Regression models for dichotomous data are ubiquitous in statistics. Besides being useful for inference on binary responses, these methods serve also as building blocks in more complex formulations, such as density regression, nonparametric classification and graphical models. Within the Bayesian framework, inference proceeds by updating the priors for the coefficients, typically set to be Gaussians, with the likelihood induced by probit or logit regressions for the responses. In this updating, the apparent absence of a tractable posterior has motivated a variety of computational methods, including Markov Chain Monte Carlo routines and algorithms which approximate the posterior. Despite being routinely implemented, Markov Chain Monte Carlo strategies face mixing or time-inefficiency issues in large p and small n studies, whereas approximate routines fail to capture the skewness typically observed in the posterior. This article proves that the posterior distribution for the probit coefficients has a unified skew-normal kernel, under Gaussian priors. Such a novel result allows efficient Bayesian inference for a wide class of applications, especially in large p and small-to-moderate n studies where state-of-the-art computational methods face notable issues. These advances are outlined in a genetic study, and further motivate the development of a wider class of conjugate priors for probit models along with methods to obtain independent and identically distributed samples from the unified skew-normal posterior.
A broad class of models that routinely appear in several fields can be expressed as partially or fully discretized Gaussian linear regressions. Besides including basic Gaussian response settings, this class also encompasses probit, multinomial probit and tobit regression, among others, thereby yielding to one of the most widely-implemented families of models in applications. The relevance of such representations has stimulated decades of research in the Bayesian field, mostly motivated by the fact that, unlike for Gaussian linear regression, the posterior distribution induced by such models do…
Correlated binary response data with covariates are ubiquitous in longitudinal or spatial studies. Among the existing statistical models the most well-known one for this type of data is the multivariate probit model, which uses a Gaussian link to model dependence at the latent level. However, a symmetric link may not be appropriate if the data are highly imbalanced. Here, we propose a multivariate skew-elliptical link model for correlated binary responses, which includes the multivariate probit model as a special case. Furthermore, we perform Bayesian inference for this new model and prove tha…
Multinomial probit (mnp) models are fundamental and widely-applied regression models for categorical data. Fasano and Durante (2022) proved that the class of unified skew-normal distributions is conjugate to several mnp sampling models. This allows to develop Monte Carlo samplers and accurate variational methods to perform Bayesian inference. In this paper, we adapt the abovementioned results for a popular special case: the discrete-choice mnp model under zero mean and independent Gaussian priors. This allows to obtain simplified expressions for the parameters of the posterior distribution and…
This article proposes Multinomial Probit Bayesian Additive Regression Trees (MPBART) as a multinomial probit extension of BART - Bayesian Additive Regression Trees (Chipman et al (2010)). MPBART is flexible to allow inclusion of predictors that describe the observed units as well as the available choice alternatives. Through two simulation studies and four real data examples, we show that MPBART exhibits very good predictive performance in comparison to other discrete choice and multiclass classification methods. To implement MPBART, we have developed an R package mpbart available freely from …
Fitted probabilities from widely used Bayesian multinomial probit models can depend strongly on the choice of a base category, which is used to uniquely identify the parameters of the model. This paper proposes a novel identification strategy, and associated prior distribution for the model parameters, that renders the prior symmetric with respect to relabeling the outcome categories. The new prior permits an efficient Gibbs algorithm that samples rank-deficient covariance matrices without resorting to Metropolis-Hastings updates.
Multinomial probit models are routinely-implemented representations for learning how the class probabilities of categorical response data change with p observed predictors. Although several frequentist methods have been developed for estimation, inference and classification within such a class of models, Bayesian inference is still lagging behind. This is due to the apparent absence of a tractable class of conjugate priors, that may facilitate posterior inference on the multinomial probit coefficients. Such an issue has motivated increasing efforts toward the development of effective Markov ch…
In this article, we consider Markov chain Monte Carlo(MCMC) algorithms for exploring the intractable posterior density associated with Bayesian probit linear mixed models under improper priors on the regression coefficients and variance components. In particular, we construct the two-block Gibbs sampler using the data augmentation (DA) techniques. Furthermore, we prove geometric ergodicity of the Gibbs sampler, which is the foundation for building central limit theorems for MCMC based estimators and subsequent inferences. The conditions for geometric convergence are similar to those guaranteei…
In this paper, we present a Weibull link (skewed) model for categorical response data arising from binomial as well as multinomial model. We show that, for such types of categorical data, the most commonly used models (logit, probit and complementary log-log) can be obtained as limiting cases. We further compare the proposed model with some other asymmetrical models. The Bayesian as well as frequentist estimation procedures for binomial and multinomial data responses are presented in details. The analysis of two data sets to show the efficiency of the proposed model is performed.
