In Bayesian statistical inference and computationally intensive frequentist inference, one is interested in obtaining samples from a high dimensional, and possibly multi-modal target density. The challenge is to obtain samples from this target without any knowledge of the normalizing constant. Several approaches to this problem rely on Monte Carlo methods. One of the simplest such methods is the rejection sampler due to von Neumann. Here we introduce an auto-validating version of the rejection sampler via interval analysis. We show that our rejection sampler does provide us with independent samples from a large class of target densities in a guaranteed manner. We illustrate the efficiency of the sampler by theory and by examples in up to 10 dimensions. Our sampler is immune to the `pathologies' of some infamous densities including the witch's hat and can rigorously draw samples from piece-wise Euclidean spaces of small phylogenetic trees.
We consider an acceptance-rejection sampler based on a deterministic driver sequence. The deterministic sequence is chosen such that the discrepancy between the empirical target distribution and the target distribution is small. We use quasi-Monte Carlo (QMC) point sets for this purpose. The empirical evidence shows convergence rates beyond the crude Monte Carlo rate of $N^{-1/2}$. We prove that the discrepancy of samples generated by the QMC acceptance-rejection sampler is bounded from above by $N^{-1/s}$. A lower bound shows that for any given driver sequence, there always exists a target de…
We present a sequential Monte Carlo sampler variant of the partial rejection control algorithm, and show that this variant can be considered as a sequential Monte Carlo sampler with a modified mutation kernel. We prove that the new sampler can reduce the variance of the incremental importance weights when compared with standard sequential Monte Carlo samplers. We provide a study of theoretical properties of the new algorithm, and make connections with some existing algorithms. Finally, the sampler is adapted for application under the challenging "likelihood free," approximate Bayesian computat…
We propose a coupled rejection-sampling method for sampling from couplings of arbitrary distributions. The method relies on accepting or rejecting coupled samples coming from dominating marginals. Contrary to existing acceptance-rejection coupling methods, the variance of the execution time of the proposed method is limited and stays finite as the two target marginals approach each other in the sense of the total variation norm. In the important special case of coupling multivariate Gaussians with different means and covariances, we derive positive lower bounds for the resulting coupling proba…
In this work we present a non-reversible, tuning- and rejection-free Markov chain Monte Carlo which naturally fits in the framework of hit-and-run. The sampler only requires access to the gradient of the log-density function, hence the normalizing constant is not needed. We prove the proposed Markov chain is invariant for the target distribution and illustrate its applicability through a wide range of examples. We show that the sampler introduced in the present paper is intimately related to the continuous sampler of Peters and de With (2012), Bouchard-Cote et al. (2017). In particular, the co…
Markov chain Monte Carlo methods have become standard tools in statistics to sample from complex probability measures. Many available techniques rely on discrete-time reversible Markov chains whose transition kernels build up over the Metropolis-Hastings algorithm. We explore and propose several original extensions of an alternative approach introduced recently in Peters and de With (2012) where the target distribution of interest is explored using a continuous-time Markov process. In the Metropolis-Hastings algorithm, a trial move to a region of lower target density, equivalently "higher ener…
Markov Chain Monte Carlo (MCMC) algorithms are widely used for stochastic optimization, sampling, and integration of mathematical objective functions, in particular, in the context of Bayesian inverse problems and parameter estimation. For decades, the algorithm of choice in MCMC simulations has been the Metropolis-Hastings (MH) algorithm. An advancement over the traditional MH-MCMC sampler is the Delayed-Rejection Adaptive Metropolis (DRAM). In this paper, we present MatDRAM, a stochastic optimization, sampling, and Monte Carlo integration toolbox in MATLAB which implements a variant of the D…
This Chapter, "ABC Samplers", is to appear in the forthcoming Handbook of Approximate Bayesian Computation (2018). It details the main ideas and algorithms used to sample from the ABC approximation to the posterior distribution, including methods based on rejection/importance sampling, MCMC and sequential Monte Carlo.
This work introduces a class of rejection-free Markov chain Monte Carlo (MCMC) samplers, named the Bouncy Hybrid Sampler, which unifies several existing methods from the literature. Examples include the Bouncy Particle Sampler of Peters and de With (2012), Bouchard-Cote et al. (2015) and the Hamiltonian MCMC. Following the introduced general framework, we derive a new sampler called the Quadratic Bouncy Hybrid Sampler. We apply this novel sampler to the problem of sampling from a truncated Gaussian distribution.
The Bouncy Particle Sampler is a novel rejection-free non-reversible sampler for differentiable probability distributions over continuous variables. We generalize the algorithm to piecewise differentiable distributions and apply it to generic binary distributions using a piecewise differentiable augmentation. We illustrate the new algorithm in a binary Markov Random Field example, and compare it to binary Hamiltonian Monte Carlo. Our results suggest that binary BPS samplers are better for easy to mix distributions.
