This is a revised and personal manuscript version of the article that has been accepted for publication by Journal of Statistical Planning and Inference
We discuss an approach for deriving robust posterior distributions from $M$-estimating functions using Approximate Bayesian Computation (ABC) methods. In particular, we use $M$-estimating functions to construct suitable summary statistics in ABC algorithms. The theoretical properties of the robust posterior distributions are discussed. Special attention is given to the application of the method to linear mixed models. Simulation results and an application to a clinical study demonstrate the usefulness of the method. An R implementation is also provided in the robustBLME package.
We propose a quasi-Bayesian method to conduct inference for the production frontier. This approach combines multiple first-stage extreme quantile estimates by the quasi-Bayesian method to produce the point estimate and confidence interval for the production frontier. We show the asymptotic properties of the proposed estimator and the validity of the inference procedure. The finite sample performance of our method is illustrated through simulations and an empirical application.
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…
Inspired by the pioneering work of Rubin (1978), we employ the potential outcomes framework to develop a finite-population Bayesian causal inference framework for randomized controlled $2^K$ factorial designs with binary outcomes, which are common in medical research. As demonstrated by simulated and empirical examples, the proposed framework corrects the well-known variance over-estimation issue of the classic "Neymanian" inference framework, under various settings.
In this article we consider Bayesian inference for partially observed Andersson-Madigan-Perlman (AMP) Gaussian chain graph (CG) models. Such models are of particular interest in applications such as biological networks and financial time series. The model itself features a variety of constraints which make both prior modeling and computational inference challenging. We develop a framework for the aforementioned challenges, using a sequential Monte Carlo (SMC) method for statistical inference. Our approach is illustrated on both simulated data as well as real case studies from university gradua…
We propose a general solution to the problem of robust Bayesian inference in complex settings where outliers may be present. In practice, the automation of robust Bayesian analyses is important in the many applications involving large and complex datasets. The proposed solution relies on a reformulation of Bayesian inference based on possibility theory, and leverages the observation that, in this context, the marginal likelihood of the data assesses the consistency between prior and likelihood rather than model fitness. Our approach does not require additional parameters in its simplest form a…
The goal of causal inference is to understand the outcome of alternative courses of action. However, all causal inference requires assumptions. Such assumptions can be more influential than in typical tasks for probabilistic modeling, and testing those assumptions is important to assess the validity of causal inference. We develop model criticism for Bayesian causal inference, building on the idea of posterior predictive checks to assess model fit. Our approach involves decomposing the problem, separately criticizing the model of treatment assignments and the model of outcomes. Conditioned on …
Verifying the correctness of Bayesian computation is challenging. This is especially true for complex models that are common in practice, as these require sophisticated model implementations and algorithms. In this paper we introduce \emph{simulation-based calibration} (SBC), a general procedure for validating inferences from Bayesian algorithms capable of generating posterior samples. This procedure not only identifies inaccurate computation and inconsistencies in model implementations but also provides graphical summaries that can indicate the nature of the problems that arise. We argue that…
The standard approach to Bayesian inference is based on the assumption that the distribution of the data belongs to the chosen model class. However, even a small violation of this assumption can have a large impact on the outcome of a Bayesian procedure. We introduce a simple, coherent approach to Bayesian inference that improves robustness to perturbations from the model: rather than condition on the data exactly, one conditions on a neighborhood of the empirical distribution. When using neighborhoods based on relative entropy estimates, the resulting "coarsened" posterior can be approximated…
In this paper the Bayesian analysis is applied to assign a probability density to the value of a quantity having a definite sign. This analysis is logically consistent with the results, positive or negative, of repeated measurements. Results are used to estimate the atom density shift in a caesium fountain clock. The comparison with the classical statistical analysis is also reported and the advantages of the Bayesian approach for the realization of the time unit are discussed.
