Linear mixed models are able to handle an extraordinary range of complications in regression-type analyses. Their most common use is to account for within-subject correlation in longitudinal data analysis. They are also the standard vehicle for smoothing spatial count data. However, when treated in full generality, mixed models can also handle spline-type smoothing and closely approximate kriging. This allows for nonparametric regression models (e.g., additive models and varying coefficient models) to be handled within the mixed model framework. The key is to allow the random effects design matrix to have general structure; hence our label general design. For continuous response data, particularly when Gaussianity of the response is reasonably assumed, computation is now quite mature and supported by the R, SAS and S-PLUS packages. Such is not the case for binary and count responses, where generalized linear mixed models (GLMMs) are required, but are hindered by the presence of intractable multivariate integrals. Software known to us supports special cases of the GLMM (e.g., PROC NLMIXED in SAS or glmmML in R) or relies on the sometimes crude Laplace-type approximation of integrals (e.g., the SAS macro glimmix or glmmPQL in R). This paper describes the fitting of general design generalized linear mixed models. A Bayesian approach is taken and Markov chain Monte Carlo (MCMC) is used for estimation and inference. In this generalized setting, MCMC requires sampling from nonstandard distributions. In this article, we demonstrate that the MCMC package WinBUGS facilitates sound fitting of general design Bayesian generalized linear mixed models in practice.
In this article, we construct a two-block Gibbs sampler using Polson et al. (2013) data augmentation technique with Polya-Gamma latent variables for Bayesian logistic linear mixed models under proper priors. Furthermore, we prove the uniform ergodicity of this Gibbs sampler, which guarantees the existence of the central limit theorems for MCMC based estimators.
Assume we observe a finite number of inspection times together with information on whether a specific event has occurred before each of these times. Suppose replicated measurements are available on multiple event times. The set of inspection times, including the number of inspections, may be different for each event. This is known as mixed case interval censored data. We consider Bayesian estimation of the distribution function of the event time while assuming it is concave. We provide sufficient conditions on the prior such that the resulting procedure is consistent from the Bayesian point of…
Although continuous density estimation has received abundant attention in the Bayesian nonparametrics literature, there is limited theory on multivariate mixed scale density estimation. In this note, we consider a general framework to jointly model continuous, count and categorical variables under a nonparametric prior, which is induced through rounding latent variables having an unknown density with respect to Lebesgue measure. For the proposed class of priors, we provide sufficient conditions for large support, strong consistency and rates of posterior contraction. These conditions allow one…
We consider nonparametric estimation of a mixed discrete-continuous distribution under anisotropic smoothness conditions and possibly increasing number of support points for the discrete part of the distribution. For these settings, we derive lower bounds on the estimation rates in the total variation distance. Next, we consider a nonparametric mixture of normals model that uses continuous latent variables for the discrete part of the observations. We show that the posterior in this model contracts at rates that are equal to the derived lower bounds up to a log factor. Thus, Bayesian mixture o…
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…
We study a parametric estimation problem related to moment condition models. As an alternative to the generalized empirical likelihood (GEL) and the generalized method of moments (GMM), a Bayesian approach to the problem can be adopted, extending the MEM procedure to parametric moment conditions. We show in particular that a large number of GEL estimators can be interpreted as a maximum entropy solution. Moreover, we provide a more general field of applications by proving the method to be robust to approximate moment conditions.
