Approximate Bayesian computation (ABC) methods permit approximate inference for intractable likelihoods when it is possible to simulate from the model. However they perform poorly for high dimensional data, and in practice must usually be used in conjunction with dimension reduction methods, resulting in a loss of accuracy which is hard to quantify or control. We propose a new ABC method for high dimensional data based on rare event methods which we refer to as RE-ABC. This uses a latent variable representation of the model. For a given parameter value, we estimate the probability of the rare event that the latent variables correspond to data roughly consistent with the observations. This is performed using sequential Monte Carlo and slice sampling to systematically search the space of latent variables. In contrast standard ABC can be viewed as using a more naive Monte Carlo estimate. We use our rare event probability estimator as a likelihood estimate within the pseudo-marginal Metropolis-Hastings algorithm for parameter inference.
We provide asymptotics showing that RE-ABC has a lower computational cost for high dimensional data than standard ABC methods. We also illustrate our approach empirically, on a Gaussian distribution and an application in infectious disease modelling.
Likelihood-free methods, such as approximate Bayesian computation, are powerful tools for practical inference problems with intractable likelihood functions. Markov chain Monte Carlo and sequential Monte Carlo variants of approximate Bayesian computation can be effective techniques for sampling posterior distributions in an approximate Bayesian computation setting. However, without careful consideration of convergence criteria and selection of proposal kernels, such methods can lead to very biased inference or computationally inefficient sampling. In contrast, rejection sampling for approximat…
In this paper, the parameter estimation of ARMA(p,q) model is given by approximate Bayesian computation algorithm. In order to improve the sampling efficiency of the algorithm, approximate Bayesian computation should select as many statistics as possible with parameter information in low dimension. Firstly, we use the autocorrelation coefficient of the first p+q order sample as the statistic and obtain an approximate Bayesian estimation of the AR coefficient, transforming the ARMA(p,q) model into the MA(q) model. Considering the first q order sample autocorrelation functions and sample varianc…
This Chapter, "A Guide to General-Purpose ABC Software", is to appear in the forthcoming Handbook of Approximate Bayesian Computation (2018). We present general-purpose software to perform Approximate Bayesian Computation (ABC) as implemented in the R-packages abc and EasyABC and the c++ program ABCtoolbox. With simple toy models we demonstrate how to perform parameter inference, model selection, validation and optimal choice of summary statistics. We demonstrate how to combine ABC with Markov Chain Monte Carlo and describe a realistic population genetics application.
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…
ABC (approximate Bayesian computation) is a general approach for dealing with models with an intractable likelihood. In this work, we derive ABC algorithms based on QMC (quasi- Monte Carlo) sequences. We show that the resulting ABC estimates have a lower variance than their Monte Carlo counter-parts. We also develop QMC variants of sequential ABC algorithms, which progressively adapt the proposal distribution and the acceptance threshold. We illustrate our QMC approach through several examples taken from the ABC literature. Keywords: Approximate Bayesian computation, Likelihood-free inference,…
Approximate Bayesian computation allows for inference of complicated probabilistic models with intractable likelihoods using model simulations. The Markov chain Monte Carlo implementation of approximate Bayesian computation is often sensitive to the tolerance parameter: low tolerance leads to poor mixing and large tolerance entails excess bias. We consider an approach using a relatively large tolerance for the Markov chain Monte Carlo sampler to ensure its sufficient mixing, and post-processing the output leading to estimators for a range of finer tolerances. We introduce an approximate confid…
Approximate Bayesian Computation (ABC) is a statistical learning technique to calibrate and select models by comparing observed data to simulated data. This technique bypasses the use of the likelihood and requires only the ability to generate synthetic data from the models of interest. We apply ABC to fit and compare insurance loss models using aggregated data. A state-of-the-art ABC implementation in Python is proposed. It uses sequential Monte Carlo to sample from the posterior distribution and the Wasserstein distance to compare the observed and synthetic data.