We propose a Bayesian approach to estimating parameters in multiclass functional models. Unordered multinomial probit, ordered multinomial probit and multinomial logistic models are considered. We use finite random series priors based on a suitable basis such as B-splines in these three multinomial models, and classify the functional data using the Bayes rule. We average over models based on the marginal likelihood estimated from Markov Chain Monte Carlo (MCMC) output. Posterior contraction rates for the three multinomial models are computed. We also consider Bayesian linear and quadratic disc…
Trinity College（都柏林圣三一学院）；Dalle Molle Institute for Artificial Intelligence Research (IDSIA)（达尔莫尔人工智能研究所（IDSIA））
Skew-Gaussian processes (SkewGPs) extend the multivariate Unified Skew-Normal distributions over finite dimensional vectors to distribution over functions. SkewGPs are more general and flexible than Gaussian processes, as SkewGPs may also represent asymmetric distributions. In a recent contribution we showed that SkewGP and probit likelihood are conjugate, which allows us to compute the exact posterior for non-parametric binary classification and preference learning. In this paper, we generalize previous results and we prove that SkewGP is conjugate with both the normal and affine probit likel…
The use of MCMC algorithms in high dimensional Bayesian problems has become routine. This has spurred so-called convergence complexity analysis, the goal of which is to ascertain how the convergence rate of a Monte Carlo Markov chain scales with sample size, $n$, and/or number of covariates, $p$. This article provides a thorough convergence complexity analysis of Albert and Chib's (1993) data augmentation algorithm for the Bayesian probit regression model. The main tools used in this analysis are drift and minorization conditions. The usual pitfalls associated with this type of analysis are av…
The Bayesian probit regression model (Albert and Chib (1993)) is popular and widely used for binary regression. While the improper flat prior for the regression coefficients is an appropriate choice in the absence of any prior information, a proper normal prior is desirable when prior information is available or in modern high dimensional settings where the number of coefficients ($p$) is greater than the sample size ($n$). For both choices of priors, the resulting posterior density is intractable and a Data Dugmentation (DA) Markov chain is used to generate approximate samples from the poster…
We present a class of sparse generalized linear models that include probit and logistic regression as special cases and offer some extra flexibility. We provide an EM algorithm for learning the parameters of these models from data. We apply our method in text classification and in simulated data and show that our method outperforms the logistic and probit models and also the elastic net, in general by a substantial margin.
We perform a Bayesian analysis of the p-variate skew-t model, providing a new parameterization, a set of non-informative priors and a sampler specifically designed to explore the posterior density of the model parameters. Extensions, such as the multivariate regression model with skewed errors and the stochastic frontiers model, are easily accommodated. A novelty introduced in the paper is given by the extension of the bivariate skew-normal model given in Liseo & Parisi (2013) to a more realistic p-variate skew-t model. We also introduce the R package mvst, which allows to estimate the multiva…
Skewed probit regression is but one example of a statistical model that generalizes a simpler model, like probit regression. All skew-symmetric distributions and link functions arise from symmetric distributions by incorporating a skewness parameter through some skewing mechanism. In this work we address some fundamental issues in skewed probit regression, and more genreally skew-symmetric distributions or skew-symmetric link functions. We address the issue of identifiability of the skewed probit model parameters by reformulating the intercept from first principles. A new standardization of th…
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The state-of-the-art approach uses a phylogenetic multivariate probit model to accommodate binary and continuous traits via a latent variable framework, and utilizes an efficient bouncy particle sampler (BPS) to tackle the computational bottleneck -- integrating many latent variables from a high-dimensional truncated normal distribution. This approach breaks down as the number…
Harvey et al. (2010) extended the Bayesian estimation method by Sahu et al. (2003) to a multivariate skew-elliptical distribution with a general skewness matrix, and applied it to Bayesian portfolio optimization with higher moments. Although their method is epochal in the sense that it can handle the skewness dependency among asset returns and incorporate higher moments into portfolio optimization, it cannot identify all elements in the skewness matrix due to label switching in the Gibbs sampler. To deal with this identification issue, we propose to modify their sampling algorithm by imposing …
Job interviews are a fundamental activity for most corporations to acquire potential candidates, and for job seekers to get well-rewarded and fulfilling career opportunities. In many cases, interviews are conducted in multiple processes such as telephone interviews and several face-to-face interviews. At each stage, candidates are evaluated in various aspects. Among them, grade evaluation, such as a rating on a 1-4 scale, might be used as a reasonable method to evaluate candidates. However, because each evaluation is based on a subjective judgment of interviewers, the aggregated evaluations ca…
A nonparametric and locally adaptive Bayesian estimator is proposed for estimating a binary regression. Flexibility is obtained by modeling the binary regression as a mixture of probit regressions with the argument of each probit regression having a thin plate spline prior with its own smoothing parameter and with the mixture weights depending on the covariates. The estimator is compared to a single spline estimator and to a recently proposed locally adaptive estimator. The methodology is illustrated by applying it to both simulated and real examples.