Bayesian tests on the symmetry of the generalized von Mises model for planar directions (Gatto and Jammalamadaka, 2007) are introduced. The generalized von Mises distribution is a flexible model that can be axially symmetric or asymmetric, unimodal or bimodal. A characterization of axial symmetry is provided and taken as null hypothesis for one of the proposed Bayesian tests. The Bayesian tests are obtained by the technique of probability perturbation. The prior probability measure is perturbed so to give a positive prior probability to the null hypothesis, which would be null otherwise. This …
The emergence of big data has led to a growing interest in so-called convergence complexity analysis, which is the study of how the convergence rate of a Monte Carlo Markov chain (for an intractable Bayesian posterior distribution) scales as the underlying data set grows in size. Convergence complexity analysis of practical Monte Carlo Markov chains on continuous state spaces is quite challenging, and there have been very few successful analyses of such chains. One fruitful analysis was recently presented by Qin and Hobert (2021b), who studied a Gibbs sampler for a simple Bayesian random effec…
We consider Bayesian model selection in generalized linear models that are high-dimensional, with the number of covariates p being large relative to the sample size n, but sparse in that the number of active covariates is small compared to p. Treating the covariates as random and adopting an asymptotic scenario in which p increases with n, we show that Bayesian model selection using certain priors on the set of models is asymptotically equivalent to selecting a model using an extended Bayesian information criterion. Moreover, we prove that the smallest true model is selected by either of these…
Exploration of the intractable posterior distributions associated with Bayesian versions of the general linear mixed model is often performed using Markov chain Monte Carlo. In particular, if a conditionally conjugate prior is used, then there is a simple two-block Gibbs sampler available. Román and Hobert [Linear Algebra Appl. 473 (2015) 54-77] showed that, when the priors are proper and the $X$ matrix has full column rank, the Markov chains underlying these Gibbs samplers are nearly always geometrically ergodic. In this paper, Román and Hobert's (2015) result is extended by allowing improper…
Bayesian analysis of data from the general linear mixed model is challenging because any nontrivial prior leads to an intractable posterior density. However, if a conditionally conjugate prior density is adopted, then there is a simple Gibbs sampler that can be employed to explore the posterior density. A popular default among the conditionally conjugate priors is an improper prior that takes a product form with a flat prior on the regression parameter, and so-called power priors on each of the variance components. In this paper, a convergence rate analysis of the corresponding Gibbs sampler i…
We review and contrast frequentist and Bayesian definitions of tolerance regions. We give conditions under which for large samples a Bayesian region also has frequentist validity, and study the latter for smaller samples in a simulation study. We discuss a computational strategy for computing a Bayesian two-sided tolerance interval for a Gaussian future variable, and apply this to the case of possibly unbalanced linear mixed models. We illustrate the method on a quality control experiment from the pharmaceutical industry.
To extend several known centered Gaussian processes, we introduce a new centered mixed self-similar Gaussian process called the mixed generalized fractional Brownian motion, which could serve as a good model for a larger class of natural phenomena. This process generalizes both the well known mixed fractional Brownian motion introduced by Cheridito [10] and the generalized fractional Brownian motion introduced by Zili [31]. We study its main stochastic properties, its non-Markovian and non-stationarity characteristics and the conditions under which it is not a semimartingale. We prove the long…
Leiden University（莱顿大学）；CWI（荷兰国家数学与计算机科学研究所）；University of Oxford（牛津大学）；University of Victoria（维多利亚大学）
We study generalized Bayesian inference under misspecification, i.e. when the model is 'wrong but useful'. Generalized Bayes equips the likelihood with a learning rate $η$. We show that for generalized linear models (GLMs), $η$-generalized Bayes concentrates around the best approximation of the truth within the model for specific $η\neq 1$, even under severely misspecified noise, as long as the tails of the true distribution are exponential. We derive MCMC samplers for generalized Bayesian lasso and logistic regression and give examples of both simulated and real-world data in which generalize…
Trinity College Dublin（都柏林圣三一学院）；Eindhoven University of Technology（埃因霍温理工大学）
A fundamental task in AI is to assess (in)dependence between mixed-type variables (text, image, sound). We propose a Bayesian kernelised correlation test of (in)dependence using a Dirichlet process model. The new measure of (in)dependence allows us to answer some fundamental questions: Based on data, are (mixed-type) variables independent? How likely is dependence/independence to hold? How high is the probability that two mixed-type variables are more than just weakly dependent? We theoretically show the properties of the approach, as well as algorithms for fast computation with it. We empiric…
Dalhousie University（达尔豪斯大学）；University of Science（理大学）；Vietnam National University（越南国立大学）；AISIA Research Lab（AISIA研究实验室）；University of Delaware（特拉华大学）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）
In this paper, we study the learning rate of generalized Bayes estimators in a general setting where the hypothesis class can be uncountable and have an irregular shape, the loss function can have heavy tails, and the optimal hypothesis may not be unique. We prove that under the multi-scale Bernstein's condition, the generalized posterior distribution concentrates around the set of optimal hypotheses and the generalized Bayes estimator can achieve fast learning rate. Our results are applied to show that the standard Bayesian linear regression is robust to heavy-tailed distributions.
