Posterior sampling for high-dimensional Bayesian inverse problems is a common challenge in real-world applications. Randomized Maximum Likelihood (RML) is an optimization based methodology that gives samples from an approximation to the posterior distribution. We develop a high-dimensional Bayesian Optimization (BO) approach based on Gaussian Process (GP) surrogate models to solve the RML problem. We demonstrate the benefits of our approach in comparison to alternative optimization methods on a variety of synthetic and real-world Bayesian inverse problems, including medical and magnetohydrodynamics applications.
We present a randomized maximum a posteriori (rMAP) method for generating approximate samples of posteriors in high dimensional Bayesian inverse problems governed by large-scale forward problems. We derive the rMAP approach by: 1) casting the problem of computing the MAP point as a stochastic optimization problem; 2) interchanging optimization and expectation; and 3) approximating the expectation with a Monte Carlo method. For a specific randomized data and prior mean, rMAP reduces to the maximum likelihood approach (RML). It can also be viewed as an iterative stochastic Newton method. An anal…
This article surveys computational methods for posterior inference with intractable likelihoods, that is where the likelihood function is unavailable in closed form, or where evaluation of the likelihood is infeasible. We review recent developments in pseudo-marginal methods, approximate Bayesian computation (ABC), the exchange algorithm, thermodynamic integration, and composite likelihood, paying particular attention to advancements in scalability for large datasets. We also mention R and MATLAB source code for implementations of these algorithms, where they are available.
Implementing Bayesian inference is often computationally challenging in applications involving complex models, and sometimes calculating the likelihood itself is difficult. Synthetic likelihood is one approach for carrying out inference when the likelihood is intractable, but it is straightforward to simulate from the model. The method constructs an approximate likelihood by taking a vector summary statistic as being multivariate normal, with the unknown mean and covariance matrix estimated by simulation for any given parameter value. Our article makes three contributions. The first shows that…
Gibbs random fields play an important role in statistics, for example the autologistic model is commonly used to model the spatial distribution of binary variables defined on a lattice. However they are complicated to work with due to an intractability of the likelihood function. It is therefore natural to consider tractable approximations to the likelihood function. Composite likelihoods offer a principled approach to constructing such approximation. The contribution of this paper is to examine the performance of a collection of composite likelihood approximations in the context of Bayesian i…
A spectral approach to Bayesian inference is presented. It pursues the emulation of the posterior probability density. The starting point is a series expansion of the likelihood function in terms of orthogonal polynomials. From this spectral likelihood expansion all statistical quantities of interest can be calculated semi-analytically. The posterior is formally represented as the product of a reference density and a linear combination of polynomial basis functions. Both the model evidence and the posterior moments are related to the expansion coefficients. This formulation avoids Markov chain…
Randomized neural networks (NNs) are an interesting alternative to conventional NNs that are more used for data modeling. The random vector functional-link (RVFL) network is an established and theoretically well-grounded randomized learning model. A key theoretical result for RVFL networks is that they provide universal approximation for continuous maps, on average, almost surely. We specialize and modify this result, and show that RFVL networks can provide functional approximations that converge in Kullback-Leibler divergence, when the target function is a probability density function. Expand…
Both Approximate Bayesian Computation (ABC) and composite likelihood methods are useful for Bayesian and frequentist inference, respectively, when the likelihood function is intractable. We propose to use composite likelihood score functions as summary statistics in ABC in order to obtain accurate approximations to the posterior distribution. This is motivated by the use of the score function of the full likelihood, and extended to general unbiased estimating functions in complex models. Moreover, we show that if the composite score is suitably standardised, the resulting ABC procedure is inva…
$α$-stable distributions are utilised as models for heavy-tailed noise in many areas of statistics, finance and signal processing engineering. However, in general, neither univariate nor multivariate $α$-stable models admit closed form densities which can be evaluated pointwise. This complicates the inferential procedure. As a result, $α$-stable models are practically limited to the univariate setting under the Bayesian paradigm, and to bivariate models under the classical framework. In this article we develop a novel Bayesian approach to modelling univariate and multivariate $α$-stable distri…
The logistic specification has been used extensively in non-Bayesian statistics to model the dependence of discrete outcomes on the values of specified covariates. Because the likelihood function is globally weakly concave estimation by maximum likelihood is generally straightforward even in commonly arising applications with scores or hundreds of parameters. In contrast Bayesian inference has proven awkward, requiring normal approximations to the likelihood or specialized adaptations of existing Markov chain Monte Carlo and data augmentation methods. This paper approaches Bayesian inference i…
