, ·) and is accepted with probability α(x, y) defined as

Limit theorems for some adaptive MCMC algorithms with subgeometric kernels

This paper deals with the ergodicity and the existence of a strong law of large numbers for adaptive Markov Chain Monte Carlo. We show that a diminishing adaptation assumption together with a drift condition for positive recurrence is enough to imply ergodicity. Strengthening the drift condition to a polynomial drift condition yields a strong law of large numbers for possibly unbounded functions. These results broaden considerably the class of adaptive MCMC algorithms for which rigorous analysis is now possible. As an example, we give a detailed analysis of the Adaptive Metropolis Algorithm of Haario et al. (2001) when the target distribution is sub-exponential in the tails.

Inference for dynamic and latent variable models via iterated, perturbed Bayes maps

Significance Many scientific challenges involve the study of stochastic dynamic systems for which only noisy or incomplete measurements are available. Inference for partially observed Markov process models provides a framework for formulating and answering questions about these systems. Except when the system is small, or approximately linear and Gaussian, state-of-the-art statistical methods are required to make efficient use of available data. Evaluation of the likelihood for a partially observed Markov process model can be formulated as a filtering problem. Iterated filtering algorithms carry out repeated Monte Carlo filtering operations to maximize the likelihood. We develop a new theoretical framework for iterated filtering and construct a new algorithm that dramatically outperforms previous approaches on a challenging inference problem in disease ecology. Iterated filtering algorithms are stochastic optimization procedures for latent variable models that recursively combine parameter perturbations with latent variable reconstruction. Previously, theoretical support for these algorithms has been based on the use of conditional moments of perturbed parameters to approximate derivatives of the log likelihood function. Here, a theoretical approach is introduced based on the convergence of an iterated Bayes map. An algorithm supported by this theory displays substantial numerical improvement on the computational challenge of inferring parameters of a partially observed Markov process.

On Russian Roulette Estimates for Bayesian Inference with Doubly-Intractable Likelihoods

A large number of statistical models are “doubly-intractable”: the likelihood normalising term, which is a function of the model parameters, is intractable, as well as the marginal likelihood (model evidence). This means that standard inference techniques to sample from the posterior, such as Markov chain Monte Carlo (MCMC), cannot be used. Examples include, but are not confined to, massive Gaussian Markov random fields, autologistic models and Exponential random graph models. A number of approximate schemes based on MCMC techniques, Approximate Bayesian computation (ABC) or analytic approximations to the posterior have been suggested, and these are reviewed here. Exact MCMC schemes, which can be applied to a subset of doubly-intractable distributions, have also been developed and are described in this paper. As yet, no general method exists which can be applied to all classes of models with doubly-intractable posteriors. In addition, taking inspiration from the Physics literature, we study an alternative method based on representing the intractable likelihood as an infinite series. Unbiased estimates of the likelihood can then be obtained by finite time stochastic truncation of the series via Russian Roulette sampling, although the estimates are not necessarily positive. Results from the Quantum Chromodynamics literature are exploited to allow the use of possibly negative estimates in a pseudo-marginal MCMC scheme such that expectations with respect to the posterior distribution are preserved. The methodology is reviewed on well-known examples such as the parameters in Ising models, the posterior for Fisher–Bingham distributions on the d-Sphere and a largescale Gaussian Markov Random Field model describing the Ozone Column data. This leads to a critical assessment of the strengths and weaknesses of the methodology with pointers to ongoing research.

Kernel estimators of asymptotic variance for adaptive Markov chain Monte Carlo

We study the asymptotic behavior of kernel estimators of asymptotic variances (or long-run variances) for a class of adaptive Markov chains. The convergence is studied both in L p and almost surely. The results also apply to Markov chains and improve on the existing literature by imposing weaker conditions. We illustrate the results with applications to the GARCH(1, 1) Markov model and to an adaptive MCMC algorithm for Bayesian logistic regression.

Discussion of “Equi-energy sampler” by Kou, Zhou and Wong

We congratulate Samuel Kou, Qing Zhou and Wing Wong [math.ST/0507080] (referred to subsequently as KZW) for this beautifully written paper, which opens a new direction in Monte Carlo computation. This discussion has two parts. First, we describe a very closely related method, multicanonical sampling (MCS), and report a simulation example that compares the equi-energy (EE) sampler with MCS. Overall, we found the two algorithms to be of comparable efficiency for the simulation problem considered. In the second part, we develop some additional convergence results for the EE sampler.

On the geometric ergodicity of Metropolis-Hastings algorithms

Under a compactness assumption, we show that a φ-irreducible and aperiodic Metropolis-Hastings chain is geometrically ergodic if and only if its rejection probability is bounded away from unity. In the particular case of the independence Metropolis-Hastings algorithm, we obtain that the whole spectrum of the induced operator is contained in (and in many cases equal to) the essential range of the rejection probability of the chain as conjectured by [Liu, J.S., 1996, Metropolized independent sampling with comparaisons to rejection sampling and importance sampling. Statistics and Computing, 6, 113–119.].

Change-Point Estimation in High-Dimensional Markov Random Field Models

This paper investigates a change-point estimation problem in the context of high-dimensional Markov random field models. Change-points represent a key feature in many dynamically evolving network structures. The change-point estimate is obtained by maximizing a profile penalized pseudo-likelihood function under a sparsity assumption. We also derive a tight bound for the estimate, up to a logarithmic factor, even in settings where the number of possible edges in the network far exceeds the sample size. The performance of the proposed estimator is evaluated on synthetic data sets and is also used to explore voting patterns in the US Senate in the 1979-2012 period.

Approximate Bayesian Computation for Exponential Random Graph Models for Large Social Networks

We consider the issue of sampling from the posterior distribution of exponential random graph (ERG) models and other statistical models with intractable normalizing constants. Existing methods based on exact sampling are either infeasible or require very long computing time. We study a class of approximate Markov chain Monte Carlo (MCMC) sampling schemes that deal with this issue. We also develop a new Metropolis–Hastings kernel to sample sparse large networks from ERG models. We illustrate the proposed methods on several examples.