No Arabic abstract
In this article, we derive a novel non-reversible, continuous-time Markov chain Monte Carlo (MCMC) sampler, called Coordinate Sampler, based on a piecewise deterministic Markov process (PDMP), which can be seen as a variant of the Zigzag sampler. In addition to proving a theoretical validation for this new sampling algorithm, we show that the Markov chain it induces exhibits geometrical ergodicity convergence, for distributions whose tails decay at least as fast as an exponential distribution and at most as fast as a Gaussian distribution. Several numerical examples highlight that our coordinate sampler is more efficient than the Zigzag sampler, in terms of effective sample size.
The R package MfUSampler provides Monte Carlo Markov Chain machinery for generating samples from multivariate probability distributions using univariate sampling algorithms such as Slice Sampler and Adaptive Rejection Sampler. The sampler function performs a full cycle of univariate sampling steps, one coordinate at a time. In each step, the latest sample values obtained for other coordinates are used to form the conditional distributions. The concept is an extension of Gibbs sampling where each step involves, not an independent sample from the conditional distribution, but a Markov transition for which the conditional distribution is invariant. The software relies on proportionality of conditional distributions to the joint distribution to implement a thin wrapper for producing conditionals. Examples illustrate basic usage as well as methods for improving performance. By encapsulating the multivariate-from-univariate logic, MfUSampler provides a reliable library for rapid prototyping of custom Bayesian models while allowing for incremental performance optimizations such as utilization of conjugacy, conditional independence, and porting function evaluations to compiled languages.
This note presents a simple and elegant sampler which could be used as an alternative to the reversible jump MCMC methodology.
In this paper, we analyze the convergence rate of a collapsed Gibbs sampler for crossed random effects models. Our results apply to a substantially larger range of models than previous works, including models that incorporate missingness mechanism and unbalanced level data. The theoretical tools involved in our analysis include a connection between relaxation time and autoregression matrix, concentration inequalities, and random matrix theory.
We consider Particle Gibbs (PG) as a tool for Bayesian analysis of non-linear non-Gaussian state-space models. PG is a Monte Carlo (MC) approximation of the standard Gibbs procedure which uses sequential MC (SMC) importance sampling inside the Gibbs procedure to update the latent and potentially high-dimensional state trajectories. We propose to combine PG with a generic and easily implementable SMC approach known as Particle Efficient Importance Sampling (PEIS). By using SMC importance sampling densities which are approximately fully globally adapted to the targeted density of the states, PEIS can substantially improve the mixing and the efficiency of the PG draws from the posterior of the states and the parameters relative to existing PG implementations. The efficiency gains achieved by PEIS are illustrated in PG applications to a univariate stochastic volatility model for asset returns, a non-Gaussian nonlinear local-level model for interest rates, and a multivariate stochastic volatility model for the realized covariance matrix of asset returns.
In many fields, researchers are interested in discovering features with substantial effect on the response from a large number of features and controlling the proportion of false discoveries. By incorporating the knockoff procedure in the Bayesian framework, we develop the Bayesian knockoff filter (BKF) for selecting features that have important effect on the response. In contrast to the fixed knockoff variables in the frequentist procedures, we allow the knockoff variables to be continuously updated in the Markov chain Monte Carlo. Based on the posterior samples and elaborated greedy selection procedures, our method can distinguish the truly important features as well as controlling the Bayesian false discovery rate at a desirable level. Numerical experiments on both synthetic and real data demonstrate the advantages of our method over existing knockoff methods and Bayesian variable selection approaches, i.e., the BKF possesses higher power and yields a lower false discovery rate.