The marginal likelihood is a well established model selection criterion in Bayesian statistics. It also allows to efficiently calculate the marginal posterior model probabilities that can be used for Bayesian model averaging of quantities of interest. For many complex models, including latent modeling approaches, marginal likelihoods are however difficult to compute. One recent promising approach for approximating the marginal likelihood is Integrated Nested Laplace Approximation (INLA), design for models with latent Gaussian structures. In this study we compare the approximations obtained wit…
Bayesian inference for models with intractable likelihood functions represents a challenging suite of problems in modern statistics. In this work we analyse the Conway-Maxwell-Poisson (COM-Poisson) distribution, a two parameter generalisation of the Poisson distribution. COM-Poisson regression modelling allows the flexibility to model dispersed count data as part of a generalised linear model (GLM) with a COM-Poisson response, where exogenous covariates control the mean and dispersion level of the response. The major difficulty with COM-Poisson regression is that the likelihood function contai…
The aim of this paper is to generalize the PAC-Bayesian theorems proved by Catoni in the classification setting to more general problems of statistical inference. We show how to control the deviations of the risk of randomized estimators. A particular attention is paid to randomized estimators drawn in a small neighborhood of classical estimators, whose study leads to control the risk of the latter. These results allow to bound the risk of very general estimation procedures, as well as to perform model selection.
Bayesian synthetic likelihood (BSL) is a popular method for performing approximate Bayesian inference when the likelihood function is intractable. In synthetic likelihood methods, the likelihood function is approximated parametrically via model simulations, and then standard likelihood-based techniques are used to perform inference. The Gaussian synthetic likelihood estimator has become ubiquitous in BSL literature, primarily for its simplicity and ease of implementation. However, it is often too restrictive and may lead to poor posterior approximations. Recently, a more flexible semi-parametr…
We propose a Bayesian elastic net that uses empirical likelihood and develop an efficient tuning of Hamiltonian Monte Carlo for posterior sampling. The proposed model relaxes the assumptions on the identity of the error distribution, performs well when the variables are highly correlated, and enables more straightforward inference by providing posterior distributions of the regression coefficients. The Hamiltonian Monte Carlo method implemented in Bayesian empirical likelihood overcomes the challenges that the posterior distribution lacks a closed analytic form and its domain is nonconvex. We …
This paper proposes a new approach for Bayesian and maximum likelihood parameter estimation for stationary Gaussian processes observed on a large lattice with missing values. We propose an MCMC approach for Bayesian inference, and a Monte Carlo EM algorithm for maximum likelihood inference. Our approach uses data augmentation and circulant embedding of the covariance matrix, and provides exact inference for the parameters and the missing data. Using simulated data and an application to satellite sea surface temperatures in the Pacific Ocean, we show that our method provides accurate inference …
Expectation-Propagation for Bayesian Empirical Likelihood Inference
College of Computing and Data Science, Nanyang Technological University（南洋理工大学计算与数据科学学院）；School of Mathematics and Statistics, The University of Melbourne（墨尔本大学数学与统计学院）
We consider Bayesian inference problems with computationally intensive likelihood functions. We propose a Gaussian process (GP) based method to approximate the joint distribution of the unknown parameters and the data. In particular, we write the joint density approximately as a product of an approximate posterior density and an exponentiated GP surrogate. We then provide an adaptive algorithm to construct such an approximation, where an active learning method is used to choose the design points. With numerical examples, we illustrate that the proposed method has competitive performance agains…
Statistical analysis of max-stable processes used to model spatial extremes has been limited by the difficulty in calculating the joint likelihood function. This precludes all standard likelihood-based approaches, including Bayesian approaches. In this paper we present a Bayesian approach through the use of approximate Bayesian computing. This circumvents the need for a joint likelihood function by instead relying on simulations from the (unavailable) likelihood. This method is compared with an alternative approach based on the composite likelihood. We demonstrate that approximate Bayesian com…
Likelihood-free Bayesian inference algorithms are popular methods for calibrating the parameters of complex, stochastic models, required when the likelihood of the observed data is intractable. These algorithms characteristically rely heavily on repeated model simulations. However, whenever the computational cost of simulation is even moderately expensive, the significant burden incurred by likelihood-free algorithms leaves them unviable in many practical applications. The multifidelity approach has been introduced (originally in the context of approximate Bayesian computation) to reduce the s…