This paper describes a new library for learning Bayesian networks from data containing discrete and continuous variables (mixed data). In addition to the classical learning methods on discretized data, this library proposes its algorithm that allows structural learning and parameters learning from mixed data without discretization since data discretization leads to information loss. This algorithm based on mixed MI score function for structural learning, and also linear regression and Gaussian distribution approximation for parameters learning. The library also offers two algorithms for enumer…
The paper is motivated from clustering problem in high-throughput mixed datasets. Clustering of such datasets can provide much insight into biological associations. An open problem in this context is to simultaneously cluster high-dimensional mixed dataset. This paper fills that gap and proposes a nonparametric Bayesian method called Gen-VariScan for biclustering of high-dimensional mixed dataset. Gen-VariScan utilizes Generalized Linear Models (GLM), and latent variable approaches to integrate mixed dataset. We make use of Poisson Dirichlet Process (PDP) to identify a lower dimensional struct…
This paper builds on recent research that focuses on regression modeling of continuous bounded data, such as proportions measured on a continuous scale. Specifically, it deals with beta regression models with mixed effects from a Bayesian approach. We use a suitable parameterization of the beta law in terms of its mean and a precision parameter, and allow both parameters to be modeled through regression structures that may involve fixed and random effects. Specification of prior distributions is discussed, computational implementation via Gibbs sampling is provided, and illustrative examples a…
Ordinal cumulative probability models (CPMs) -- also known as cumulative link models -- such as the proportional odds regression model are typically used for discrete ordered outcomes, but can accommodate both continuous and mixed discrete/continuous outcomes since these are also ordered. Recent papers describe ordinal CPMs in this setting using non-parametric maximum likelihood estimation. We formulate a Bayesian CPM for continuous or mixed outcome data. Bayesian CPMs inherit many of the benefits of frequentist CPMs and have advantages with regard to interpretation, flexibility, and exact inf…
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 …
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…
Brain and Spine Institute（脑与脊柱研究所）；ETH（苏黎世联邦理工学院）；INSERM（法国国家健康与医学研究院）
This note is concerned with an accurate and computationally efficient variational bayesian treatment of mixed-effects modelling. We focus on group studies, i.e. empirical studies that report multiple measurements acquired in multiple subjects. When approached from a bayesian perspective, such mixed-effects models typically rely upon a hierarchical generative model of the data, whereby both within- and between-subject effects contribute to the overall observed variance. The ensuing VB scheme can be used to assess statistical significance at the group level and/or to capture inter-individual dif…
Institute for Computing and Information Sciences（计算与信息科学研究所）；Radboud University Nijmegen（拉德堡德大学奈梅亨分校）
We consider the problem of learning parameters of latent variable models from mixed (continuous and ordinal) data with missing values. We propose a novel Bayesian Gaussian copula factor (BGCF) approach that is consistent under certain conditions and that is quite robust to the violations of these conditions. In simulations, BGCF substantially outperforms two state-of-the-art alternative approaches. An illustration on the `Holzinger & Swineford 1939' dataset indicates that BGCF is favorable over the so-called robust maximum likelihood (MLR) even if the data match the assumptions of MLR.
