Likelihood-free inference for simulator-based statistical models has developed rapidly from its infancy to a useful tool for practitioners. However, models with more than a handful of parameters still generally remain a challenge for the Approximate Bayesian Computation (ABC) based inference. To advance the possibilities for performing likelihood-free inference in higher dimensional parameter spaces, we introduce an extension of the popular Bayesian optimisation based approach to approximate discrepancy functions in a probabilistic manner which lends itself to an efficient exploration of the parameter space. Our approach achieves computational scalability for higher dimensional parameter spaces by using separate acquisition functions and discrepancies for each parameter. The efficient additive acquisition structure is combined with exponentiated loss -likelihood to provide a misspecification-robust characterisation of the marginal posterior distribution for all model parameters. The method successfully performs computationally efficient inference in a 100-dimensional space on canonical examples and compares favourably to existing modularised ABC methods. We further illustrate the potential of this approach by fitting a bacterial transmission dynamics model to a real data set, which provides biologically coherent results on strain competition in a 30-dimensional parameter space.
Misspecification-robust Sequential Neural Likelihood for Simulation-based Inference
School of Mathematical Sciences（数学科学学院）；Centre for Data Science（数据科学中心）；Queensland University of Technology（昆士兰科技大学）；Institute of Operations Research and Analytics（运营研究与分析研究所）；National University of Singapore（新加坡国立大学）；Department of Econometrics and Business Statistics（计量经济学与商务统计系）；Monash University（莫纳什大学）
We propose Posterior Bootstrap, a set of algorithms extending Weighted Likelihood Bootstrap, to properly incorporate prior information and address the problem of model misspecification in Bayesian inference. We consider two approaches to incorporating prior knowledge: the first is based on penalization of the Weighted Likelihood Bootstrap objective function, and the second uses pseudo-samples from the prior predictive distribution. We also propose methodology for hierarchical models, which was not previously known for methods based on Weighted Likelihood Bootstrap. Edgeworth expansions guide t…
We study two practically important cases of model based clustering using Gaussian Mixture Models: (1) when there is misspecification and (2) on high dimensional data, in the light of recent advances in Gradient Descent (GD) based optimization using Automatic Differentiation (AD). Our simulation studies show that EM has better clustering performance, measured by Adjusted Rand Index, compared to GD in cases of misspecification, whereas on high dimensional data GD outperforms EM. We observe that both with EM and GD there are many solutions with high likelihood but poor cluster interpretation. To …
Model misspecification is a long-standing enigma of the Bayesian inference framework as posteriors tend to get overly concentrated on ill-informed parameter values towards the large sample limit. Tempering of the likelihood has been established as a safer way to do updates from prior to posterior in the presence of model misspecification. At one extreme tempering can ignore the data altogether and at the other extreme it provides the standard Bayes' update when no misspecification is assumed to be present. However, it is an open issue how to best recognize misspecification and choose a suitabl…
Model misspecification constitutes a major obstacle to reliable inference in many inverse problems. Inverse problems in seismology, for example, are particularly affected by misspecification of wave propagation velocities. In this paper, we focus on a specific seismic inverse problem - full-waveform moment tensor inversion - and develop a Bayesian framework that seeks robustness to velocity misspecification. A novel element of our framework is the use of transport-Lagrangian (TL) distances between observed and model predicted waveforms to specify a loss function, and the use of this loss to de…
Cluster of Excellence SimTech（SimTech卓越集群）；University of Stuttgart（斯图加特大学）；Heidelberg University（海德堡大学）；Cluster of Excellence STRUCTURES（STRUCTURES卓越集群）
Neural density estimators have proven remarkably powerful in performing efficient simulation-based Bayesian inference in various research domains. In particular, the BayesFlow framework uses a two-step approach to enable amortized parameter estimation in settings where the likelihood function is implicitly defined by a simulation program. But how faithful is such inference when simulations are poor representations of reality? In this paper, we conceptualize the types of model misspecification arising in simulation-based inference and systematically investigate the performance of the BayesFlow …
Simulation-based Bayesian inference under model misspecification
