Many problems in science and engineering require uncertainty quantification that accounts for observed data. For example, in computational neuroscience, Neural Population Models (NPMs) are mechanistic models that describe brain physiology in a range of different states. Within computational neuroscience there is growing interest in the inverse problem of inferring NPM parameters from recordings such as the EEG (Electroencephalogram). Uncertainty quantification is essential in this application area in order to infer the mechanistic effect of interventions such as anaesthesia. This paper presents C++ software for Bayesian uncertainty quantification in the parameters of NPMs from approximately stationary data using Markov Chain Monte Carlo (MCMC). Modern MCMC methods require first order (and in some cases higher order) derivatives of the posterior density. The software presented offers two distinct methods of evaluating derivatives: finite differences and exact derivatives obtained through Algorithmic Differentiation (AD). For AD, two different implementations are used: the open source Stan Math Library and the commercially licenced dco/c++ tool distributed by NAG (Numerical Algorithms Group). The use of derivative information in MCMC sampling is demonstrated through a simple example, the noise-driven harmonic oscillator. And different methods for computing derivatives are compared. The software is written in a modular object-oriented way such that it can be extended to derivative based MCMC for other scientific domains.
Bayesian methods are critical for quantifying the behaviors of systems. They capture our uncertainty about a system's behavior using probability distributions and update this understanding as new information becomes available. Probabilistic predictions that incorporate this uncertainty can then be made to evaluate system performance and make decisions. While Bayesian methods are very useful, they are often computationally intensive. This necessitates the development of more efficient algorithms. Here, we discuss a group of population Markov Chain Monte Carlo (MCMC) methods for Bayesian updatin…
In this paper, we introduce efficient ensemble Markov Chain Monte Carlo (MCMC) sampling methods for Bayesian computations in the univariate stochastic volatility model. We compare the performance of our ensemble MCMC methods with an improved version of a recent sampler of Kastner and Fruwirth-Schnatter (2014). We show that ensemble samplers are more efficient than this state of the art sampler by a factor of about 3.1, on a data set simulated from the stochastic volatility model. This performance gain is achieved without the ensemble MCMC sampler relying on the assumption that the latent proce…
With larger data at their disposal, scientists are emboldened to tackle complex questions that require sophisticated statistical models. It is not unusual for the latter to have likelihood functions that elude analytical formulations. Even under such adversity, when one can simulate from the sampling distribution, Bayesian analysis can be conducted using approximate methods such as Approximate Bayesian Computation (ABC) or Bayesian Synthetic Likelihood (BSL). A significant drawback of these methods is that the number of required simulations can be prohibitively large, thus severely limiting th…
In geostatistics, Gaussian random fields are often used to model heterogeneities of soil or subsurface parameters. To give spatial approximations of these random fields, they are discretized. Then, different techniques of geostatistical inversion are used to condition them on measurement data. Among these techniques, Markov chain Monte Carlo (MCMC) techniques stand out, because they yield asymptotically unbiased conditional realizations. However, standard Markov Chain Monte Carlo (MCMC) methods suffer the curse of dimensionality when refining the discretization. This means that their efficienc…
Proximal Markov Chain Monte Carlo is a novel construct that lies at the intersection of Bayesian computation and convex optimization, which helped popularize the use of nondifferentiable priors in Bayesian statistics. Existing formulations of proximal MCMC, however, require hyperparameters and regularization parameters to be prespecified. In this work, we extend the paradigm of proximal MCMC through introducing a novel new class of nondifferentiable priors called epigraph priors. As a proof of concept, we place trend filtering, which was originally a nonparametric regression problem, in a para…
Stochastic gradient Markov chain Monte Carlo (MCMC) algorithms have received much attention in Bayesian computing for big data problems, but they are only applicable to a small class of problems for which the parameter space has a fixed dimension and the log-posterior density is differentiable with respect to the parameters. This paper proposes an extended stochastic gradient MCMC lgoriathm which, by introducing appropriate latent variables, can be applied to more general large-scale Bayesian computing problems, such as those involving dimension jumping and missing data. Numerical studies show…