We consider the problems of hypothesis testing and model comparison under a flexible Bayesian linear regression model whose formulation is closely connected with the linear mixed effect model and the parametric models for SNP set analysis in genetic association studies. We derive a class of analytic approximate Bayes factors and illustrate their connections with a variety of frequentist test statistics, including the Wald statistic and the variance component score statistic. Taking advantage of Bayesian model averaging and hierarchical modeling, we demonstrate some distinct advantages and flex…
Gaussian random field (GRF) models are widely used in spatial statistics to capture spatially correlated error. We investigate the results of replacing Gaussian processes with Laplace moving averages (LMAs) in spatial generalized linear mixed models (SGLMMs). We demonstrate that LMAs offer improved predictive power when the data exhibits localized spikes in the response. SGLMMs with LMAs are shown to maintain analogous parameter inference and similar computing to Gaussian SGLMMs. We propose a novel discrete space LMA model for irregular lattices and construct conjugate samplers for LMAs with g…
We investigate the issue of bandwidth estimation in a nonparametric functional regression model with function-valued, continuous real-valued and discrete-valued regressors under the framework of unknown error density. Extending from the recent work of Shang (2013, Computational Statistics & Data Analysis), we approximate the unknown error density by a kernel density estimator of residuals, where the regression function is estimated by the functional Nadaraya-Watson estimator that admits mixed types of regressors. We derive a kernel likelihood and posterior density for the bandwidth parameters …
The mixed-logit model is a flexible tool in transportation choice analysis, which provides valuable insights into inter and intra-individual behavioural heterogeneity. However, applications of mixed-logit models are limited by the high computational and data requirements for model estimation. When estimating on small samples, the Bayesian estimation approach becomes vulnerable to over and under-fitting. This is problematic for investigating the behaviour of specific population sub-groups or market segments with low data availability. Similar challenges arise when transferring an existing model…
Generalized linear mixed models (GLMM) encompass large class of statistical models, with a vast range of applications areas. GLMM extends the linear mixed models allowing for different types of response variable. Three most common data types are continuous, counts and binary and standard distributions for these types of response variables are Gaussian, Poisson and Binomial, respectively. Despite that flexibility, there are situations where the response variable is continuous, but bounded, such as rates, percentages, indexes and proportions. In such situations the usual GLMM's are not adequate …
Mixed effects regression models are widely used by language researchers. However, these regressions are implemented with an algorithm which may not converge on a solution. While convergence issues in linear mixed effects models can often be addressed with careful experiment design and model building, logistic mixed effects models introduce the possibility of separation or quasi-separation, which can cause problems for model estimation that result in convergence errors or in unreasonable model estimates. These problems cannot be solved by experiment or model design. In this paper, we discuss (q…
Variational inference methods have been shown to lead to significant improvements in the computational efficiency of approximate Bayesian inference in mixed multinomial logit models when compared to standard Markov-chain Monte Carlo (MCMC) methods without compromising accuracy. However, despite their demonstrated efficiency gains, existing methods still suffer from important limitations that prevent them to scale to very large datasets, while providing the flexibility to allow for rich prior distributions and to capture complex posterior distributions. In this paper, we propose an Amortized Va…
This paper demonstrates the advantages of sharing information about unknown features of covariates across multiple model components in various nonparametric regression problems including multivariate, heteroscedastic, and semi-continuous responses. In this paper, we present methodology which allows for information to be shared nonparametrically across various model components using Bayesian sum-of-tree models. Our simulation results demonstrate that sharing of information across related model components is often very beneficial, particularly in sparse high-dimensional problems in which variabl…
ONERA（法国国家航空航天研究中心）；Université de Toulouse（图卢兹大学）；ISAE-SUPAERO（法国国立高等航空航天学院）
Bayesian optimization methods have been successfully applied to black box optimization problems that are expensive to evaluate. In this paper, we adapt the so-called super effcient global optimization algorithm to solve more accurately mixed constrained problems. The proposed approach handles constraints by means of upper trust bound, the latter encourages exploration of the feasible domain by combining the mean prediction and the associated uncertainty function given by the Gaussian processes. On top of that, a refinement procedure, based on a learning rate criterion, is introduced to enhance…
The use of Bayesian information criterion (BIC) in the model selection procedure is under the assumption that the observations are independent and identically distributed (i.i.d.). However, in practice, we do not always have i.i.d. samples. For example, clustered observations tend to be more similar within the same group, and longitudinal data is collected by measuring the same subject repeatedly. In these scenarios, the assumption in BIC is not satisfied. The concept of effective sample size is brought up and improved BIC is defined by replacing the sample size in the original BIC expression …