As a special example of piecewise deterministic Markov process, bouncy particle sampler is a rejection-free, irreversible Markov chain Monte Carlo algorithm and can draw samples from target distribution efficiently. We generalize bouncy particle sampler in terms of its transition dynamics. In BPS, the transition dynamic at event time is deterministic, but in GBPS, it is random. With the help of this randomness, GBPS can overcome the reducibility problem in BPS without refreshement.
MCMC using $\textit{bouncy}$ Hamiltonian dynamics: A unifying framework for Hamiltonian Monte Carlo and piecewise deterministic Markov process samplers
In phylogenetic inference one is interested in obtaining samples from the posterior distribution over the tree space on the basis of some observed DNA sequence data. The challenge is to obtain samples from this target distribution without any knowledge of the normalizing constant. One of the simplest sampling methods is the rejection sampler due to von Neumann. Here we introduce an auto-validating version of the rejection sampler, via interval analysis, to rigorously draw samples from posterior distributions, based on homologous primate mitochondrial DNA, over small phylogenetic tree spaces.
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…
We propose a new Monte Carlo algorithm for complex discrete distributions. The algorithm is motivated by the N-Fold Way, which is an ingenious event-driven MCMC sampler that avoids rejection moves at any specific state. The N-Fold Way can however get "trapped" in cycles. We surmount this problem by modifying the sampling process. This correction does introduce bias, but the bias is subsequently corrected with a carefully engineered importance sampler.
University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）；University of British Columbia（不列颠哥伦比亚大学）
Sampling the parameters of high-dimensional Continuous Time Markov Chains (CTMC) is a challenging problem with important applications in many fields of applied statistics. In this work a recently proposed type of non-reversible rejection-free Markov Chain Monte Carlo (MCMC) sampler, the Bouncy Particle Sampler (BPS), is brought to bear to this problem. BPS has demonstrated its favorable computational efficiency compared with state-of-the-art MCMC algorithms, however to date applications to real-data scenario were scarce. An important aspect of the practical implementation of BPS is the simulat…
University of Cambridge（剑桥大学）；ETH Zürich（苏黎世联邦理工学院）
Stochastic gradient Markov Chain Monte Carlo algorithms are popular samplers for approximate inference, but they are generally biased. We show that many recent versions of these methods (e.g. Chen et al. (2014)) cannot be corrected using Metropolis-Hastings rejection sampling, because their acceptance probability is always zero. We can fix this by employing a sampler with realizable backwards trajectories, such as Gradient-Guided Monte Carlo (Horowitz, 1991), which generalizes stochastic gradient Langevin dynamics (Welling and Teh, 2011) and Hamiltonian Monte Carlo. We show that this sampler c…
Most Markov chain Monte Carlo methods operate in discrete time and are reversible with respect to the target probability. Nevertheless, it is now understood that the use of non-reversible Markov chains can be beneficial in many contexts. In particular, the recently-proposed Bouncy Particle Sampler leverages a continuous-time and non-reversible Markov process and empirically shows state-of-the-art performances when used to explore certain probability densities; however, its implementation typically requires the computation of local upper bounds on the gradient of the log target density. We pres…
Stanford University（斯坦福大学）；Google Research（谷歌研究院）；New York University（纽约大学）
Energy-based models (EBMs) are powerful probabilistic models, but suffer from intractable sampling and density evaluation due to the partition function. As a result, inference in EBMs relies on approximate sampling algorithms, leading to a mismatch between the model and inference. Motivated by this, we consider the sampler-induced distribution as the model of interest and maximize the likelihood of this model. This yields a class of energy-inspired models (EIMs) that incorporate learned energy functions while still providing exact samples and tractable log-likelihood lower bounds. We describe …
Approximate Bayesian computation (ABC) is computationally intensive for complex model simulators. To exploit expensive simulations, data-resampling via bootstrapping can be employed to obtain many artificial datasets at little cost. However, when using this approach within ABC, the posterior variance is inflated, thus resulting in biased posterior inference. Here we use stratified Monte Carlo to considerably reduce the bias induced by data resampling. We also show empirically that it is possible to obtain reliable inference using a larger than usual ABC threshold. Finally, we show that with st…
We propose approaches for testing implementations of Markov Chain Monte Carlo methods as well as of general Monte Carlo methods. Based on statistical hypothesis tests, these approaches can be used in a unit testing framework to, for example, check if individual steps in a Gibbs sampler or a reversible jump MCMC have the desired invariant distribution. Two exact tests for assessing whether a given Markov chain has a specified invariant distribution are discussed. These and other tests of Monte Carlo methods can be embedded into a sequential method that allows low expected effort if the simulati…