We address the problem of providing inference from a Bayesian perspective for parameters selected after viewing the data. We present a Bayesian framework for providing inference for selected parameters, based on the observation that providing Bayesian inference for selected parameters is a truncated data problem. We show that if the prior for the parameter is non-informative, or if the parameter is a "fixed" unknown constant, then it is necessary to adjust the Bayesian inference for selection. Our second contribution is the introduction of Bayesian False Discovery Rate controlling methodology,…
This survey covers state-of-the-art Bayesian techniques for the estimation of mixtures. It complements the earlier Marin, Mengersen and Robert (2005) by studying new types of distributions, the multinomial, latent class and t distributions. It also exhibits closed form solutions for Bayesian inference in some discrete setups. Lastly, it sheds a new light on the computation of Bayes factors via the approximation of Chib (1995).
We revisit and generalize the concept of composite likelihood as a method to make a probabilistic inference by aggregation of multiple Bayesian agents, thereby defining a class of predictive models which we call composite Bayesian. This perspective gives insight to choose the weights associated with composite likelihood, either a priori or via learning; in the latter case, they may be tuned so as to minimize prediction cross-entropy, yielding an easy-to-solve convex problem. We argue that composite Bayesian inference is a middle way between generative and discriminative models that trades off …
This note is commenting on Ronald Gallant's (2015) reflections on the construction of Bayesian prior distributions from moment conditions. The main conclusion is that the paper does not deliver a working principle that could justify inference based on such priors.
This paper provides a review of Approximate Bayesian Computation (ABC) methods for carrying out Bayesian posterior inference, through the lens of density estimation. We describe several recent algorithms and make connection with traditional approaches. We show advantages and limitations of models based on parametric approaches and we then draw attention to developments in machine learning, which we believe have the potential to make ABC scalable to higher dimensions and may be the future direction for research in this area.
For many decades, statisticians have made attempts to prepare the Bayesian omelette without breaking the Bayesian eggs; that is, to obtain probabilistic likelihood-based inferences without relying on informative prior distributions. A recent example is Murray Aitkin's recent book, {\em Statistical Inference}, which presents an approach to statistical hypothesis testing based on comparisons of posterior distributions of likelihoods under competing models. Aitkin develops and illustrates his method using some simple examples of inference from iid data and two-way tests of independence. We analyz…
Cluster sampling is common in survey practice, and the corresponding inference has been predominantly design-based. We develop a Bayesian framework for cluster sampling and account for the design effect in the outcome modeling. We consider a two-stage cluster sampling design where the clusters are first selected with probability proportional to cluster size, and then units are randomly sampled inside selected clusters. Challenges arise when the sizes of nonsampled cluster are unknown. We propose nonparametric and parametric Bayesian approaches for predicting the unknown cluster sizes, with thi…
In Bayesian inference, an unknown measurement uncertainty is often quantified in terms of a Gamma distributed precision parameter, which is impractical when prior information on the standard deviation of the measurement uncertainty shall be utilised during inference. This paper thus introduces a method for transforming between a gamma distributed precision parameter and the distribution of the associated standard deviation. The proposed method is based on numerical optimisation and shows adequate results for a wide range of scenarios.
We introduce priors and algorithms to perform Bayesian inference in Gaussian models defined by acyclic directed mixed graphs. Such a class of graphs, composed of directed and bi-directed edges, is a representation of conditional independencies that is closed under marginalization and arises naturally from causal models which allow for unmeasured confounding. Monte Carlo methods and a variational approximation for such models are presented. Our algorithms for Bayesian inference allow the evaluation of posterior distributions for several quantities of interest, including causal effects that are …
In this paper, the panel count data analysis for recurrent events is considered. Such analysis is useful for studying tumor or infection recurrences in both clinical trial and observational studies. A bivariate Gaussian Cox process model is proposed to jointly model the observation process and the recurrent event process. Bayesian nonparametric inference is proposed for simultaneously estimating regression parameters, bivariate frailty effects and baseline intensity functions. Inference is done through Markov chain Monte Carlo, with fully developed computational techniques. Predictive inferenc…
We introduce new estimation methods for a sub-class of the Gaussian scale mixture models for wavelet trees by Wainwright, Simoncelli & Willsky that rely on modern results for composite likelihoods and approximate Bayesian inference. Our methodology is illustrated for denoising and edge detection problems in two-dimensional images.
