Testing the (in)equality of variances is an important problem in many statistical applications. We develop default Bayes factor tests to assess the (in)equality of two or more population variances, as well as a test for whether the population variances equal a specific value. The resulting test can be used to check assumptions for commonly used procedures such as the $t$-test or ANOVA, or test substantive hypotheses concerning variances directly. We show that our Bayes factor fulfills a number of desiderata. Researchers may have directed hypotheses such as $σ_{1}^{2} > σ_{2}^{2}$, they may want to extend $\mathcal{H}_{0}$ to have a null-region, or wish to combine hypotheses about equality with hypotheses about inequality, for example $σ_{1}^{2} = σ_{2}^{2} > (σ_{3}^{2}, σ_{4}^{2})$. We extend our Bayes factor test to allow for these deviations from our proposed default and illustrate it on a number of practical examples. Our procedure is implemented in the R package $bfvartest$.
The multivariate normal linear model is one of the most widely employed models for statistical inference in applied research. Special cases include (multivariate) t testing, (M)AN(C)OVA, (multivariate) multiple regression, and repeated measures analysis. Statistical procedures for model selection where the models may have equality and order constraints on the model parameters of interest are limited however. This paper presents a default Bayes factor for this model selection problem. The default Bayes factor is based on generalized fractional Bayes methodology where different fractions are use…
This paper presents objective priors for robust Bayesian estimation against outliers based on divergences. The minimum $γ$-divergence estimator is well-known to work well estimation against heavy contamination. The robust Bayesian methods by using quasi-posterior distributions based on divergences have been also proposed in recent years. In objective Bayesian framework, the selection of default prior distributions under such quasi-posterior distributions is an important problem. In this study, we provide some properties of reference and moment matching priors under the quasi-posterior distribu…
We provide a framework for assessing the default nature of a prior distribution using the property of regular variation, which we study for global-local shrinkage priors. In particular, we demonstrate the horseshoe priors, originally designed to handle sparsity, also possess regular variation and thus are appropriate for default Bayesian analysis. To illustrate our methodology, we solve a problem of non-informative priors due to Efron (1973), who showed standard flat non-informative priors in high-dimensional normal means model can be highly informative for nonlinear parameters of interest. We…
Due to their great flexibility, nonparametric Bayes methods have proven to be a valuable tool for discovering complicated patterns in data. The term "nonparametric Bayes" suggests that these methods inherit model-free operating characteristics of classical nonparametric methods, as well as coherent uncertainty assessments provided by Bayesian procedures. However, as the authors say in the conclusion to their article, nonparametric Bayesian methods may be more aptly described as "massively parametric." Furthermore, I argue that many of the default nonparametric Bayes procedures are only Bayesia…
Measures of association play a central role in the social sciences to quantify the strength of a linear relationship between the variables of interest. In many applications researchers can translate scientific expectations to hypotheses with equality and/or order constraints on these measures of association. In this paper a Bayes factor test is proposed for testing multiple hypotheses with constraints on the measures of association between ordinal and/or continuous variables, possibly after correcting for certain covariates. This test can be used to obtain a direct answer to the research quest…
In this paper we present a Bayesian competing risk proportional hazards model to describe mortgage defaults and prepayments. We develop Bayesian inference for the model using Markov chain Monte Carlo methods. Implementation of the model is illustrated using actual default/prepayment data and additional insights that can be obtained from the Bayesian analysis are discussed.