In Part I (arXiv:1911.00619) of this article, we proposed an importance sampling algorithm to compute rare-event probabilities in forward uncertainty quantification problems. The algorithm, which we termed the "Bayesian Inverse Monte Carlo (BIMC) method", was shown to be optimal for problems in which the input-output operator is nearly linear. But applying the original BIMC to highly nonlinear systems can lead to several different failure modes. In this paper, we modify the BIMC method to extend its applicability to a wider class of systems. The modified algorithm, which we call "Adaptive-BIMC…
The estimation of rare event or failure probabilities in high dimensions is of interest in many areas of science and technology. We consider problems where the rare event is expressed in terms of a computationally costly numerical model. Importance sampling with the cross-entropy method offers an efficient way to address such problems provided that a suitable parametric family of biasing densities is employed. Although some existing parametric distribution families are designed to perform efficiently in high dimensions, their applicability within the cross-entropy method is limited to problems…
Some discussions of D. Fearnhead and D. Prangle's Read Paper "Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation"
Multifidelity approximate Bayesian computation (MF-ABC) is a likelihood-free technique for parameter inference that exploits model approximations to significantly increase the speed of ABC algorithms (Prescott and Baker, 2020). Previous work has considered MF-ABC only in the context of rejection sampling, which does not explore parameter space particularly efficiently. In this work, we integrate the multifidelity approach with the ABC sequential Monte Carlo (ABC-SMC) algorithm into a new MF-ABC-SMC algorithm. We show that the improvements generated by each of ABC-SMC and MF-ABC to the efficien…
Approximate Bayesian computation (ABC) has gained popularity in recent years owing to its easy implementation, nice interpretation and good performance. Its advantages are more visible when one encounters complex models where maximum likelihood estimation as well as Bayesian analysis via Markov chain Monte Carlo demand prohibitively large amount of time. This paper examines properties of ABC both from a theoretical as well as from a computational point of view.We consolidate the ABC theory by proving theorems related to its limiting behaviour. In particular, we consider partial posteriors, whi…
Bayesian inference for exponential family random graph models (ERGMs) is a doubly-intractable problem because of the intractability of both the likelihood and posterior normalizing factor. Auxiliary variable based Markov Chain Monte Carlo (MCMC) methods for this problem are asymptotically exact but computationally demanding, and are difficult to extend to modified ERGM families. In this work, we propose a kernel-based approximate Bayesian computation algorithm for fitting ERGMs. By employing an adaptive importance sampling technique, we greatly improve the efficiency of the sampling step. Thou…
This Chapter, "Overview of Approximate Bayesian Computation", is to appear as the first chapter in the forthcoming Handbook of Approximate Bayesian Computation (2018). It details the main ideas and concepts behind ABC methods with many examples and illustrations.
By the nature of their construction, many statistical models for extremes result in likelihood functions that are computationally prohibitive to evaluate. This is consequently problematic for the purposes of likelihood-based inference. With a focus on the Bayesian framework, this chapter examines the use of approximate Bayesian computation (ABC) techniques for the fitting and analysis of statistical models for extremes. After introducing the ideas behind ABC algorithms and methods, we demonstrate their application to extremal models in stereology and spatial extremes.