We describe a simple method for making inference on a functional of a multivariate distribution. The method is based on a copula representation of the multivariate distribution and it is based on the properties of an Approximate Bayesian Monte Carlo algorithm, where the proposed values of the functional of interest are weighed in terms of their empirical likelihood. This method is particularly useful when the "true" likelihood function associated with the working model is too costly to evaluate or when the working model is only partially specified.
Analysis of competing risks data plays an important role in the lifetime data analysis. Recently Feizjavadian and Hashemi (Computational Statistics and Data Analysis, vol. 82, 19-34, 2015) provided a classical inference of a competing risks data set using four-parameter Marshall-Olkin bivariate Weibull distribution when the failure of an unit at a particular time point can happen due to more than one cause. The aim of this paper is to provide the Bayesian analysis of the same model based on a very flexible Gamma-Dirichlet prior on the scale parameters. It is observed that the Bayesian inferenc…
We propose a general formalism of iterated random functions with semigroup property, under which exact and approximate Bayesian posterior updates can be viewed as specific instances. A convergence theory for iterated random functions is presented. As an application of the general theory we analyze convergence behaviors of exact and approximate message-passing algorithms that arise in a sequential change point detection problem formulated via a latent variable directed graphical model. The sequential inference algorithm and its supporting theory are illustrated by simulated examples.
Bayesian, frequentist and fiducial (BFF) inferences are much more congruous than they have been perceived historically in the scientific community (cf., Reid and Cox 2015; Kass 2011; Efron 1998). Most practitioners are probably more familiar with the two dominant statistical inferential paradigms, Bayesian inference and frequentist inference. The third, lesser known fiducial inference paradigm was pioneered by R.A. Fisher in an attempt to define an inversion procedure for inference as an alternative to Bayes' theorem. Although each paradigm has its own strengths and limitations subject to thei…
We combine Bayesian prediction and weighted inference as a unified approach to survey inference. The general principles of Bayesian analysis imply that models for survey outcomes should be conditional on all variables that affect the probability of inclusion. We incorporate the weighting variables under the framework of multilevel regression and poststratification, as a byproduct generating model-based weights after smoothing. We investigate deep interactions and introduce structured prior distributions for smoothing and stability of estimates. The computation is done via Stan and implemented …
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…
We present new methodologies for Bayesian inference on the rate parameters of a discretely observed continuous-time Markov jump processes with a countably infinite state space. The usual method of choice for inference, particle Markov chain Monte Carlo (particle MCMC), struggles when the observation noise is small. We consider the most challenging regime of exact observations and provide two new methodologies for inference in this case: the minimal extended state space algorithm (MESA) and the nearly minimal extended state space algorithm (nMESA). By extending the Markov chain Monte Carlo stat…
Variational approaches to approximate Bayesian inference provide very efficient means of performing parameter estimation and model selection. Among these, so-called variational-Laplace or VL schemes rely on Gaussian approximations to posterior densities on model parameters. In this note, we review the main variants of VL approaches, that follow from considering nonlinear models of continuous and/or categorical data. En passant, we also derive a few novel theoretical results that complete the portfolio of existing analyses of variational Bayesian approaches, including investigations of their as…
We empirically show that Bayesian inference can be inconsistent under misspecification in simple linear regression problems, both in a model averaging/selection and in a Bayesian ridge regression setting. We use the standard linear model, which assumes homoskedasticity, whereas the data are heteroskedastic, and observe that the posterior puts its mass on ever more high-dimensional models as the sample size increases. To remedy the problem, we equip the likelihood in Bayes' theorem with an exponent called the learning rate, and we propose the Safe Bayesian method to learn the learning rate from…
We formulate Bayesian updates in Markov processes by means of path integral techniques and derive the imaginary-time Schrödinger equation with likelihood to direct the inference incorporated as a potential for the posterior probability distribution
We introduce the concepts of Bayesian lens, characterizing the bidirectional structure of exact Bayesian inference, and statistical game, formalizing the optimization objectives of approximate inference problems. We prove that Bayesian inversions compose according to the compositional lens pattern, and exemplify statistical games with a number of classic statistical concepts, from maximum likelihood estimation to generalized variational Bayesian methods. This paper is the first in a series laying the foundations for a compositional account of the theory of active inference, and we therefore pa…
BayesPy is an open-source Python software package for performing variational Bayesian inference. It is based on the variational message passing framework and supports conjugate exponential family models. By removing the tedious task of implementing the variational Bayesian update equations, the user can construct models faster and in a less error-prone way. Simple syntax, flexible model construction and efficient inference make BayesPy suitable for both average and expert Bayesian users. It also supports some advanced methods such as stochastic and collapsed variational inference.