Istituto Dalle Molle di Studi sull’Intelligenza Artificiale (IDSIA)（达勒莫勒人工智能研究所（IDSIA））；Ecole Polytechnique Fédérale de Lausanne (EPFL)（洛桑联邦理工学院（EPFL））
We commonly assume that data are a homogeneous set of observations when learning the structure of Bayesian networks. However, they often comprise different data sets that are related but not homogeneous because they have been collected in different ways or from different populations. In our previous work (Azzimonti, Corani and Scutari, 2021), we proposed a closed-form Bayesian Hierarchical Dirichlet score for discrete data that pools information across related data sets to learn a single encompassing network structure, while taking into account the differences in their probabilistic structures…
University of Oxford（牛津大学）；Amazon（亚马逊）；RMIT University（皇家墨尔本理工大学）
High-dimensional black-box optimisation remains an important yet notoriously challenging problem. Despite the success of Bayesian optimisation methods on continuous domains, domains that are categorical, or that mix continuous and categorical variables, remain challenging. We propose a novel solution -- we combine local optimisation with a tailored kernel design, effectively handling high-dimensional categorical and mixed search spaces, whilst retaining sample efficiency. We further derive convergence guarantee for the proposed approach. Finally, we demonstrate empirically that our method outp…
Many real-world optimisation problems are defined over both categorical and continuous variables, yet efficient optimisation methods such asBayesian Optimisation (BO) are not designed tohandle such mixed-variable search spaces. Recent approaches to this problem cast the selection of the categorical variables as a bandit problem, operating independently alongside a BO component which optimises the continuous variables. In this paper, we adopt a holistic view and aim to consolidate optimisation of the categorical and continuous sub-spaces under a single acquisition metric. We derive candidates f…
An augmented Lagrangian (AL) can convert a constrained optimization problem into a sequence of simpler (e.g., unconstrained) problems, which are then usually solved with local solvers. Recently, surrogate-based Bayesian optimization (BO) sub-solvers have been successfully deployed in the AL framework for a more global search in the presence of inequality constraints; however, a drawback was that expected improvement (EI) evaluations relied on Monte Carlo. Here we introduce an alternative slack variable AL, and show that in this formulation the EI may be evaluated with library routines. The sla…
With the arrival of the R packages nlme and lme4, linear mixed models (LMMs) have come to be widely used in experimentally-driven areas like psychology, linguistics, and cognitive science. This tutorial provides a practical introduction to fitting LMMs in a Bayesian framework using the probabilistic programming language Stan. We choose Stan (rather than WinBUGS or JAGS) because it provides an elegant and scalable framework for fitting models in most of the standard applications of LMMs. We ease the reader into fitting increasingly complex LMMs, first using a two-condition repeated measures sel…
Boosting methods are widely used in statistical learning to deal with high-dimensional data due to their variable selection feature. However, those methods lack straightforward ways to construct estimators for the precision of the parameters such as variance or confidence interval, which can be achieved by conventional statistical methods like Bayesian inference. In this paper, we propose a new inference method "BayesBoost" that combines boosting and Bayesian for linear mixed models to make the uncertainty estimation for the random effects possible on the one hand. On the other hand, the new m…
Most real optimization problems are defined over a mixed search space where the variables are both discrete and continuous. In engineering applications, the objective function is typically calculated with a numerically costly black-box simulation.General mixed and costly optimization problems are therefore of a great practical interest, yet their resolution remains in a large part an open scientific question. In this article, costly mixed problems are approached through Gaussian processes where the discrete variables are relaxed into continuous latent variables. The continuous space is more ea…
Bayesian Optimization (BO) has become a core method for solving expensive black-box optimization problems. While much research focussed on the choice of the acquisition function, we focus on online length-scale adaption and the choice of kernel function. Instead of choosing hyperparameters in view of maximum likelihood on past data, we propose to use the acquisition function to decide on hyperparameter adaptation more robustly and in view of the future optimization progress. Further, we propose a particular kernel function that includes non-stationarity and local anisotropy and thereby implici…
University of Cambridge（剑桥大学）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）；ETH Zurich（苏黎世联邦理工学院）
The optimization of expensive to evaluate, black-box, mixed-variable functions, i.e. functions that have continuous and discrete inputs, is a difficult and yet pervasive problem in science and engineering. In Bayesian optimization (BO), special cases of this problem that consider fully continuous or fully discrete domains have been widely studied. However, few methods exist for mixed-variable domains and none of them can handle discrete constraints that arise in many real-world applications. In this paper, we introduce MiVaBo, a novel BO algorithm for the efficient optimization of mixed-variab…
