Generalized Bayes posterior distributions are formed by putting a fractional power on the likelihood before combining with the prior via Bayes's formula. This fractional power, which is often viewed as a remedy for potential model misspecification bias, is called the learning rate, and a number of data-driven learning rate selection methods have been proposed in the recent literature. Each of these proposals has a different focus, a different target they aim to achieve, which makes them difficult to compare. In this paper, we provide a direct head-to-head comparison of these learning rate selection methods in various misspecified model scenarios, in terms of several relevant metrics, in particular, coverage probability of the generalized Bayes credible regions. In some examples all the methods perform well, while in others the misspecification is too severe to be overcome, but we find that the so-called generalized posterior calibration algorithm tends to outperform the others in terms of credible region coverage probability.
This paper introduces the parallel hierarchical sampler (PHS), a Markov chain Monte Carlo algorithm using several chains simultaneously. The connections between PHS and the parallel tempering (PT) algorithm are illustrated, convergence of PHS joint transition kernel is proved and and its practical advantages are emphasized. We illustrate the inferences obtained using PHS, parallel tempering and the Metropolis-Hastings algorithm for three Bayesian model selection problems, namely Gaussian clustering, the selection of covariates for a linear regression model and the selection of the structure of…
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 propose a general algorithmic framework for Bayesian model selection. A spike-and-slab Laplacian prior is introduced to model the underlying structural assumption. Using the notion of effective resistance, we derive an EM-type algorithm with closed-form iterations to efficiently explore possible candidates for Bayesian model selection. The deterministic nature of the proposed algorithm makes it more scalable to large-scale and high-dimensional data sets compared with existing stochastic search algorithms. When applied to sparse linear regression, our framework recovers the EMVS algorithm [R…
Often the underlying system of differential equations driving a stochastic dynamical system is assumed to be known, with inference conditioned on this assumption. We present a Bayesian framework for discovering this system of differential equations under assumptions that align with real-life scenarios, including the availability of relatively sparse data. Further, we discuss computational strategies that are critical in teasing out the important details about the dynamical system and algorithmic innovations to solve for acute parameter interdependence in the absence of rich data. This gives a …
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.
In this paper we extend existing Bayesian methods for variable selection in Gaussian process regression, to select both the regression terms and the active covariates in the spatial correlation structure. We then use the estimated posterior probabilities to choose between relatively few modes through cross-validation, and consequently improve prediction.
Selecting a subset of variables for linear models remains an active area of research. This paper reviews many of the recent contributions to the Bayesian model selection and shrinkage prior literature. A posterior variable selection summary is proposed, which distills a full posterior distribution over regression coefficients into a sequence of sparse linear predictors.
This note is a discussion of the article "Bayesian model selection based on proper scoring rules" by A.P. Dawid and M. Musio, to appear in Bayesian Analysis. While appreciating the concepts behind the use of proper scoring rules, including the inclusion of improper priors, we point out here some possible practical difficulties with the advocated approach.
We consider Bayesian logistic regression models with group-structured covariates. In high-dimensional settings, it is often assumed that only small portion of groups are significant, thus consistent group selection is of significant importance. While consistent frequentist group selection methods have been proposed, theoretical properties of Bayesian group selection methods for logistic regression models have not been investigated yet. In this paper, we consider a hierarchical group spike and slab prior for logistic regression models in high-dimensional settings. Under mild conditions, we esta…
This article is an invited discussion of the article by Gronau and Wagenmakers (2018) that can be found at https://dx.doi.org/10.1007/s42113-018-0011-7.
Until recently, the use of Bayesian inference in population genetics was limited to a few cases because for many realistic population genetic models the likelihood function cannot be calculated analytically . The situation changed with the advent of likelihood-free inference algorithms, often subsumed under the term Approximate Bayesian Computation (ABC). A key innovation was the use of a post-sampling regression adjustment, allowing larger tolerance values and as such shifting computation time to realistic orders of magnitude (see Beaumont et al., 2002). Here we propose a reformulation of the…
We consider a context-dependent ranking and selection problem. The best design is not universal but depends on the contexts. Under a Bayesian framework, we develop a dynamic sampling scheme for context-dependent optimization (DSCO) to efficiently learn and select the best designs in all contexts. The proposed sampling scheme is proved to be consistent. Numerical experiments show that the proposed sampling scheme significantly improves the efficiency in context-dependent ranking and selection.