Simulation models often lack tractable likelihood functions, making likelihood-free inference methods indispensable. Approximate Bayesian computation generates likelihood-free posterior samples by comparing simulated and observed data through some distance measure, but existing approaches are often poorly suited to time series simulators, for example due to an independent and identically distributed data assumption. In this paper, we propose to use path signatures in approximate Bayesian computation to handle the sequential nature of time series. We provide theoretical guarantees on the result…
We propose a novel approach to approximate Bayesian computation (ABC) that seeks to cater for possible misspecification of the assumed model. This new approach can be equally applied to rejection-based ABC and to popular regression adjustment ABC. We demonstrate that this new approach mitigates the poor performance of regression adjusted ABC that can eventuate when the model is misspecified. In addition, this new adjustment approach allows us to detect which features of the observed data can not be reliably reproduced by the assumed model. A series of simulated and empirical examples illustrat…
This chapter will appear in the forthcoming Handbook of Approximate Bayesian Computation (2018). The conceptual and methodological framework that underpins approximate Bayesian computation (ABC) is targetted primarily towards problems in which the likelihood is either challenging or missing. ABC uses a simulation-based non-parametric estimate of the likelihood of a summary statistic and assumes that the generation of data from the model is computationally cheap. This chapter reviews two alternative approaches for estimating the intractable likelihood, with the goal of reducing the necessary mo…
A new recalibration post-processing method is presented to improve the quality of the posterior approximation when using Approximate Bayesian Computation (ABC) algorithms. Recalibration may be used in conjunction with existing post-processing methods, such as regression-adjustments. In addition, this work extends and strengthens the links between ABC and indirect inference algorithms, allowing more extensive use of misspecified auxiliary models in the ABC context. The method is illustrated using simulated examples to demonstrate the effects of recalibration under various conditions, and throug…
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…
Approximate Bayesian computation (ABC) is a well-established family of Monte Carlo methods for performing approximate Bayesian inference in the case where an ``implicit'' model is used for the data: when the data model can be simulated, but the likelihood cannot easily be pointwise evaluated. A fundamental property of standard ABC approaches is that the number of Monte Carlo points required to achieve a given accuracy scales exponentially with the dimension of the data. Prangle et al. (2018) proposes a Markov chain Monte Carlo (MCMC) method that uses a rare event sequential Monte Carlo (SMC) a…
We present asymptotic results for the regression-adjusted version of approximate Bayesian computation introduced by Beaumont(2002). We show that for an appropriate choice of the bandwidth, regression adjustment will lead to a posterior that, asymptotically, correctly quantifies uncertainty. Furthermore, for such a choice of bandwidth we can implement an importance sampling algorithm to sample from the posterior whose acceptance probability tends to unity as the data sample size increases. This compares favourably to results for standard approximate Bayesian computation, where the only way to o…
We analyze the computational efficiency of approximate Bayesian computation (ABC), which approximates a likelihood function by drawing pseudo-samples from the associated model. For the rejection sampling version of ABC, it is known that multiple pseudo-samples cannot substantially increase (and can substantially decrease) the efficiency of the algorithm as compared to employing a high-variance estimate based on a single pseudo-sample. We show that this conclusion also holds for a Markov chain Monte Carlo version of ABC, implying that it is unnecessary to tune the number of pseudo-samples used …
Approximate Bayesian computation (ABC) is a widely used inference method in Bayesian statistics to bypass the point-wise computation of the likelihood. In this paper we develop theoretical bounds for the distance between the statistics used in ABC. We show that some versions of ABC are inherently robust to misspecification. The bounds are given in the form of oracle inequalities for a finite sample size. The dependence on the dimension of the parameter space and the number of statistics is made explicit. The results are shown to be amenable to oracle inequalities in parameter space. We apply o…
This document is due to appear as a chapter of the forthcoming Handbook of Approximate Bayesian Computation (ABC) edited by S. Sisson, Y. Fan, and M. Beaumont. Since the earliest work on ABC, it has been recognised that using summary statistics is essential to produce useful inference results. This is because ABC suffers from a curse of dimensionality effect, whereby using high dimensional inputs causes large approximation errors in the output. It is therefore crucial to find low dimensional summaries which are informative about the parameter inference or model choice task at hand. This chapte…
We present a procedure to diagnose model misspecification in situations where inference is performed using approximate Bayesian computation. We demonstrate theoretically, and empirically that this procedure can consistently detect the presence of model misspecification. Our examples demonstrates that this approach delivers good finite-sample performance and is computational less onerous than existing approaches, all of which require re-running the inference algorithm. An empirical application to modelling exchange rate log returns using a g-and-k distribution completes the paper.