We present a Bayesian inference scheme for scaled Brownian motion, and investigate its performance on synthetic data for parameter estimation and model selection in a combined inference with fractional Brownian motion. We include the possibility of measurement noise in both models. We find that for trajectories of a few hundred time points the procedure is able to resolve well the true model and parameters. Using the prior of the synthetic data generation process also for the inference, the approach is optimal based on decision theory. We include a comparison with inference using a prior diffe…
The notion of Craig interpolant, used as a form of explanation in automated reasoning, is adapted from logical inference to statistical inference and used to explain inferences made by neural networks. The method produces explanations that are at the same time concise, understandable and precise.
Fitting models to data using Bayesian inference is quite common, but when each point in parameter space gives a curve, fitting the curve to a data set requires new nuisance parameters, which specify the metric embedding the one-dimensional curve into the higher-dimensional space occupied by the data. A generic formalism for curve fitting in the context of Bayesian inference is developed which shows how the aforementioned metric arises. The result is a natural generalization of previous works, and is compared to oft-used frequentist approaches and similar Bayesian techniques.
We discuss Bayesian inference for parameters selected using the data. First, we provide a critical analysis of the existing positions in the literature regarding the correct Bayesian approach under selection. Second, we propose two types of non-informative priors for selection models. These priors may be employed to produce a posterior distribution in the absence of prior information as well as to provide well-calibrated frequentist inference for the selected parameter. We test the proposed priors empirically in several scenarios.
We present a new probabilistic method for detecting, deblending, and cataloging astronomical sources called the Bayesian Light Source Separator (BLISS). BLISS is based on deep generative models, which embed neural networks within a Bayesian model. For posterior inference, BLISS uses a new form of variational inference known as Forward Amortized Variational Inference. The BLISS inference routine is fast, requiring a single forward pass of the encoder networks on a GPU once the encoder networks are trained. BLISS can perform fully Bayesian inference on megapixel images in seconds, and produces h…
Machine learning provides algorithms that can learn from data and make inferences or predictions on data. Bayesian networks are a class of graphical models that allow to represent a collection of random variables and their condititional dependencies by directed acyclic graphs. In this paper, an inference algorithm for the hidden random variables of a Bayesian network is given by using the tropicalization of the marginal distribution of the observed variables. By restricting the topological structure to graded networks, an inference algorithm for graded Bayesian networks will be established tha…
Modern deep neural network models suffer from adversarial examples, i.e. confidently misclassified points in the input space. It has been shown that Bayesian neural networks are a promising approach for detecting adversarial points, but careful analysis is problematic due to the complexity of these models. Recently Gilmer et al. (2018) introduced adversarial spheres, a toy set-up that simplifies both practical and theoretical analysis of the problem. In this work, we use the adversarial sphere set-up to understand the properties of approximate Bayesian inference methods for a linear model in a…
Many modern data analysis problems involve inferences from streaming data. However, streaming data is not easily amenable to the standard probabilistic modeling approaches, which assume that we condition on finite data. We develop population variational Bayes, a new approach for using Bayesian modeling to analyze streams of data. It approximates a new type of distribution, the population posterior, which combines the notion of a population distribution of the data with Bayesian inference in a probabilistic model. We study our method with latent Dirichlet allocation and Dirichlet process mixtur…
In this paper, a scale mixture of Normal distributions model is developed for classification and clustering of data having outliers and missing values. The classification method, based on a mixture model, focuses on the introduction of latent variables that gives us the possibility to handle sensitivity of model to outliers and to allow a less restrictive modelling of missing data. Inference is processed through a Variational Bayesian Approximation and a Bayesian treatment is adopted for model learning, supervised classification and clustering.