We deal with Bayesian inference for Beta autoregressive processes. We restrict our attention to the class of conditionally linear processes. These processes are particularly suitable for forecasting purposes, but are difficult to estimate due to the constraints on the parameter space. We provide a full Bayesian approach to the estimation and include the parameter restrictions in the inference problem by a suitable specification of the prior distributions. Moreover in a Bayesian framework parameter estimation and model choice can be solved simultaneously. In particular we suggest a Markov-Chain…
Integrative analyses based on statistically relevant associations between genomics and a wealth of intermediary phenotypes (such as imaging) provide vital insights into their clinical relevance in terms of the disease mechanisms. Estimates for uncertainty in the resulting integrative models are however unreliable unless inference accounts for the selection of these associations with accuracy. In this article, we develop selection-aware Bayesian methods which: (i) counteract the impact of model selection bias through a "selection-aware posterior" in a flexible class of integrative Bayesian mode…
Challenging research in various fields has driven a wide range of methodological advances in variable selection for regression models with high-dimensional predictors. In comparison, selection of nonlinear functions in models with additive predictors has been considered only more recently. Several competing suggestions have been developed at about the same time and often do not refer to each other. This article provides a state-of-the-art review on function selection, focusing on penalized likelihood and Bayesian concepts, relating various approaches to each other in a unified framework. In an…
In the era of big data, variable selection is a key technology for handling high-dimensional problems with a small sample size but a large number of covariables. Different variable selection methods were proposed for different models, such as linear model, logistic model and generalized linear model. However, fewer works focused on variable selection for single index models, especially, for single index logistic model, due to the difficulty arose from the unknown link function and the slow mixing rate of MCMC algorithm for traditional logistic model. In this paper, we proposed a Bayesian varia…
In this note we introduce linear regression with basis functions in order to apply Bayesian model selection. The goal is to incorporate Occam's razor as provided by Bayes analysis in order to automatically pick the model optimally able to explain the data without overfitting.
In this paper, we consider Bayesian variable selection problem of linear regression model with global-local shrinkage priors on the regression coefficients. We propose a variable selection procedure that select a variable if the ratio of the posterior mean to the ordinary least square estimate of the corresponding coefficient is greater than $1/2$. Under the assumption of orthogonal designs, we show that if the local parameters have polynomial-tailed priors, our proposed method enjoys the oracle property in the sense that it can achieve variable selection consistency and optimal estimation rat…
While the Bayesian Information Criterion (BIC) and Akaike Information Criterion (AIC) are powerful tools for model selection in linear regression, they are built on different prior assumptions and thereby apply to different data generation scenarios. We show that in the finite-dimensional case their respective assumptions can be unified within an augmented model-plus-noise space and construct a prior in this space which inherits the beneficial properties of both AIC and BIC. This allows us to adapt the BIC to be robust against misspecified models where the signal to noise ratio is low.
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.
Heckman selection model is the most popular econometric model in analysis of data with sample selection. However, selection models with Normal errors cannot accommodate heavy tails in the error distribution. Recently, Marchenko and Genton proposed a selection-t model to perform frequentist' robust analysis of sample selection. Instead of using their maximum likelihood estimates, our paper develops new Bayesian procedures for the selection-t models with either continuous or binary outcomes. By exploiting the Normal mixture representation of the t distribution, we can use data augmentation to im…
Spike-and-slab and horseshoe regression are arguably the most popular Bayesian variable selection approaches for linear regression models. However, their performance can deteriorate if outliers and heteroskedasticity are present in the data, which are common features in many real-world statistics and machine learning applications. In this work, we propose a Bayesian nonparametric approach to linear regression that performs variable selection while accounting for outliers and heteroskedasticity. Our proposed model is an instance of a Dirichlet process scale mixture model with the advantage that…
We propose a cautious Bayesian variable selection routine by investigating the sensitivity of a hierarchical model, where the regression coefficients are specified by spike and slab priors. We exploit the use of latent variables to understand the importance of the co-variates. These latent variables also allow us to obtain the size of the model space which is an important aspect of high dimensional problems. In our approach, instead of fixing a single prior, we adopt a specific type of robust Bayesian analysis, where we consider a set of priors within the same parametric family to specify the …
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…
In this paper we briefly review the main methodological aspects concerned with the application of the Bayesian approach to model choice and model averaging in the context of variable selection in regression models. This includes prior elicitation, summaries of the posterior distribution and computational strategies. We then examine and compare various publicly available {\tt R}-packages for its practical implementation summarizing and explaining the differences between packages and giving recommendations for applied users. We find that all packages reviewed lead to very similar results, but th…
Decision-making often involves ranking and selection. For example, to assemble a team of political forecasters, we might begin by narrowing our choice set to the candidates we are confident rank among the top 10% in forecasting ability. Unfortunately, we do not know each candidate's true ability but observe a noisy estimate of it. This paper develops new Bayesian algorithms to rank and select candidates based on noisy estimates. Using simulations based on empirical data, we show that our algorithms often outperform frequentist ranking and selection algorithms. Our Bayesian ranking algorithms y…
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.