We consider geothermal inverse problems and uncertainty quantification from a Bayesian perspective. Our main goal is to make standard, `out-of-the-box' Markov chain Monte Carlo (MCMC) sampling more feasible for complex simulation models by using suitable approximations. To do this, we first show how to pose both the inverse and prediction problems in a hierarchical Bayesian framework. We then show how to incorporate so-called posterior-informed model approximation error into this hierarchical framework, using a modified form of the Bayesian approximation error (BAE) approach. This enables the …
We present an R package bssm for Bayesian non-linear/non-Gaussian state space modelling. Unlike the existing packages, bssm allows for easy-to-use approximate inference based on Gaussian approximations such as the Laplace approximation and the extended Kalman filter. The package accommodates also discretely observed latent diffusion processes. The inference is based on fully automatic, adaptive Markov chain Monte Carlo (MCMC) on the hyperparameters, with optional importance sampling post-correction to eliminate any approximation bias. The package implements also a direct pseudo-marginal MCMC a…
This paper introduces a framework for speeding up Bayesian inference conducted in presence of large datasets. We design a Markov chain whose transition kernel uses an (unknown) fraction of (fixed size) of the available data that is randomly refreshed throughout the algorithm. Inspired by the Approximate Bayesian Computation (ABC) literature, the subsampling process is guided by the fidelity to the observed data, as measured by summary statistics. The resulting algorithm, Informed Sub-Sampling MCMC (ISS-MCMC), is a generic and flexible approach which, contrary to existing scalable methodologies…
Uncertainty quantification is a critical missing component in radio interferometric imaging that will only become increasingly important as the big-data era of radio interferometry emerges. Since radio interferometric imaging requires solving a high-dimensional, ill-posed inverse problem, uncertainty quantification is difficult but also critical to the accurate scientific interpretation of radio observations. Statistical sampling approaches to perform Bayesian inference, like Markov Chain Monte Carlo (MCMC) sampling, can in principle recover the full posterior distribution of the image, from w…
Bayesian neural networks via MCMC: a Python-based tutorial
School of Mathematics and Statistics, UNSW Sydney（新南威尔士大学悉尼分校数学与统计学院）；Pingala Institute of Artificial Intelligence（平加拉人工智能研究院）；University of Sydney（悉尼大学）
In this paper, we perform Bayesian Inference to analyze spatial tree count data from the Timiskaming and Abitibi River forests in Ontario, Canada. We consider a Bayesian Generalized Linear Geostatistical Model and implement a Markov Chain Monte Carlo algorithm to sample from its posterior distribution. How spatial predictions for new sites in the forests change as the amount of training data is reduced is studied and compared with a Logistic Regression model without a spatial effect. Finally, we discuss a stratified sampling approach for selecting subsets of data that allows for potential bett…
This paper introduces a new neural network based prior for real valued functions on $\mathbb R^d$ which, by construction, is more easily and cheaply scaled up in the domain dimension $d$ compared to the usual Karhunen-Loève function space prior. The new prior is a Gaussian neural network prior, where each weight and bias has an independent Gaussian prior, but with the key difference that the variances decrease in the width of the network in such a way that the resulting function is \emph{almost surely} well defined in the limit of an infinite width network. We show that in a Bayesian treatment…
Bayesian inference under a set of priors, called robust Bayesian analysis, allows for estimation of parameters within a model and quantification of epistemic uncertainty in quantities of interest by bounded (or imprecise) probability. Iterative importance sampling can be used to estimate bounds on the quantity of interest by optimizing over the set of priors. A method for iterative importance sampling when the robust Bayesian inference rely on Markov chain Monte Carlo (MCMC) sampling is proposed. To accommodate the MCMC sampling in iterative importance sampling, a new expression for the effect…
TNO（荷兰应用科学研究组织）；Utrecht University（乌得勒支大学）；University of Amsterdam（阿姆斯特丹大学）
We introduce and characterise the performance of the Markov chain Monte Carlo (MCMC) inference method Prune Sampling for discrete and deterministic Bayesian networks (BNs). We developed a procedure to obtain the performance of a MCMC sampling method in the limit of infinite simulation time, extrapolated from relatively short simulations. This approach was used to conduct a study to compare the accuracy, rate of convergence and the time consumption of Prune Sampling with two conventional MCMC sampling methods: Gibbs- and Metropolis sampling. We show that Markov chains created by Prune Sampling …
Light and Widely Applicable (LWA-) MCMC is a novel approximation of the Metropolis-Hastings kernel targeting a posterior distribution defined on a large number of observations. Inspired by Approximate Bayesian Computation, we design a Markov chain whose transition makes use of an unknown but fixed, fraction of the available data, where the random choice of sub-sample is guided by the fidelity of this sub-sample to the observed data, as measured by summary (or sufficient) statistics. LWA-MCMC is a generic and flexible approach, as illustrated by the diverse set of examples which we explore. In …