We derive the Jeffreys prior for the parameter of the Multivariate Ewens Distribution and study some of its properties. In particular, we show that this prior is proper and has no finite moments. We also investigate the impact of this default prior on the a priori distribution of the number of species and the a priori probability of discovery of a new species, which are usually employed in subjective prior elicitation. The effect of the Jeffreys prior for posterior inference is illustrated using examples arising in the context of inference for species sampling models and Dirichlet process mixt…
Banks and financial institutions all over the world manage portfolios containing tens of thousands of customers. Not all customers are high credit-worthy, and many possess varying degrees of risk to the Bank or financial institutions that lend money to these customers. Hence assessment of credit risk is paramount in the field of credit risk management. This paper discusses the use of Bayesian principles and simulation-techniques to estimate and calibrate the default probability of credit ratings. The methodology is a two-phase approach where, in the first phase, a posterior density of default …
Managing risk at the aggregate level is crucial for banks and financial institutions as required by the Basel III framework. In this paper, we introduce discrete time Bayesian state space models with Poisson measurements to model aggregate mortgage default rate. We discuss parameter updating, filtering, smoothing, forecasting and estimation using Markov chain Monte Carlo methods. In addition, we investigate the dynamic behavior of the default rate and the effects of macroeconomic variables. We illustrate the use of the proposed models using actual U.S. residential mortgage data and discuss ins…
We propose a non-parametric, two-sample Bayesian test for checking whether or not two data sets share a common distribution. The test makes use of data splitting ideas and does not require priors for high-dimensional parameter vectors as do other nonparametric Bayesian procedures. We provide evidence that the new procedure provides more stable Bayes factors than do methods based on Pólya trees. Somewhat surprisingly, the behavior of the proposed Bayes factors when the two distributions are the same is usually superior to that of Pólya tree Bayes factors. We showcase the effectiveness of the te…
Multiple imputation is a common approach for dealing with missing values in statistical databases. The imputer fills in missing values with draws from predictive models estimated from the observed data, resulting in multiple, completed versions of the database. Researchers have developed a variety of default routines to implement multiple imputation; however, there has been limited research comparing the performance of these methods, particularly for categorical data. We use simulation studies to compare repeated sampling properties of three default multiple imputation methods for categorical …
With the advent of so-called default Bayesian hypothesis tests, scientists in applied fields have gained access to a powerful and principled method for testing hypotheses. However, such default tests usually come with a compromise, requiring the analyst to accept a one-size-fits-all approach to hypothesis testing. Further, such tests may not have the flexibility to test problems the scientist really cares about. In this tutorial, I demonstrate a flexible approach to generalizing one specific default test (the JZS t-test; Rouder et al., 2009) that is becoming increasingly popular in the social …
This paper proposes a strategy for regularized estimation in multi-way contingency tables, which are common in meta-analyses and multi-center clinical trials. Our approach is based on data augmentation, and appeals heavily to a novel class of Polya-Gamma distributions. Our main contributions are to build up the relevant distributional theory and to demonstrate three useful features of this data-augmentation scheme. First, it leads to simple EM and Gibbs-sampling algorithms for posterior inference, circumventing the need for analytic approximations, numerical integration, Metropolis--Hastings, …
Scientific theories can often be formulated using equality and order constraints on the relative effects in a linear regression model. For example, it may be expected that the effect of the first predictor is larger than the effect of the second predictor, and the second predictor is expected to be larger than the third predictor. The goal is then to test such expectations against competing scientific expectations or theories. In this paper a simple default Bayes factor test is proposed for testing multiple hypotheses with equality and order constraints on the effects of interest. The proposed…
Credit risk modelling is an integral part of the global financial system. While there has been great attention paid to neural network models for credit default prediction, such models often lack the required interpretation mechanisms and measures of the uncertainty around their predictions. This work develops and compares Bayesian Neural Networks(BNNs) for credit card default modelling. This includes a BNNs trained by Gaussian approximation and the first implementation of BNNs trained by Hybrid Monte Carlo(HMC) in credit risk modelling. The results on the Taiwan Credit Dataset show that BNNs w…
This note is a discussion commenting on the paper by Ly et al. on "Harold Jeffreys's Default Bayes Factor Hypothesis Tests: Explanation, Extension, and Application in Psychology" and on the perceived shortcomings of the classical Bayesian approach to testing, while reporting on an alternative approach advanced by Kamary, Mengersen, Robert and Rousseau (2014. arxiv:1412.2044) as a solution to this quintessential inference problem.