Convergence fragility in probit Bayesian kernel machine regression implemented in the bkmr R package for binary-outcome environmental mixture analyses: a simulation study
Chiba University（千叶大学）；Institute of Science Tokyo（东京科学大学）；Tokyo University of Science（东京理科大学）；Meisei University（明海大学）
Insurance risks data typically exhibit skewed behaviour. In this paper, we propose a Bayesian approach to capture the main features of these datasets. This work extends the methodology introduced in Villa and Walker (2014a) by considering an extra parameter which captures the skewness of the data. In particular, a skewed Student-t distribution is considered. Two datasets are analysed: the Danish fire losses and the US indemnity loss. The analysis is carried with an objective Bayesian approach. For the discrete parameter representing the number of the degrees of freedom, we adopt a novel prior …
This paper describes a new Bayesian interpretation of a class of skew--Student $t$ distributions. We consider a hierarchical normal model with unknown covariance matrix and show that by imposing different restrictions on the parameter space, corresponding Bayes predictive density estimators under Kullback-Leibler loss function embrace some well-known skew--Student $t$ distributions. We show that obtained estimators perform better in terms of frequentist risk function over regular Bayes predictive density estimators. We apply our proposed methods to estimate future densities of medical data: th…
Skewed generalizations of the normal distribution have been a topic of great interest in the statistics community due to their diverse applications across several domains. One of the most popular skew normal distributions, due to its intuitive appeal, is the Azzalini's skew normal distribution. However, due to the nature of the distribution it suffers from serious inferential problems. Interestingly, the Bayesian approach has been shown to mitigate these issues. Recently, another skew normal distribution, the Geometric skew normal distribution, which is structurally different from Azzalini's s…
We consider probabilistic multinomial probit classification using Gaussian process (GP) priors. The challenges with the multiclass GP classification are the integration over the non-Gaussian posterior distribution, and the increase of the number of unknown latent variables as the number of target classes grows. Expectation propagation (EP) has proven to be a very accurate method for approximate inference but the existing EP approaches for the multinomial probit GP classification rely on numerical quadratures or independence assumptions between the latent values from different classes to facili…
Multivariate stochastic volatility models with skew distributions are proposed. Exploiting Cholesky stochastic volatility modeling, univariate stochastic volatility processes with leverage effect and generalized hyperbolic skew t-distributions are embedded to multivariate analysis with time-varying correlations. Bayesian prior works allow this approach to provide parsimonious skew structure and to easily scale up for high-dimensional problem. Analyses of daily stock returns are illustrated. Empirical results show that the time-varying correlations and the sparse skew structure contribute to im…
The multivariate extended skew-normal distribution allows for accommodating raw data which are skewed and heavy tailed, and has at least three appealing statistical properties, namely closure under conditioning, affine transformations, and marginalization. In this paper we propose a Bayesian computational approach based on a sequential Monte Carlo (SMC) sampler to estimate such distributions. The practical implementation of each step of the algorithm is discussed and the elicitation of prior distributions takes into consideration some unusual behaviour of the likelihood function and the corres…
A brief comment on A variational Bayesian approach for inverse problems with skew-t error distributions (Guha et al., Journal of Computational Physics 301 (2015) 377-393) is given in this letter.