We consider the bridge linear regression modeling, which can produce a sparse or non-sparse model. A crucial point in the model building process is the selection of adjusted parameters including a regularization parameter and a tuning parameter in bridge regression models. The choice of the adjusted parameters can be viewed as a model selection and evaluation problem. We propose a model selection criterion for evaluating bridge regression models in terms of Bayesian approach. This selection criterion enables us to select the adjusted parameters objectively. We investigate the effectiveness of …
We introduce the concept of conjugate prior models for a given likelihood function in Bayesian spatial inversion. The conjugate class of prior models can be selection extended and still remain conjugate. We demonstrate the generality of selection Gaussian prior models, representing multi-modality, skewness and heavy-tailedness. For Gauss-linear likelihood functions, the posterior model is also selection Gaussian. The model parameters of the posterior pdf are explisite functions of the model parameters of the likelihood and prior models - and the actual observations, of course. Efficient algori…
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…
It is common practice to use Laplace approximations to compute marginal likelihoods in Bayesian versions of generalised linear models (GLM). Marginal likelihoods combined with model priors are then used in different search algorithms to compute the posterior marginal probabilities of models and individual covariates. This allows performing Bayesian model selection and model averaging. For large sample sizes, even the Laplace approximation becomes computationally challenging because the optimisation routine involved needs to evaluate the likelihood on the full set of data in multiple iterations…
An important task in building regression models is to decide which regressors should be included in the final model. In a Bayesian approach, variable selection can be performed using mixture priors with a spike and a slab component for the effects subject to selection. As the spike is concentrated at zero, variable selection is based on the probability of assigning the corresponding regression effect to the slab component. These posterior inclusion probabilities can be determined by MCMC sampling. In this paper we compare the MCMC implementations for several spike and slab priors with regard t…
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.
An important aspect of Bayesian model selection is how to deal with huge model spaces, since exhaustive enumeration of all the models entertained is unfeasible and inferences have to be based on the very small proportion of models visited. This is the case for the variable selection problem, with a moderate to large number of possible explanatory variables being considered in this paper. We review some of the strategies proposed in the literature and argue that inferences based on empirical frequencies via Markov Chain Monte Carlo sampling of the posterior distribution outperforms recently pro…
We propose a novel Bayesian model selection technique on linear mixed-effects models to compare multiple treatments with a control. A fully Bayesian approach is implemented to estimate the marginal inclusion probabilities that provide a direct measure of the difference between treatments and the control, along with the model-averaged posterior distributions. Default priors are proposed for model selection incorporating domain knowledge and a component-wise Gibbs sampler is developed for efficient posterior computation. We demonstrate the proposed method based on simulated data and an experimen…
Bayesian Variable Selection in Generalized Linear Models
University of Trento（特伦托大学）；Fondazione Bruno Kessler (FBK)（布鲁诺·孔塞雷基金会）；BCAM — Basque Center for Applied Mathematics（巴斯克应用数学中心）；Ikerbasque — Basque Foundation for Science（巴斯克科学基金会）
The class of chain event graph models is a generalisation of the class of discrete Bayesian networks, retaining most of the structural advantages of the Bayesian network for model interrogation, propagation and learning, while more naturally encoding asymmetric state spaces and the order in which events happen. In this paper we demonstrate how with complete sampling, conjugate closed form model selection based on product Dirichlet priors is possible, and prove that suitable homogeneity assumptions characterise the product Dirichlet prior on this class of models. We demonstrate our techniques u…
Rice University（莱斯大学）；Department of Statistics（统计系）
Subset selection is a valuable tool for interpretable learning, scientific discovery, and data compression. However, classical subset selection is often avoided due to selection instability, lack of regularization, and difficulties with post-selection inference. We address these challenges from a Bayesian perspective. Given any Bayesian predictive model $\mathcal{M}$, we extract a family of near-optimal subsets of variables for linear prediction or classification. This strategy deemphasizes the role of a single "best" subset and instead advances the broader perspective that often many subsets …
