We introduce a novel procedure for obtaining cross-validated predictive estimates for Bayesian hierarchical regression models (BHRMs). Bayesian hierarchical models are popular for their ability to model complex dependence structures and provide probabilistic uncertainty estimates, but can be computationally expensive to run. Cross-validation (CV) is therefore not a common practice to evaluate the predictive performance of BHRMs. Our method circumvents the need to re-run computationally costly estimation methods for each cross-validation fold and makes CV more feasible for large BHRMs. By conditioning on the variance-covariance parameters, we shift the CV problem from probability-based sampling to a simple and familiar optimization problem. In many cases, this produces estimates which are equivalent to full CV. We provide theoretical results and demonstrate its efficacy on publicly available data and in simulations.
We propose a nonparametric Bayesian factor regression model that accounts for uncertainty in the number of factors, and the relationship between factors. To accomplish this, we propose a sparse variant of the Indian Buffet Process and couple this with a hierarchical model over factors, based on Kingman's coalescent. We apply this model to two problems (factor analysis and factor regression) in gene-expression data analysis.
We propose a practical and scalable Gaussian process model for large-scale nonlinear probabilistic regression. Our mixture-of-experts model is conceptually simple and hierarchically recombines computations for an overall approximation of a full Gaussian process. Closed-form and distributed computations allow for efficient and massive parallelisation while keeping the memory consumption small. Given sufficient computing resources, our model can handle arbitrarily large data sets, without explicit sparse approximations. We provide strong experimental evidence that our model can be applied to lar…
We propose nonparametric Bayesian estimators for causal inference exploiting Regression Discontinuity/Kink (RD/RK) under sharp and fuzzy designs. Our estimators are based on Gaussian Process (GP) regression and classification. The GP methods are powerful probabilistic machine learning approaches that are advantageous in terms of derivative estimation and uncertainty quantification, facilitating RK estimation and inference of RD/RK models. These estimators are extended to hierarchical GP models with an intermediate Bayesian neural network layer and can be characterized as hybrid deep learning m…
University of Sheffield（谢菲尔德大学）；University of Oxford（牛津大学）
This paper introduces a new sparse spatio-temporal structured Gaussian process regression framework for online and offline Bayesian inference. This is the first framework that gives a time-evolving representation of the interdependencies between the components of the sparse signal of interest. A hierarchical Gaussian process describes such structure and the interdependencies are represented via the covariance matrices of the prior distributions. The inference is based on the expectation propagation method and the theoretical derivation of the posterior distribution is provided in the paper. Th…
Standard Gaussian Process (GP) regression, a powerful machine learning tool, is computationally expensive when it is applied to large datasets, and potentially inaccurate when data points are sparsely distributed in a high-dimensional feature space. To address these challenges, a new multiscale, sparsified GP algorithm is formulated, with the goal of application to large scientific computing datasets. In this approach, the data is partitioned into clusters and the cluster centers are used to define a reduced training set, resulting in an improvement over standard GPs in terms of training and e…
University of Washington（华盛顿大学）；University of Maryland, College Park（马里兰大学帕克分校）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）
One of the challenges in model-based control of stochastic dynamical systems is that the state transition dynamics are involved, and it is not easy or efficient to make good-quality predictions of the states. Moreover, there are not many representational models for the majority of autonomous systems, as it is not easy to build a compact model that captures the entire dynamical subtleties and uncertainties. In this work, we present a hierarchical Bayesian linear regression model with local features to learn the dynamics of a micro-robotic system as well as two simpler examples, consisting of a …
We propose the supervised hierarchical Dirichlet process (sHDP), a nonparametric generative model for the joint distribution of a group of observations and a response variable directly associated with that whole group. We compare the sHDP with another leading method for regression on grouped data, the supervised latent Dirichlet allocation (sLDA) model. We evaluate our method on two real-world classification problems and two real-world regression problems. Bayesian nonparametric regression models based on the Dirichlet process, such as the Dirichlet process-generalised linear models (DP-GLM) h…
Collected data, which is used for analysis or prediction tasks, often have a hierarchical structure, for example, data from various people performing the same task. Modeling the data's structure can improve the reliability of the derived results and prediction performance of newly unobserved data. Bayesian modeling provides a tool-kit for designing hierarchical models. However, Markov Chain Monte Carlo methods which are commonly used for parameter estimation are computationally expensive. This often renders its use for many applications not applicable. However, variational Bayesian methods all…
Radboud University（拉德堡德大学）；Radboud University Medical Centre（拉德堡德大学医学中心）；University of Oslo（奥斯陆大学）；Oslo University Hospital（奥斯陆大学医院）；King’s College London（伦敦国王学院）
Clinical neuroimaging has recently witnessed explosive growth in data availability which brings studying heterogeneity in clinical cohorts to the spotlight. Normative modeling is an emerging statistical tool for achieving this objective. However, its application remains technically challenging due to difficulties in properly dealing with nuisance variation, for example due to variability in image acquisition devices. Here, in a fully probabilistic framework, we propose an application of hierarchical Bayesian regression (HBR) for multi-site normative modeling. Our experimental results confirm t…
Considering the flexibility and applicability of Bayesian modeling, in this work we revise the main characteristics of two hierarchical models in a regression setting. We study the full probabilistic structure of the models along with the full conditional distribution for each model parameter. Under our hierarchical extensions, we allow the mean of the second stage of the model to have a linear dependency on a set of covariates. The Gibbs sampling algorithms used to obtain samples when fitting the models are fully described and derived. In addition, we consider a case study in which the plant …
MIT CSAIL（麻省理工学院计算机科学与人工智能实验室）；Broad Institute（博德研究所）