Estimation of finite mixture models when the mixing distribution support is unknown is an important problem. This paper gives a new approach based on a marginal likelihood for the unknown support. Motivated by a Bayesian Dirichlet prior model, a computationally efficient stochastic approximation version of the marginal likelihood is proposed and large-sample theory is presented. By restricting the support to a finite grid, a simulated annealing method is employed to maximize the marginal likelihood and estimate the support. Real and simulated data examples show that this novel stochastic appro…
Bayesian models often involve a small set of hyperparameters determined by maximizing the marginal likelihood. Bayesian optimization is a popular iterative method where a Gaussian process posterior of the underlying function is sequentially updated by new function evaluations. An acquisition strategy uses this posterior distribution to decide where to place the next function evaluation. We propose a novel Bayesian optimization framework for situations where the user controls the computational effort, and therefore the precision of the function evaluations. This is a common situation in econome…
Approximate Bayesian computation (ABC) methods, which are applicable when the likelihood is difficult or impossible to calculate, are an active topic of current research. Most current ABC algorithms directly approximate the posterior distribution, but an alternative, less common strategy is to approximate the likelihood function. This has several advantages. First, in some problems, it is easier to approximate the likelihood than to approximate the posterior. Second, an approximation to the likelihood allows reference analyses to be constructed based solely on the likelihood. Third, it is stra…
Adaptive approaches, allowing for more flexible trial design, have been proposed for individually randomized trials to save time or reduce sample size. However, adaptive designs for cluster-randomized trials in which groups of participants rather than individuals are randomized to treatment arms are less common. Motivated by a cluster-randomized trial designed to assess the effectiveness of a machine-learning based clinical decision support system for physicians treating patients with depression, two Bayesian adaptive designs for cluster-randomized trials are proposed to allow for early stoppi…
Likelihood-free methods are an established approach for performing approximate Bayesian inference for models with intractable likelihood functions. However, they can be computationally demanding. Bayesian synthetic likelihood (BSL) is a popular such method that approximates the likelihood function of the summary statistic with a known, tractable distribution -- typically Gaussian -- and then performs statistical inference using standard likelihood-based techniques. However, as the number of summary statistics grows, the number of model simulations required to accurately estimate the covariance…
Bayesian synthetic likelihood (BSL) is now an established method for conducting approximate Bayesian inference in models where, due to the intractability of the likelihood function, exact Bayesian approaches are either infeasible or computationally too demanding. Implicit in the application of BSL is the assumption that the data generating process (DGP) can produce simulated summary statistics that capture the behaviour of the observed summary statistics. We demonstrate that if this compatibility between the actual and assumed DGP is not satisfied, i.e., if the model is misspecified, BSL can y…
Bayesian synthetic likelihood (BSL) is now a well established method for performing approximate Bayesian parameter estimation for simulation-based models that do not possess a tractable likelihood function. BSL approximates an intractable likelihood function of a carefully chosen summary statistic at a parameter value with a multivariate normal distribution. The mean and covariance matrix of this normal distribution are estimated from independent simulations of the model. Due to the parametric assumption implicit in BSL, it can be preferred to its non-parametric competitor, approximate Bayesia…
Helsinki Institute for Information Technology HIIT（赫尔辛基信息技术研究所）；Aalto University（阿尔托大学）；University of Edinburgh（爱丁堡大学）
We consider Bayesian inference when only a limited number of noisy log-likelihood evaluations can be obtained. This occurs for example when complex simulator-based statistical models are fitted to data, and synthetic likelihood (SL) method is used to form the noisy log-likelihood estimates using computationally costly forward simulations. We frame the inference task as a sequential Bayesian experimental design problem, where the log-likelihood function is modelled with a hierarchical Gaussian process (GP) surrogate model, which is used to efficiently select additional log-likelihood evaluation…
In this paper we propose a new sampling-free approach to solve Bayesian model inversion problems that is an extension of the previously proposed spectral likelihood expansions (SLE) method. Our approach, called stochastic spectral likelihood embedding (SSLE), uses the recently presented stochastic spectral embedding (SSE) method for local spectral expansion refinement to approximate the likelihood function at the core of Bayesian inversion problems. We show that, similar to SLE, this approach results in analytical expressions for key statistics of the Bayesian posterior distribution, such as e…