School of Mathematical Sciences, Queensland University of Technology（昆士兰科技大学数学科学学院）；Centre for Data Science, Queensland University of Technology（昆士兰科技大学数据科学中心）；Department of Econometrics and Business Statistics, Monash University（莫纳什大学计量经济学与商业统计系）；Department of Statistics and Data Science, National University of Singapore（新加坡国立大学统计与数据科学系）；Institute for Adaptive & Neural Computation, University of Edinburgh（爱丁堡大学自适应与神经计算研究所）；Centre of Excellence for the Mathematical Analysis of Cellular Systems, Queensland University of Technology（昆士兰科技大学细胞系统数学分析卓越中心）
Aided by advances in neural density estimation, considerable progress has been made in recent years towards a suite of simulation-based inference (SBI) methods capable of performing flexible, black-box, approximate Bayesian inference for stochastic simulation models. While it has been demonstrated that neural SBI methods can provide accurate posterior approximations, the simulation studies establishing these results have considered only well-specified problems -- that is, where the model and the data generating process coincide exactly. However, the behaviour of such algorithms in the case of …
We present non-asymptotic two-sided bounds to the log-marginal likelihood in Bayesian inference. The classical Laplace approximation is recovered as the leading term. Our derivation permits model misspecification and allows the parameter dimension to grow with the sample size. We do not make any assumptions about the asymptotic shape of the posterior, and instead require certain regularity conditions on the likelihood ratio and that the posterior to be sufficiently concentrated.
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…
This paper presents recent methodological advances to perform simulation-based inference (SBI) of a general class of Bayesian hierarchical models (BHMs), while checking for model misspecification. Our approach is based on a two-step framework. First, the latent function that appears as second layer of the BHM is inferred and used to diagnose possible model misspecification. Second, target parameters of the trusted model are inferred via SBI. Simulations used in the first step are recycled for score compression, which is necessary to the second step. As a proof of concept, we apply our framewor…
Misspecification-robust amortised simulation-based inference using variational methods
Institute of Astronomy, University of Cambridge（天文研究所，剑桥大学）；Statistical Laboratory, University of Cambridge（统计实验室，剑桥大学）；Kavli Institute for Cosmology, University of Cambridge（宇宙学研究所，剑桥大学）；Institute of Astrophysics, FORTH（天体物理学研究所，福蒂斯研究所）
Bayesian variable selection often assumes normality, but the effects of model misspecification are not sufficiently understood. There are sound reasons behind this assumption, particularly for large $p$: ease of interpretation, analytical and computational convenience. More flexible frameworks exist, including semi- or non-parametric models, often at the cost of some tractability. We propose a simple extension of the Normal model that allows for skewness and thicker-than-normal tails but preserves tractability. It leads to easy interpretation and a log-concave likelihood that facilitates optim…
A successful model for high-dimensional spatial extremes should, in principle, be able to describe both weakening extremal dependence at increasing levels and changes in the type of extremal dependence class as a function of the distance between locations. Furthermore, the model should allow for computationally tractable inference using inference methods that efficiently extract information from data and that are robust to model misspecification. In this paper, we demonstrate how to fulfil all these requirements by developing a comprehensive methodological workflow for efficient Bayesian model…
Typical Bayesian inference requires parameter identification via likelihood parameterization, which has invited criticism for being less flexible than the Frequentist framework and subject to misspecification. Though misspecification may be avoided by functional parameter inference under a nonparametric model space, there does not exist a flexible Bayesian semiparametric model that would allow full control over the marginal prior over any general functional parameter. We present the technique of $θ$-augmentation which helps us manipulate nonparametric models into semiparametric ones that direc…
Columbia University（哥伦比亚大学）；Northwestern University（西北大学）
$α$-posteriors and their variational approximations distort standard posterior inference by downweighting the likelihood and introducing variational approximation errors. We show that such distortions, if tuned appropriately, reduce the Kullback-Leibler (KL) divergence from the true, but perhaps infeasible, posterior distribution when there is potential parametric model misspecification. To make this point, we derive a Bernstein-von Mises theorem showing convergence in total variation distance of $α$-posteriors and their variational approximations to limiting Gaussian distributions. We use the…