The University of Tokyo（东京大学）；RIKEN AIP（理化学研究所先进智能项目中心）
Approximate Bayesian computation (ABC) is a likelihood-free inference method that has been employed in various applications. However, ABC can be sensitive to outliers if a data discrepancy measure is chosen inappropriately. In this paper, we propose to use a nearest-neighbor-based $γ$-divergence estimator as a data discrepancy measure. We show that our estimator possesses a suitable theoretical robustness property called the redescending property. In addition, our estimator enjoys various desirable properties such as high flexibility, asymptotic unbiasedness, almost sure convergence, and linea…
We propose a new methodology to perform mineralogic inversion from wellbore logs based on a Bayesian linear regression model. Our method essentially relies on three steps. The first step makes use of Approximate Bayesian Computation (ABC) and selects from the Bayesian generator a set of candidates-volumes corresponding closely to the wellbore data responses. The second step gathers these candidates through a density-based clustering algorithm. A mineral scenario is assigned to each cluster through direct mineralogical inversion, and we provide a confidence estimate for each lithological hypoth…
In the following article we consider approximate Bayesian computation (ABC) inference. We introduce a method for numerically approximating ABC posteriors using the multilevel Monte Carlo (MLMC). A sequential Monte Carlo version of the approach is developed and it is shown under some assumptions that for a given level of mean square error, this method for ABC has a lower cost than i.i.d. sampling from the most accurate ABC approximation. Several numerical examples are given.
How can heuristic strategies emerge from smaller building blocks? We propose Approximate Bayesian Computation as a computational solution to this problem. As a first proof of concept, we demonstrate how a heuristic decision strategy such as Take The Best (TTB) can be learned from smaller, probabilistically updated building blocks. Based on a self-reinforcing sampling scheme, different building blocks are combined and, over time, tree-like non-compensatory heuristics emerge. This new algorithm, coined Approximately Bayesian Computed Take The Best (ABC-TTB), is able to recover a data set that wa…
This paper proposes a new Bayesian approach to estimate the Gini coefficient from the Lorenz curve based on grouped data. The proposed approach assumes a hypothetical income distribution and estimates the parameter by directly working on the likelihood function implied by the Lorenz curve of the income distribution from the grouped data. It inherits the advantages of two existing approaches through which the Gini coefficient can be estimated more accurately and a straightforward interpretation about the underlying income distribution is provided. Since the likelihood function is implicitly def…
Many statistical applications involve models for which it is difficult to evaluate the likelihood, but from which it is relatively easy to sample. Approximate Bayesian computation is a likelihood-free method for implementing Bayesian inference in such cases. We present results on the asymptotic variance of estimators obtained using approximate Bayesian computation in a large-data limit. Our key assumption is that the data are summarized by a fixed-dimensional summary statistic that obeys a central limit theorem. We prove asymptotic normality of the mean of the approximate Bayesian computation …
In many instances, the application of approximate Bayesian methods is hampered by two practical features: 1) the requirement to project the data down to low-dimensional summary, including the choice of this projection, which ultimately yields inefficient inference; 2) a possible lack of robustness to deviations from the underlying model structure. Motivated by these efficiency and robustness concerns, we construct a new Bayesian method that can deliver efficient estimators when the underlying model is well-specified, and which is simultaneously robust to certain forms of model misspecification…
We derive the optimal proposal density for Approximate Bayesian Computation (ABC) using Sequential Monte Carlo (SMC) (or Population Monte Carlo, PMC). The criterion for optimality is that the SMC/PMC-ABC sampler maximise the effective number of samples per parameter proposal. The optimal proposal density represents the optimal trade-off between favoring high acceptance rate and reducing the variance of the importance weights of accepted samples. We discuss two convenient approximations of this proposal and show that the optimal proposal density gives a significant boost in the expected samplin…
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 …
Controlled branching processes are stochastic growth population models in which the number of individuals with reproductive capacity in each generation is controlled by a random control function. The purpose of this work is to examine the Approximate Bayesian Computation (ABC) methods and to propose appropriate summary statistics for them in the context of these processes. This methodology enables to approximate the posterior distribution of the parameters of interest satisfactorily without explicit likelihood calculations and under a minimal set of assumptions. In particular, the tolerance re…