Bayesian synthetic likelihood (BSL) is a popular method for estimating the parameter posterior distribution for complex statistical models and stochastic processes that possess a computationally intractable likelihood function. Instead of evaluating the likelihood, BSL approximates the likelihood of a judiciously chosen summary statistic of the data via model simulation and density estimation. Compared to alternative methods such as approximate Bayesian computation (ABC), BSL requires little tuning and requires less model simulations than ABC when the chosen summary statistic is high-dimension…
Some statistical models are specified via a data generating process for which the likelihood function cannot be computed in closed form. Standard likelihood-based inference is then not feasible but the model parameters can be inferred by finding the values which yield simulated data that resemble the observed data. This approach faces at least two major difficulties: The first difficulty is the choice of the discrepancy measure which is used to judge whether the simulated data resemble the observed data. The second difficulty is the computationally efficient identification of regions in the pa…
Generalised Bayesian inference updates prior beliefs using a loss function, rather than a likelihood, and can therefore be used to confer robustness against possible mis-specification of the likelihood. Here we consider generalised Bayesian inference with a Stein discrepancy as a loss function, motivated by applications in which the likelihood contains an intractable normalisation constant. In this context, the Stein discrepancy circumvents evaluation of the normalisation constant and produces generalised posteriors that are either closed form or accessible using standard Markov chain Monte Ca…
Approximate Bayesian computation (ABC) has become an essential tool for the analysis of complex stochastic models when the likelihood function is numerically unavailable. However, the well-established statistical method of empirical likelihood provides another route to such settings that bypasses simulations from the model and the choices of the ABC parameters (summary statistics, distance, tolerance), while being convergent in the number of observations. Furthermore, bypassing model simulations may lead to significant time savings in complex models, for instance those found in population gene…
The popular Bayesian meta-analysis expressed by Bayesian normal-normal hierarchical model (NNHM) synthesizes knowledge from several studies and is highly relevant in practice. Moreover, NNHM is the simplest Bayesian hierarchical model (BHM), which illustrates problems typical in more complex BHMs. Until now, it has been unclear to what extent the data determines the marginal posterior distributions of the parameters in NNHM. To address this issue we computed the second derivative of the Bhattacharyya coefficient with respect to the weighted likelihood, defined the total empirical determinacy (…
We consider the problem of approximate Bayesian parameter inference in non-linear state-space models with intractable likelihoods. Sequential Monte Carlo with approximate Bayesian computations (SMC-ABC) is one approach to approximate the likelihood in this type of models. However, such approximations can be noisy and computationally costly which hinders efficient implementations using standard methods based on optimisation and Monte Carlo methods. We propose a computationally efficient novel method based on the combination of Gaussian process optimisation and SMC-ABC to create a Laplace approx…
In this paper we revisit the weighted likelihood bootstrap, a method that generates samples from an approximate Bayesian posterior of a parametric model. We show that the same method can be derived, without approximation, under a Bayesian nonparametric model with the parameter of interest defined as minimising an expected negative log-likelihood under an unknown sampling distribution. This interpretation enables us to extend the weighted likelihood bootstrap to posterior sampling for parameters minimizing an expected loss. We call this method the loss-likelihood bootstrap. We make a connection…
The paper addresses joint sparsity selection in the regression coefficient matrix and the error precision (inverse covariance) matrix for high-dimensional multivariate regression models in the Bayesian paradigm. The selected sparsity patterns are crucial to help understand the network of relationships between the predictor and response variables, as well as the conditional relationships among the latter. While Bayesian methods have the advantage of providing natural uncertainty quantification through posterior inclusion probabilities and credible intervals, current Bayesian approaches either r…
Composite likelihoods are increasingly used in applications where the full likelihood is analytically unknown or computationally prohibitive. Although the maximum composite likelihood estimator has frequentist properties akin to those of the usual maximum likelihood estimator, Bayesian inference based on composite likelihoods has yet to be explored. In this paper we investigate the use of the Metropolis--Hastings algorithm to compute a pseudo-posterior distribution based on the composite likelihood. Two methodologies for adjusting the algorithm are presented and their performance on approximat…
Two data-dependent information metrics are developed to quantify the information of the prior and likelihood functions within a parametric Bayesian model, one of which is closely related to the reference priors from Berger, Bernardo, and Sun, and information measure introduced by Lindley. A combination of theoretical, empirical, and computational support provides evidence that these information-theoretic metrics may be useful diagnostic tools when performing a Bayesian analysis.