University of Warwick（华威大学）；The Alan Turing Institute（艾伦·图灵研究所）
We introduce a framework for inference in general state-space hidden Markov models (HMMs) under likelihood misspecification. In particular, we leverage the loss-theoretic perspective of Generalized Bayesian Inference (GBI) to define generalised filtering recursions in HMMs, that can tackle the problem of inference under model misspecification. In doing so, we arrive at principled procedures for robust inference against observation contamination by utilising the $β$-divergence. Operationalising the proposed framework is made possible via sequential Monte Carlo methods (SMC), where most standard…
Imperial College London（帝国理工学院）；University College London（伦敦大学学院）；University of Cambridge（剑桥大学）
Gaussian processes are ubiquitous in machine learning, statistics, and applied mathematics. They provide a flexible modelling framework for approximating functions, whilst simultaneously quantifying uncertainty. However, this is only true when the model is well-specified, which is often not the case in practice. In this paper, we study the properties of Gaussian process means when the smoothness of the model and the likelihood function are misspecified. In this setting, an important theoretical question of practial relevance is how accurate the Gaussian process approximations will be given the…
In this paper we are interested in empirical likelihood (EL) as a method of estimation, and we address the following two problems: (1) selecting among various empirical discrepancies in an EL framework and (2) demonstrating that EL has a well-defined probabilistic interpretation that would justify its use in a Bayesian context. Using the large deviations approach, a Bayesian law of large numbers is developed that implies that EL and the Bayesian maximum a posteriori probability (MAP) estimators are consistent under misspecification and that EL can be viewed as an asymptotic form of MAP. Estima…
CREST（Crest研究中心）；ENSAE（法国国立统计与经济管理学院）；Institut Polytechnique de Paris（巴黎理工学院）；RIKEN Center for AI Project（理化学研究所人工智能项目中心）
In some misspecified settings, the posterior distribution in Bayesian statistics may lead to inconsistent estimates. To fix this issue, it has been suggested to replace the likelihood by a pseudo-likelihood, that is the exponential of a loss function enjoying suitable robustness properties. In this paper, we build a pseudo-likelihood based on the Maximum Mean Discrepancy, defined via an embedding of probability distributions into a reproducing kernel Hilbert space. We show that this MMD-Bayes posterior is consistent and robust to model misspecification. As the posterior obtained in this way mi…
Standard Bayesian inference is known to be sensitive to model misspecification, leading to unreliable uncertainty quantification and poor predictive performance. However, finding generally applicable and computationally feasible methods for robust Bayesian inference under misspecification has proven to be a difficult challenge. An intriguing, easy-to-use, and widely applicable approach is to use bagging on the Bayesian posterior ("BayesBag"); that is, to use the average of posterior distributions conditioned on bootstrapped datasets. In this paper, we develop the asymptotic theory of BayesBag,…
Model selection is crucial to high-dimensional learning and inference for contemporary big data applications in pinpointing the best set of covariates among a sequence of candidate interpretable models. Most existing work assumes implicitly that the models are correctly specified or have fixed dimensionality. Yet both features of model misspecification and high dimensionality are prevalent in practice. In this paper, we exploit the framework of model selection principles in misspecified models originated in Lv and Liu (2014) and investigate the asymptotic expansion of Bayesian principle of mod…
Inference problems with incomplete observations often aim at estimating population properties of unobserved quantities. One simple way to accomplish this estimation is to impute the unobserved quantities of interest at the individual level and then take an empirical average of the imputed values. We show that this simple imputation estimator can provide partial protection against model misspecification. We illustrate imputation estimators' robustness to model specification on three examples: mixture model-based clustering, estimation of genotype frequencies in population genetics, and estimati…
We give an overview of statistical models and likelihood, together with two of its variants: penalized and hierarchical likelihood. The Kullback-Leibler divergence is referred to repeatedly, for defining the misspecification risk of a model, for grounding the likelihood and the likelihood crossvalidation which can be used for choosing weights in penalized likelihood. Families of penalized likelihood and sieves estimators are shown to be equivalent. The similarity of these likelihood with a posteriori distributions in a Bayesian approach is considered.