Nonlinear non-Gaussian state-space models arise in numerous applications in statistics and signal processing. In this context, one of the most successful and popular approximation techniques is the Sequential Monte Carlo (SMC) algorithm, also known as particle filtering. Nevertheless, this method tends to be inefficient when applied to high dimensional problems. In this paper, we focus on another class of sequential inference methods, namely the Sequential Markov Chain Monte Carlo (SMCMC) techniques, which represent a promising alternative to SMC methods. After providing a unifying framework f…
Markov Chain Monte Carlo (MCMC) is a well-established family of algorithms primarily used in Bayesian statistics to sample from a target distribution when direct sampling is challenging. Existing work on Bayesian decision trees uses MCMC. Unfortunately, this can be slow, especially when considering large volumes of data. It is hard to parallelise the accept-reject component of the MCMC. None-the-less, we propose two methods for exploiting parallelism in the MCMC: in the first, we replace the MCMC with another numerical Bayesian approach, the Sequential Monte Carlo (SMC) sampler, which has the …
We propose a very fast approximate Markov Chain Monte Carlo (MCMC) sampling framework that is applicable to a large class of sparse Bayesian inference problems, where the computational cost per iteration in several models is of order $O(ns)$, where $n$ is the sample size, and $s$ the underlying sparsity of the model. This cost can be further reduced by data sub-sampling when stochastic gradient Langevin dynamics are employed. The algorithm is an extension of the asynchronous Gibbs sampler of Johnson et al. (2013), but can be viewed from a statistical perspective as a form of Bayesian iterated …
Amsterdam Business School（阿姆斯特丹商学院）；University of Amsterdam（阿姆斯特丹大学）；The Ohio State University（俄亥俄州立大学）；University of Tilburg（蒂尔堡大学）
Decision trees are flexible models that are well suited for many statistical regression problems. In a Bayesian framework for regression trees, Markov Chain Monte Carlo (MCMC) search algorithms are required to generate samples of tree models according to their posterior probabilities. The critical component of such an MCMC algorithm is to construct good Metropolis-Hastings steps for updating the tree topology. However, such algorithms frequently suffering from local mode stickiness and poor mixing. As a result, the algorithms are slow to converge. Hitherto, authors have primarily used discrete…
Autoencoders gained popularity in the deep learning revolution given their ability to compress data and provide dimensionality reduction. Although prominent deep learning methods have been used to enhance autoencoders, the need to provide robust uncertainty quantification remains a challenge. This has been addressed with variational autoencoders so far. Bayesian inference via Markov Chain Monte Carlo (MCMC) sampling has faced several limitations for large models; however, recent advances in parallel computing and advanced proposal schemes have opened routes less traveled. This paper presents B…
The University of Manchester（曼彻斯特大学）；Oak Ridge National Laboratory（橡树岭国家实验室）
Markov chain Monte Carlo (MCMC) methods have not been broadly adopted in Bayesian neural networks (BNNs). This paper initially reviews the main challenges in sampling from the parameter posterior of a neural network via MCMC. Such challenges culminate to lack of convergence to the parameter posterior. Nevertheless, this paper shows that a non-converged Markov chain, generated via MCMC sampling from the parameter space of a neural network, can yield via Bayesian marginalization a valuable posterior predictive distribution of the output of the neural network. Classification examples based on mul…
Spectral subsampling MCMC was recently proposed to speed up Markov chain Monte Carlo (MCMC) for long stationary univariate time series by subsampling periodogram observations in the frequency domain. This article extends the approach to multivariate time series using a multivariate generalisation of the Whittle likelihood. To assess the computational gains from spectral subsampling in challenging problems, a multivariate generalisation of the autoregressive tempered fractionally integrated moving average model (ARTFIMA) is introduced and some of its properties derived. Bayesian inference based…
Accept-reject based Markov chain Monte Carlo (MCMC) algorithms have traditionally utilised acceptance probabilities that can be explicitly written as a function of the ratio of the target density at the two contested points. This feature is rendered almost useless in Bayesian posteriors with unknown functional forms. We introduce a new family of MCMC acceptance probabilities that has the distinguishing feature of not being a function of the ratio of the target density at the two points. We present two stable Bernoulli factories that generate events within this class of acceptance probabilities…