Minimization of a stochastic cost function is commonly used for approximate sampling in high-dimensional Bayesian inverse problems with Gaussian prior distributions and multimodal posterior distributions. The density of the samples generated by minimization is not the desired target density, unless the observation operator is linear, but the distribution of samples is useful as a proposal density for importance sampling or for Markov chain Monte Carlo methods. In this paper, we focus on applications to sampling from multimodal posterior distributions in high dimensions. We first show that samp…
This article presents a Bayesian inferential method where the likelihood for a model is unknown but where data can easily be simulated from the model. We discretize simulated (continuous) data to estimate the implicit likelihood in a Bayesian analysis employing a Markov chain Monte Carlo algorithm. Three examples are presented as well as a small study on some of the method's properties.
We develop simple methods for constructing likelihoods and parameter priors for learning about the parameters and structure of a Bayesian network. In particular, we introduce several assumptions that permit the construction of likelihoods and parameter priors for a large number of Bayesian-network structures from a small set of assessments. The most notable assumption is that of likelihood equivalence, which says that data can not help to discriminate network structures that encode the same assertions of conditional independence. We describe the constructions that follow from these assumptions…
We consider the use of randomised forward models and log-likelihoods within the Bayesian approach to inverse problems. Such random approximations to the exact forward model or log-likelihood arise naturally when a computationally expensive model is approximated using a cheaper stochastic surrogate, as in Gaussian process emulation (kriging), or in the field of probabilistic numerical methods. We show that the Hellinger distance between the exact and approximate Bayesian posteriors is bounded by moments of the difference between the true and approximate log-likelihoods. Example applications of …
Bayesian approaches to data analysis and machine learning are widespread and popular as they provide intuitive yet rigorous axioms for learning from data; see Bernardo and Smith (2004) and Bishop (2006). However, this rigour comes with a caveat that the Bayesian model is a precise reflection of Nature. There has been a recent trend to address potential model misspecification by raising the likelihood function to a power, primarily for robustness reasons, though not exclusively. In this paper we provide a coherent specification of the power parameter once the Bayesian model has been specified i…
Works, briefly surveyed here, are concerned with two basic methods: Maximum Probability and Bayesian Maximum Probability; as well as with their asymptotic instances: Relative Entropy Maximization and Maximum Non-parametric Likelihood. Parametric and empirical extensions of the latter methods - Empirical Maximum Maximum Entropy and Empirical Likelihood - are also mentioned. The methods are viewed as tools for solving certain ill-posed inverse problems, called Pi-problem, Phi-problem, respectively. Within the two classes of problems, probabilistic justification and interpretation of the respecti…
Department of Basic Neuroscience, University of Geneva（日内瓦大学基础神经科学系）
Variational Bayesian Monte Carlo (VBMC) is a recently introduced framework that uses Gaussian process surrogates to perform approximate Bayesian inference in models with black-box, non-cheap likelihoods. In this work, we extend VBMC to deal with noisy log-likelihood evaluations, such as those arising from simulation-based models. We introduce new `global' acquisition functions, such as expected information gain (EIG) and variational interquantile range (VIQR), which are robust to noise and can be efficiently evaluated within the VBMC setting. In a novel, challenging, noisy-inference benchmark …
We study a parametric estimation problem related to moment condition models. As an alternative to the generalized empirical likelihood (GEL) and the generalized method of moments (GMM), a Bayesian approach to the problem can be adopted, extending the MEM procedure to parametric moment conditions. We show in particular that a large number of GEL estimators can be interpreted as a maximum entropy solution. Moreover, we provide a more general field of applications by proving the method to be robust to approximate moment conditions.
After an autoencoder (AE) has learnt to reconstruct one dataset, it might be expected that the likelihood on an out-of-distribution (OOD) input would be low. This has been studied as an approach to detect OOD inputs. Recent work showed this intuitive approach can fail for the dataset pairs FashionMNIST vs MNIST. This paper suggests this is due to the use of Bernoulli likelihood and analyses why this is the case, proposing two fixes: 1) Compute the uncertainty of likelihood estimate by using a Bayesian version of the AE. 2) Use alternative distributions to model the likelihood.