We study the computational complexity of Markov chain Monte Carlo (MCMC) methods for high-dimensional Bayesian linear regression under sparsity constraints. We first show that a Bayesian approach can achieve variable-selection consistency under relatively mild conditions on the design matrix. We then demonstrate that the statistical criterion of posterior concentration need not imply the computational desideratum of rapid mixing of the MCMC algorithm. By introducing a truncated sparsity prior for variable selection, we provide a set of conditions that guarantee both variable-selection consiste…
A general Bayesian framework for model selection on random network models regarding their features is considered. The goal is to develop a principle Bayesian model selection approach to compare different fittable, not necessarily nested, models for inference on those network realisations. The criterion for random network models regarding the comparison is formulated via Bayes factors and penalizing using the mostwidely used loss functions. Parametrizations are different in different spaces. To overcome this problem we incorporate and encode different aspects of complexities in terms of observa…
Approximate Bayesian computation (ABC) is a class of algorithmic methods in Bayesian inference using statistical summaries and computer simulations. ABC has become popular in evolutionary genetics and in other branches of biology. However model selection under ABC algorithms has been a subject of intense debate during the recent years. Here we propose novel approaches to model selection based on posterior predictive distributions and approximations of the deviance. We argue that this framework can settle some contradictions between the computation of model probabilities and posterior predictiv…
Motivated by examples from genetic association studies, this paper considers the model selection problem in a general complex linear model system and in a Bayesian framework. We discuss formulating model selection problems and incorporating context-dependent {\it a priori} information through different levels of prior specifications. We also derive analytic Bayes factors and their approximations to facilitate model selection and discuss their theoretical and computational properties. We demonstrate our Bayesian approach based on an implemented Markov Chain Monte Carlo (MCMC) algorithm in simul…
Bayesian methods - either based on Bayes Factors or BIC - are now widely used for model selection. One property that might reasonably be demanded of any model selection method is that if a model ${M}_{1}$ is preferred to a model ${M}_{0}$, when these two models are expressed as members of one model class $\mathbb{M}$, this preference is preserved when they are embedded in a different class $\mathbb{M}'$. However, we illustrate in this paper that with the usual implementation of these common Bayesian procedures this property does not hold true even approximately. We therefore contend that to us…
In this paper we review the concepts of Bayesian evidence and Bayes factors, also known as log odds ratios, and their application to model selection. The theory is presented along with a discussion of analytic, approximate and numerical techniques. Specific attention is paid to the Laplace approximation, variational Bayes, importance sampling, thermodynamic integration, and nested sampling and its recent variants. Analogies to statistical physics, from which many of these techniques originate, are discussed in order to provide readers with deeper insights that may lead to new techniques. The u…
We present a Bayesian model selection approach to estimate the intrinsic dimensionality of a high-dimensional dataset. To this end, we introduce a novel formulation of the probabilisitic principal component analysis model based on a normal-gamma prior distribution. In this context, we exhibit a closed-form expression of the marginal likelihood which allows to infer an optimal number of components. We also propose a heuristic based on the expected shape of the marginal likelihood curve in order to choose the hyperparameters. In non-asymptotic frameworks, we show on simulated data that this exac…
Gaussian graphical models are used for determining conditional relationships between variables. This is accomplished by identifying off-diagonal elements in the inverse-covariance matrix that are non-zero. When the ratio of variables (p) to observations (n) approaches one, the maximum likelihood estimator of the covariance matrix becomes unstable and requires shrinkage estimation. Whereas several classical (frequentist) methods have been introduced to address this issue, fully Bayesian methods remain relatively uncommon in practice and methodological literatures. Here we introduce a Bayesian m…