P-splines provide a flexible setting for modeling nonlinear model components based on a discretized penalty structure with a relatively simple computational backbone. Under a Bayesian inferential framework based on Markov chain Monte Carlo, estimates of model coefficients in P-splines models are typically obtained by means of Metropolis-type algorithms. These algorithms rely on a proposal distribution that has to be carefully chosen to generate Markov chains that efficiently explore the parameter space. To avoid such a sensitive tuning choice, we extend the Gibbs sampler to Bayesian P-splines …
Alternating Diffusion for Proximal Sampling with Zeroth Order Queries
Graduate School of Information Science and Technology, The University of Tokyo（东京大学信息科学与技术研究生院）；Institute of High Performance Computing, Agency for Science, Technology and Research（科技研究局高性能计算研究所）；Centre for Frontier AI Research, Agency for Science, Technology and Research（科技研究局前沿人工智能研究中心）；College of Computing and Data Science, Nanyang Technological University（南洋理工大学计算与数据科学学院）
"Particle methods" are sequential Monte Carlo algorithms, typically involving importance sampling, that are used to estimate and sample from joint and marginal densities from a collection of a, presumably increasing, number of random variables. In particular, a particle filter aims to estimate the current state $X_{n}$ of a stochastic system that is not directly observable by estimating a posterior distribution $π(x_{n}|y_{1},y_{2}, \ldots, y_{n})$ where the $\{Y_{n}\}$ are observations related to the $\{X_{n}\}$ through some measurement model $π(y_{n}|x_{n})$. A particle smoother aims to esti…
Recent crash frequency studies incorporate spatiotemporal correlations, but these studies have two key limitations: i) none of these studies accounts for temporal variation in model parameters; and ii) Gibbs sampler suffers from convergence issues due to non-conjugacy. To address the first limitation, we propose a new count data model that identifies the underlying temporal patterns of the regression parameters while simultaneously allowing for time-varying spatial correlation. The model is also extended to incorporate heterogeneity in non-temporal parameters across spatial units. We tackle th…
Department of Computer Science, University of Rochester（计算机科学系，罗切斯特大学）；Goergen Institute for Data Science and Artificial Intelligence (GIDS-AI)（数据科学与人工智能研究所（GIDS-AI））
In the Bayesian community, an ongoing imperative is to develop efficient algorithms. An appealing approach is to form a hybrid algorithm by combining ideas from competing existing techniques. This paper addresses issues in designing hybrid methods by considering selected case studies: the delayed rejection algorithm, the pinball sampler, the Metropolis adjusted Langevin algorithm, and the population Monte Carlo algorithm. We observe that even if each component of a hybrid algorithm has individual strengths, they may not contribute equally or even positively when they are combined. Moreover, ev…
Hamiltonian Monte Carlo (HMC) is a widely used sampler for continuous probability distributions. In many cases, the underlying Hamiltonian dynamics exhibit a phenomenon of resonance which decreases the efficiency of the algorithm and makes it very sensitive to hyperparameter values. This issue can be tackled efficiently, either via the use of trajectory length randomization (RHMC) or via partial momentum refreshment. The second approach is connected to the kinetic Langevin diffusion, and has been mostly investigated through the use of Generalized HMC (GHMC). However, GHMC induces momentum flip…
Habitat selection models are used in ecology to link the distribution of animals to environmental covariates, and identify habitats that are important for conservation. The most widely used models of this type, resource selection functions, assume independence between the observed locations of an animal. This is unrealistic when location data display spatio-temporal autocorrelation. Alternatively, step selection functions embed habitat selection in a model of animal movement, to account for the autocorrelation. However, inferences from step selection functions depend on the movement model, and…
Approximate Bayesian Computation (ABC) methods are increasingly used for inference in situations in which the likelihood function is either computationally costly or intractable to evaluate. Extensions of the basic ABC rejection algorithm have improved the computational efficiency of the procedure and broadened its applicability. The ABC-Population Monte Carlo (ABC-PMC) approach of Beaumont et al. (2009) has become a popular choice for approximate sampling from the posterior. ABC-PMC is a sequential sampler with an iteratively decreasing value of the tolerance, which specifies how close the si…
In recent years dynamical modelling has been provided with a range of breakthrough methods to perform exact Bayesian inference. However it is often computationally unfeasible to apply exact statistical methodologies in the context of large datasets and complex models. This paper considers a nonlinear stochastic differential equation model observed with correlated measurement errors and an application to protein folding modelling. An Approximate Bayesian Computation (ABC) MCMC algorithm is suggested to allow inference for model parameters within reasonable time constraints. The ABC algorithm us…