The rapid development of computing power and efficient Markov Chain Monte Carlo (MCMC) simulation algorithms have revolutionized Bayesian statistics, making it a highly practical inference method in applied work. However, MCMC algorithms tend to be computationally demanding, and are particularly slow for large datasets. Data subsampling has recently been suggested as a way to make MCMC methods scalable on massively large data, utilizing efficient sampling schemes and estimators from the survey sampling literature. These developments tend to be unknown by many survey statisticians who tradition…
University of California, Irvine（加州大学尔湾分校）；Google（谷歌）；Yahoo Labs（雅虎实验室）；University of Amsterdam（阿姆斯特丹大学）
Despite having various attractive qualities such as high prediction accuracy and the ability to quantify uncertainty and avoid over-fitting, Bayesian Matrix Factorization has not been widely adopted because of the prohibitive cost of inference. In this paper, we propose a scalable distributed Bayesian matrix factorization algorithm using stochastic gradient MCMC. Our algorithm, based on Distributed Stochastic Gradient Langevin Dynamics, can not only match the prediction accuracy of standard MCMC methods like Gibbs sampling, but at the same time is as fast and simple as stochastic gradient desc…
This paper concerns differentially private Bayesian estimation of the parameters of a population distribution, when a statistic of a sample from that population is shared in noise to provide differential privacy. This work mainly addresses two problems: (1) What statistic of the sample should be shared privately? For the first question, i.e., the one about statistic selection, we promote using the Fisher information. We find out that, the statistic that is most informative in a non-privacy setting may not be the optimal choice under the privacy restrictions. We provide several examples to supp…
Bayesian estimation methods for sparse blind deconvolution problems conventionally employ Bernoulli-Gaussian (BG) prior for modeling sparse sequences and utilize Markov Chain Monte Carlo (MCMC) methods for the estimation of unknowns. However, the discrete nature of the BG model creates computational bottlenecks, preventing efficient exploration of the probability space even with the recently proposed enhanced sampler schemes. To address this issue, we propose an alternative MCMC method by modeling the sparse sequences using the Normal-Inverse-Gamma (NIG) prior. We derive effective Gibbs sample…
Comparison of parallel SMC and MCMC for Bayesian deep learning
Mathematics Department, University of Manchester（曼彻斯特大学数学系）；Department of Electrical and Computer Engineering, Southern Methodist University（南方 Methodist 大学电气与计算机工程系）；DEVCOM US Army Research Laboratory（美国陆军研发实验室）；Department of Electrical and Computer Engineering, University of Illinois Chicago（伊利诺伊大学芝加哥分校电气与计算机工程系）；Cognizant AI Labs（Cognizant AI 实验室）；Quantum Information Science Section, Oak Ridge National Laboratory（橡树岭国家实验室量子信息科学部）；Tulane University（Tulane 大学）
Stochastic gradient Markov chain Monte Carlo (SG-MCMC) has become increasingly popular for simulating posterior samples in large-scale Bayesian modeling. However, existing SG-MCMC schemes are not tailored to any specific probabilistic model, even a simple modification of the underlying dynamical system requires significant physical intuition. This paper presents the first meta-learning algorithm that allows automated design for the underlying continuous dynamics of an SG-MCMC sampler. The learned sampler generalizes Hamiltonian dynamics with state-dependent drift and diffusion, enabling fast t…
Many Bayesian inference problems involve target distributions whose density functions are computationally expensive to evaluate. Replacing the target density with a local approximation based on a small number of carefully chosen density evaluations can significantly reduce the computational expense of Markov chain Monte Carlo (MCMC) sampling. Moreover, continual refinement of the local approximation can guarantee asymptotically exact sampling. We devise a new strategy for balancing the decay rate of the bias due to the approximation with that of the MCMC variance. We prove that the error of th…
We consider batch size selection for a general class of multivariate batch means variance estimators, which are computationally viable for high-dimensional Markov chain Monte Carlo simulations. We derive the asymptotic mean squared error for this class of estimators. Further, we propose a parametric technique for estimating optimal batch sizes and discuss practical issues regarding the estimating process. Vector auto-regressive, Bayesian logistic regression, and Bayesian dynamic space-time examples illustrate the quality of the estimation procedure where the proposed optimal batch sizes outper…
Technische Universität München（慕尼黑工业大学）；Siemens AG（西门子股份公司）；LTCI, Télécom ParisTech, Université Paris-Saclay（巴黎萨克雷大学巴黎电信学院LTCI实验室）
We introduce Tempered Geodesic Markov Chain Monte Carlo (TG-MCMC) algorithm for initializing pose graph optimization problems, arising in various scenarios such as SFM (structure from motion) or SLAM (simultaneous localization and mapping). TG-MCMC is first of its kind as it unites asymptotically global non-convex optimization on the spherical manifold of quaternions with posterior sampling, in order to provide both reliable initial poses and uncertainty estimates that are informative about the quality of individual solutions. We devise rigorous theoretical convergence guarantees for our metho…