Bayesian additive regression tree (BART) models have seen increased attention in recent years as a general-purpose nonparametric modeling technique. BART combines the flexibility of modern machine learning techniques with the principled uncertainty quantification of Bayesian inference, and it has been shown to be uniquely appropriate for addressing the high-noise problems that occur commonly in many areas of science, including medicine and the social sciences. This paper introduces the SoftBart package for fitting the Soft BART algorithm of Linero and Yang (2018). In addition to improving upon…
It has become increasingly common to collect high-dimensional binary response data; for example, with the emergence of new sampling techniques in ecology. In smaller dimensions, multivariate probit (MVP) models are routinely used for inferences. However, algorithms for fitting such models face issues in scaling up to high dimensions due to the intractability of the likelihood, involving an integral over a multivariate normal distribution having no analytic form. Although a variety of algorithms have been proposed to approximate this intractable integral, these approaches are difficult to imple…
Non-Gaussian mixture models are gaining increasing attention for mixture model-based clustering particularly when dealing with data that exhibit features such as skewness and heavy tails. Here, such a mixture distribution is presented, based on the multivariate normal inverse Gaussian (MNIG) distribution. For parameter estimation of the mixture, a Bayesian approach via Gibbs sampler is used; for this, a novel approach to simulate univariate generalized inverse Gaussian random variables and matrix generalized inverse Gaussian random matrices is provided. The proposed algorithm will be applied t…
Motivated by the analysis of the distribution of university grades, which is usually asymmetric, we discuss two informative priors for the shape parameter of the skew-normal distribution, showing that they lead to closed-form full-conditional posterior distributions, particularly useful in MCMC computation. Gibbs sampling algorithms are discussed for the joint vector of parameters, given independent prior distributions for the location and scale parameters. Simulation studies are performed to assess the performance of Gibbs samplers and to compare the choice of informative priors against a non…
We present a proposal to deal with the non-normality issue in the context of regression models with measurement errors when both the response and the explanatory variable are observed with error. We extend the normal model by jointly modeling the unobserved covariate and the random errors by a finite mixture of scale mixture of skew-normal distributions. This approach allows us to model data with great flexibility, accommodating skewness, heavy tails, and multi-modality.
University of Limerick（利默里克大学）；Dalle Molle Institute for Artificial Intelligence Research (IDSIA)（达勒莫勒人工智能研究所（IDSIA））
Gaussian processes (GPs) are distributions over functions, which provide a Bayesian nonparametric approach to regression and classification. In spite of their success, GPs have limited use in some applications, for example, in some cases a symmetric distribution with respect to its mean is an unreasonable model. This implies, for instance, that the mean and the median coincide, while the mean and median in an asymmetric (skewed) distribution can be different numbers. In this paper, we propose Skew-Gaussian processes (SkewGPs) as a non-parametric prior over functions. A SkewGP extends the multi…
Most Item Response Theory (IRT) models for dichotomous responses are based on probit or logit link functions which assume a symmetric relationship between the probability of a correct response and the latent traits of individuals submitted to a test. This assumption restricts the use of those models to the case in which all items have a symmetric behaviour. On the other hand, asymmetric models proposed in the literature impose that all the items in a test have an asymmetric behaviour. This assumption is inappropriate for great part of the tests which are, in general, composed by both symmetric…
An efficient adaptive dimension selection algorithm for multidimensional probit graded response models
KLATASDS-MOE；School of Statistics, East China Normal University（东华大学统计学院）；Zhiyuan School of Liberal Arts,Beijing Institute of Petrochemical Technology（北京石油化学工业技术学院人文学院）
We formalise and generalise the definition of the family of univariate double two--piece distributions, obtained by using a density--based transformation of unimodal symmetric continuous distributions with a shape parameter. The resulting distributions contain five interpretable parameters that control the mode, as well as the scale and shape in each direction. Four-parameter subfamilies of this class of distributions that capture different types of asymmetry are discussed. We propose interpretable scale and location-invariant benchmark priors and derive conditions for the propriety of the cor…
The marginal likelihood is a well established model selection criterion in Bayesian statistics. It also allows to efficiently calculate the marginal posterior model probabilities that can be used for Bayesian model averaging of quantities of interest. For many complex models, including latent modeling approaches, marginal likelihoods are however difficult to compute. One recent promising approach for approximating the marginal likelihood is Integrated Nested Laplace Approximation (INLA), design for models with latent Gaussian structures. In this study we compare the approximations obtained wit…
Frequentist and likelihood methods of inference based on the multivariate skew-normal model encounter several technical difficulties with this model. In spite of the popularity of this class of densities, there are no broadly satisfactory solutions for estimation and testing problems. A general population Monte Carlo algorithm is proposed which: 1) exploits the latent structure stochastic representation of skew-normal random variables to provide a full Bayesian analysis of the model and 2) accounts for the presence of constraints in the parameter space. The proposed approach can be defined as …