We exploit a suitable moment-based characterization of the mixture of Poisson distribution for developing Bayesian inference for the unknown size of a finite population whose units are subject to multiple occurrences during an enumeration sampling stage. This is a particularly challenging setting for which many other attempts have been made for inferring the unknown characteristics of the population. Here we put particular emphasis on the construction of a default prior elicitation of the characteristics of the mixing distribution. We assess the comparative performance of our approach in real …
In social and biomedical sciences testing in contingency tables often involves order restrictions on cell-probabilities parameters. We develop objective Bayes methods for order-constrained testing and model comparison when observations arise under product binomial or multinomial sampling. Specifically, we consider tests for monotone order of the parameters against equality of all parameters. Our strategy combines in a unified way both the intrinsic prior methodology and the encompassing prior approach in order to compute Bayes factors and posterior model probabilities. Performance of our metho…
We propose an objective Bayesian approach to the selection of covariates and their penalised splines transformations in generalised additive models. Specification of a reasonable default prior for the model parameters and combination with a multiplicity-correction prior for the models themselves is crucial for this task. Here we use well-studied and well-behaved continuous mixtures of g-priors as default priors. We introduce the methodology in the normal model and extend it to non-normal exponential families. A simulation study and an application from the literature illustrate the proposed app…
When the sample size is not too small, M-estimators of regression coefficients are approximately normal and unbiased. This leads to the familiar frequentist inference in terms of normality-based confidence intervals and p-values. From a Bayesian perspective, use of the (improper) uniform prior yields matching results in the sense that posterior quantiles agree with one-sided confidence bounds. For this, and various other reasons, the uniform prior is often considered objective or non-informative. In spite of this, we argue that the uniform prior is not suitable as a default prior for inference…
This article concerns testing for equality of distribution between groups. We focus on screening variables with shared distributional features such as common support, modes and patterns of skewness. We propose a Bayesian testing method using kernel mixtures, which improves performance by borrowing information across the different variables and groups through shared kernels and a common probability of group differences. The inclusion of shared kernels in a finite mixture, with Dirichlet priors on the weights, leads to a simple framework for testing that scales well for high-dimensional data. We…
For Bayesian D-optimal design, we define a singular prior distribution for the model parameters as a prior distribution such that the determinant of the Fisher information matrix has a prior geometric mean of zero for all designs. For such a prior distribution, the Bayesian D-optimality criterion fails to select a design. For the exponential decay model, we characterize singularity of the prior distribution in terms of the expectations of a few elementary transformations of the parameter. For a compartmental model and several multi-parameter generalized linear models, we establish sufficient c…
We consider evaluating improper priors in a formal Bayes setting according to the consequences of their use. Let $Φ$ be a class of functions on the parameter space and consider estimating elements of $Φ$ under quadratic loss. If the formal Bayes estimator of every function in $Φ$ is admissible, then the prior is strongly admissible with respect to $Φ$. Eaton's method for establishing strong admissibility is based on studying the stability properties of a particular Markov chain associated with the inferential setting. In previous work, this was handled differently depending upon whether $ϕ\in …
Bayesian hypothesis testing is re-examined from the perspective of an a priori assessment of the test statistic distribution under the alternative. By assessing the distribution of an observable test statistic, rather than prior parameter values, we provide a practical default Bayes factor which is straightforward to interpret. To illustrate our methodology, we provide examples where evidence for a Bayesian strikingly supports the null, but leads to rejection under a classical test. Finally, we conclude with directions for future research.