Approximate Bayesian computation (ABC) using a sequential Monte Carlo method provides a comprehensive platform for parameter estimation, model selection and sensitivity analysis in differential equations. However, this method, like other Monte Carlo methods, incurs a significant computational cost as it requires explicit numerical integration of differential equations to carry out inference. In this paper we propose a novel method for circumventing the requirement of explicit integration by using derivatives of Gaussian processes to smooth the observations from which parameters are estimated. …
We study batch normalisation in the context of variational inference methods in Bayesian neural networks, such as mean-field or MC Dropout. We show that batch-normalisation does not affect the optimum of the evidence lower bound (ELBO). Furthermore, we study the Monte Carlo Batch Normalisation (MCBN) algorithm, proposed as an approximate inference technique parallel to MC Dropout, and show that for larger batch sizes, MCBN fails to capture epistemic uncertainty. Finally, we provide insights into what is required to fix this failure, namely having to view the mini-batch size as a variational pa…
Phylogeny is the field of modelling the temporal discrete dynamics of speciation. Complex models can nowadays be studied using the Approximate Bayesian Computation approach which avoids likelihood calculations. The field's progression is hampered by the lack of robust software to estimate the numerous parameters of the speciation process. In this work we present an R package, pcmabc, based on Approximate Bayesian Computations, that implements three novel phylogenetic algorithms for trait-dependent speciation modelling. Our phylogenetic comparative methodology takes into account both the simula…
Accurate information on patterns of introduction and spread of non-native species is essential for making predictions and management decisions. In many cases, estimating unknown rates of introduction and spread from observed data requires evaluating intractable variable-dimensional integrals. In general, inference on the large class of models containing latent variables of large or variable dimension precludes exact sampling techniques. Approximate Bayesian computation (ABC) methods provide an alternative to exact sampling but rely on inefficient conditional simulation of the latent variables.…
Bernstein Center for Computational Neuroscience（伯恩斯坦计算神经科学中心）
A common problem in natural sciences is the comparison of competing models in the light of observed data. Bayesian model comparison provides a statistically sound framework for this comparison based on the evidence each model provides for the data. However, this framework relies on the calculation of likelihood functions which are intractable for most models used in practice. Previous approaches in the field of Approximate Bayesian Computation (ABC) circumvent the evaluation of the likelihood and estimate the model evidence based on rejection sampling, but they are typically computationally in…
The aghq package for implementing approximate Bayesian inference using adaptive quadrature is introduced. The method and software are described, and use of the package in making approximate Bayesian inferences in several challenging low- and high-dimensional models is illustrated. Examples include an infectious disease model; an astrostatistical model for estimating the mass of the Milky Way; two examples in non-Gaussian model-based geostatistics including one incorporating zero-inflation which is not easily fit using other methods; and a model for zero-inflated, overdispersed count data. The …
We propose a novel Bayesian nonparametric method for hierarchical modelling on a set of related density functions, where grouped data in the form of samples from each density function are available. Borrowing strength across the groups is a major challenge in this context. To address this problem, we introduce a hierarchically structured prior, defined over a set of univariate density functions, using convenient transformations of Gaussian processes. Inference is performed through approximate Bayesian computation (ABC), via a novel functional regression adjustment. The performance of the propo…
Rich data generating mechanisms are ubiquitous in this age of information and require complex statistical models to draw meaningful inference. While Bayesian analysis has seen enormous development in the last 30 years, benefitting from the impetus given by the successful application of Markov chain Monte Carlo (MCMC) sampling, the combination of big data and complex models conspire to produce significant challenges for the traditional MCMC algorithms. We review modern algorithmic developments addressing the latter and compare their performance using numerical experiments.
Current literature on posterior approximation for Bayesian inference offers many alternative methods. Does our chosen approximation scheme work well on the observed data? The best existing generic diagnostic tools treating this kind of question by looking at performance averaged over data space, or otherwise lack diagnostic detail. However, if the approximation is bad for most data, but good at the observed data, then we may discard a useful approximation. We give graphical diagnostics for posterior approximation at the observed data. We estimate a "distortion map" that acts on univariate marg…
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…