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…
Bayesian methods have proven themselves to be successful across a wide range of scientific problems and have many well-documented advantages over competing methods. However, these methods run into difficulties for two major and prevalent classes of problems: handling data sets with outliers and dealing with model misspecification. We outline the drawbacks of previous solutions to both of these problems and propose a new method as an alternative. When working with the new method, the data is summarized through a set of insufficient statistics, targeting inferential quantities of interest, and t…
Although neural networks are powerful function approximators, the underlying modelling assumptions ultimately define the likelihood and thus the hypothesis class they are parameterizing. In classification, these assumptions are minimal as the commonly employed softmax is capable of representing any categorical distribution. In regression, however, restrictive assumptions on the type of continuous distribution to be realized are typically placed, like the dominant choice of training via mean-squared error and its underlying Gaussianity assumption. Recently, modelling advances allow to be agnost…
We show that forms of Bayesian and MDL inference that are often applied to classification problems can be *inconsistent*. This means there exists a learning problem such that for all amounts of data the generalization errors of the MDL classifier and the Bayes classifier relative to the Bayesian posterior both remain bounded away from the smallest achievable generalization error.
In this paper we consider the problem of inference in statistical models characterized by moment restrictions by casting the problem within the Exponentially Tilted Empirical Likelihood (ETEL) framework. Because the ETEL function has a well defined probabilistic interpretation and plays the role of a nonparametric likelihood, a fully Bayesian semiparametric framework can be developed. We establish a number of powerful results surrounding the Bayesian ETEL framework in such models. One major concern driving our work is the possibility of misspecification. To accommodate this possibility, we sho…
We propose information criteria that measure the prediction risk of a predictive density based on the Bayesian marginal likelihood from a frequentist point of view. We derive criteria for selecting variables in linear regression models, assuming a prior distribution of the regression coefficients. Then, we discuss the relationship between the proposed criteria and related criteria. There are three advantages of our method. First, this is a compromise between the frequentist and Bayesian standpoints because it evaluates the frequentist's risk of the Bayesian model. Thus, it is less influenced b…
Robust Predictive Uncertainty and Double Descent in Contaminated Bayesian Random Features
The University of Manchester, UK（英国曼彻斯特大学）；University of Pisa, Italy（意大利比萨大学）；Nanyang Technological University, Singapore（新加坡南洋理工大学）；Max Planck Institute for Mathematics in the Sciences, Germany（德国马克斯·普朗克数学研究所）
The University of Sydney（悉尼大学）；CSIRO（澳大利亚联邦科学与工业研究组织）；NVIDIA（英伟达）
In likelihood-free settings where likelihood evaluations are intractable, approximate Bayesian computation (ABC) addresses the formidable inference task to discover plausible parameters of simulation programs that explain the observations. However, they demand large quantities of simulation calls. Critically, hyperparameters that determine measures of simulation discrepancy crucially balance inference accuracy and sample efficiency, yet are difficult to tune. In this paper, we present kernel embedding likelihood-free inference (KELFI), a holistic framework that automatically learns model hyper…
We present Sequential Neural Likelihood (SNL), a new method for Bayesian inference in simulator models, where the likelihood is intractable but simulating data from the model is possible. SNL trains an autoregressive flow on simulated data in order to learn a model of the likelihood in the region of high posterior density. A sequential training procedure guides simulations and reduces simulation cost by orders of magnitude. We show that SNL is more robust, more accurate and requires less tuning than related neural-based methods, and we discuss diagnostics for assessing calibration, convergence…
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…