Computational convenience has led to widespread use of Bayesian inference with vague or flat priors to analyze state-space models in ecology. Vague priors are claimed to be objective and to let the data speak. Neither of these claims is valid. Statisticians have criticized the use of vague priors from philosophical to computational to pragmatic reasons. Ecologists, however, dismiss such criticisms as empty philosophical wonderings with no practical implications. We illustrate that use of vague priors in population viability analysis and occupancy models can have significant impact on the analy…
In this paper, I develop a formula for estimating Bayes factors directly from minimal summary statistics produced in repeated measures analysis of variance designs. The formula, which requires knowing only the $F$-statistic, the number of subjects, and the number of repeated measurements per subject, is based on the BIC approximation of the Bayes factor, a common default method for Bayesian computation with linear models. In addition to providing computational examples, I report a simulation study in which I demonstrate that the formula compares favorably to a recently developed, more complex …
There has been a tremendous methodological development of Bayes factors for hypothesis testing in the social and behavioral sciences, and related fields. This development is due to the flexibility of the Bayes factor for testing multiple hypotheses simultaneously, the ability to test complex hypotheses involving equality as well as order constraints on the parameters of interest, and the interpretability of the outcome as the weight of evidence provided by the data in support of competing scientific theories. The available software tools for Bayesian hypothesis testing are still limited howeve…
This paper develops new insights into quantitative methods for the validation of computational model prediction. Four types of methods are investigated, namely classical and Bayesian hypothesis testing, a reliability-based method, and an area metric-based method. Traditional Bayesian hypothesis testing is extended based on interval hypotheses on distribution parameters and equality hypotheses on probability distributions, in order to validate models with deterministic/stochastic output for given inputs. Two types of validation experiments are considered - fully characterized (all the model/exp…
Motivated by the statistical evaluation of complex computer models, we deal with the issue of objective prior specification for the parameters of Gaussian processes. In particular, we derive the Jeffreys-rule, independence Jeffreys and reference priors for this situation, and prove that the resulting posterior distributions are proper under a quite general set of conditions. A proper flat prior strategy, based on maximum likelihood estimates, is also considered, and all priors are then compared on the grounds of the frequentist properties of the ensuing Bayesian procedures. Computational issue…
This is a companion paper to Yarkoni and Westfall (2017), which describes the Python package Bambi for estimating Bayesian generalized linear mixed models using a simple interface. Here I give the statistical details underlying the default, weakly informative priors used in all models when the user does not specify the priors. Our approach is to first deduce what the variances of the slopes would be if we were instead to have defined the priors on the partial correlation scale, and then to set independent Normal priors on the slopes with variances equal to these implied variances. Our approach…
We recently proposed a general algorithm for approximating nonstandard Bayesian posterior distributions by minimization of their Kullback-Leibler divergence with respect to a more convenient approximating distribution. In this note we offer details on how to efficiently implement this algorithm in practice. We also suggest default choices for the form of the posterior approximation, the number of iterations, the step size, and other user choices. By using these defaults it becomes possible to construct good posterior approximations for hierarchical models completely automatically.
Testing the equality of two proportions is a common procedure in science, especially in medicine and public health. In these domains it is crucial to be able to quantify evidence for the absence of a treatment effect. Bayesian hypothesis testing by means of the Bayes factor provides one avenue to do so, requiring the specification of prior distributions for parameters. The most popular analysis approach views the comparison of proportions from a contingency table perspective, assigning prior distributions directly to the two proportions. Another, less popular approach views the problem from a …
On the Computational Efficiency of Bayesian Additive Regression Trees: An Asymptotic Analysis
Department of Statistics and Data Science, National University of Singapore（统计与数据科学系，新加坡国立大学）；Department of Statistics, UC Berkeley（统计系，加州大学伯克利分校）；Department of Electrical Engineering and Computer Sciences, UC Berkeley（电气工程与计算机科学系，加州大学伯克利分校）；Center for Computational Biology, UC Berkeley（计算生物学中心，加州大学伯克利分校）
The Savage-Dickey density ratio is a specific expression of the Bayes factor when testing a precise (equality constrained) hypothesis against an unrestricted alternative. The expression greatly simplifies the computation of the Bayes factor at the cost of assuming a specific form of the prior under the precise hypothesis as a function of the unrestricted prior. A generalization was proposed by Verdinelli and Wasserman (1995) such that the priors can be freely specified under both hypotheses while keeping the computational advantage. This paper presents an extension of this generalization when …
Gaussian factor models have proven widely useful for parsimoniously characterizing dependence in multivariate data. There is a rich literature on their extension to mixed categorical and continuous variables, using latent Gaussian variables or through generalized latent trait models acommodating measurements in the exponential family. However, when generalizing to non-Gaussian measured variables the latent variables typically influence both the dependence structure and the form of the marginal distributions, complicating interpretation and introducing artifacts. To address this problem we prop…
Assuming a banded structure is one of the common practice in the estimation of high-dimensional precision matrix. In this case, estimating the bandwidth of the precision matrix is a crucial initial step for subsequent analysis. Although there exist some consistent frequentist tests for the bandwidth parameter, bandwidth selection consistency for precision matrices has not been established in a Bayesian framework. In this paper, we propose a prior distribution tailored to the bandwidth estimation of high-dimensional precision matrices. The banded structure is imposed via the Cholesky factor fro…
We propose optimal Bayesian two-sample tests for testing equality of high-dimensional mean vectors and covariance matrices between two populations. In many applications including genomics and medical imaging, it is natural to assume that only a few entries of two mean vectors or covariance matrices are different. Many existing tests that rely on aggregating the difference between empirical means or covariance matrices are not optimal or yield low power under such setups. Motivated by this, we develop Bayesian two-sample tests employing a divide-and-conquer idea, which is powerful especially wh…
This paper introduces the R package BayesVarSel which implements objective Bayesian methodology for hypothesis testing and variable selection in linear models. The package computes posterior probabilities of the competing hypotheses/models and provides a suite of tools, specifically proposed in the literature, to properly summarize the results. Additionally, \ourpack\ is armed with functions to compute several types of model averaging estimations and predictions with weights given by the posterior probabilities. BayesVarSel contains exact algorithms to perform fast computations in problems of …
Uniformly most powerful Bayesian tests (UMPBT's) are an objective class of Bayesian hypothesis tests that can be considered the Bayesian counterpart of classical uniformly most powerful tests. Because the rejection regions of UMPBT's can be matched to the rejection regions of classical uniformly most powerful tests (UMPTs), UMPBT's provide a mechanism for calibrating Bayesian evidence thresholds, Bayes factors, classical significance levels and p-values. The purpose of this article is to expand the application of UMPBT's outside the class of exponential family models. Specifically, we introduc…
In this paper, we propose novel, fully Bayesian non-parametric tests for one-sample and two-sample multivariate location problems. We model the underlying distribution using a Dirichlet process prior, and develop a testing procedure based on the posterior credible region for the spatial median functional of the distribution. For the one-sample problem, we fail to reject the null hypothesis if the credible set contains the null value. For the two-sample problem, we form a credible set for the difference of the spatial medians of the two samples and we fail to reject the null hypothesis of equal…
Bayesian Species Distribution Models using Hierarchical Decomposition Priors
Department of Economics University of Modena and Reggio Emilia（摩德纳和雷焦艾米利亚大学经济系）；Department of Statistical Sciences University of Bologna（博洛尼亚大学统计科学系）；Department of Life Sciences and Systems Biology University of Turin（都灵大学生命科学与系统生物学系）
Correlated proportions arise in longitudinal (panel) studies. A typical example is the ``opinion swing'' problem: ``Has the proportion of people favoring a politician changed after his recent speech to the nation on TV?''. Since the same group of individuals is interviewed before and after the speech, the two proportions are correlated. A natural null hypothesis to be tested is whether the corresponding population proportions are equal. A standard Bayesian approach to this problem has already been considered in the literature, based on a Dirichlet prior for the cell-probabilities of the underl…