Hierarchical Bayesian methods enable information sharing across multiple related regression problems. While standard practice is to model regression parameters (effects) as (1) exchangeable across datasets and (2) correlated to differing degrees across covariates, we show that this approach exhibits poor statistical performance when the number of covariates exceeds the number of datasets. For instance, in statistical genetics, we might regress dozens of traits (defining datasets) for thousands of individuals (responses) on up to millions of genetic variants (covariates). When an analyst has mo…
Geographic Information Systems (GIS) and related technologies have generated substantial interest among statisticians with regard to scalable methodologies for analyzing large spatial datasets. A variety of scalable spatial process models have been proposed that can be easily embedded within a hierarchical modeling framework to carry out Bayesian inference. While the focus of statistical research has mostly been directed toward innovative and more complex model development, relatively limited attention has been accorded to approaches for easily implementable scalable hierarchical models for th…
Technische Universität Berlin（柏林工业大学）；University of California, San Francisco（加利福尼亚大学旧金山分校）；Central China Normal University（华中师范大学）；BIFOLD – Berlin Institute for the Foundations of Learning and Data（柏林学习与数据基础研究所）；Korea University（高丽大学）；Max Planck Institute for Informatics（马克斯·普朗克信息学研究所）；Physikalisch-Technische Bundesanstalt（德国联邦物理技术研究院）；Charité – Universitätsmedizin Berlin（柏林夏里特医学院）；Bernstein Center for Computational Neuroscience（伯恩斯坦计算神经科学中心）
Several problems in neuroimaging and beyond require inference on the parameters of multi-task sparse hierarchical regression models. Examples include M/EEG inverse problems, neural encoding models for task-based fMRI analyses, and climate science. In these domains, both the model parameters to be inferred and the measurement noise may exhibit a complex spatio-temporal structure. Existing work either neglects the temporal structure or leads to computationally demanding inference schemes. Overcoming these limitations, we devise a novel flexible hierarchical Bayesian framework within which the sp…
The problem of selecting the most useful features from a great many (eg, thousands) of candidates arises in many areas of modern sciences. An interesting problem from genomic research is that, from thousands of genes that are active (expressed) in certain tissue cells, we want to find the genes that can be used to separate tissues of different classes (eg. cancer and normal). In this paper, we report our empirical experiences of using Bayesian logistic regression based on heavy-tailed priors with moderately small degree freedom (such as 1) and very small scale, and using Hamiltonian Monte Carl…
We propose a novel Bayesian nonparametric method for hierarchical modelling on a set of related density functions, where grouped data in the form of samples from each density function are available. Borrowing strength across the groups is a major challenge in this context. To address this problem, we introduce a hierarchically structured prior, defined over a set of univariate density functions, using convenient transformations of Gaussian processes. Inference is performed through approximate Bayesian computation (ABC), via a novel functional regression adjustment. The performance of the propo…
In many applications, survey data are collected from different survey centers in different regions. It happens that in some circumstances, response variables are completely observed while the covariates have missing values. In this paper, we propose a joint spatial regression model for the response variable and missing covariates via a sequence of one-dimensional conditional spatial regression models. We further construct a joint spatial model for missing covariate data mechanisms. The properties of the proposed models are examined and a Markov chain Monte Carlo sampling algorithm is used to s…
Variable selection methods with nonlocal priors have been widely studied in linear regression models, and their theoretical and empirical performances have been reported. However, the crucial model selection properties for hierarchical nonlocal priors in high-dimensional generalized linear regression have rarely been investigated. In this paper, we consider a hierarchical nonlocal prior for high-dimensional logistic regression models and investigate theoretical properties of the posterior distribution. Specifically, a product moment (pMOM) nonlocal prior is imposed over the regression coeffici…
Diversity and inclusion, or D and I, is a topic that sparks the interest of companies, research groups, and individuals alike. Recently in the United States, renewed focus has been placed on fair and equitable pay practices, which are a key component of promoting diversity in the workplace. Despite the increased demand for reliable pay equity analysis, the challenges of conducting this type of analysis on industry data have not been adequately addressed. This paper explains a few limitations of current approaches to pay equity analysis by gender and improves on them with a Bayesian hierarchica…
In this paper a new Bayesian model for sparse linear regression with a spatio-temporal structure is proposed. It incorporates the structural assumptions based on a hierarchical Gaussian process prior for spike and slab coefficients. We design an inference algorithm based on Expectation Propagation and evaluate the model over the real data.
In low-resource settings where vital registration of death is not routine it is often of critical interest to determine and study the cause of death (COD) for individuals and the cause-specific mortality fraction (CSMF) for populations. Post-mortem autopsies, considered the gold standard for COD assignment, are often difficult or impossible to implement due to deaths occurring outside the hospital, expense, and/or cultural norms. For this reason, Verbal Autopsies (VAs) are commonly conducted, consisting of a questionnaire administered to next of kin recording demographic information, known med…
Reducing the global burden of stillbirths is important to improving child and maternal health. Of interest is understanding patterns in the timing of stillbirths -- that is, whether they occur in the intra- or antepartum period -- because stillbirths that occur intrapartum are largely preventable. However, data availability on the timing of stillbirths is highly variable across the world, with low- and middle-income countries generally having few reliable observations. In this paper we develop a Bayesian penalized splines regression framework to estimate the proportion of stillbirths that are …
The choice of tuning parameters in Bayesian variable selection is a critical problem in modern statistics. In particular, for Bayesian linear regression with non-local priors, the scale parameter in the non-local prior density is an important tuning parameter which reflects the dispersion of the non-local prior density around zero, and implicitly determines the size of the regression coefficients that will be shrunk to zero. Current approaches treat the scale parameter as given, and suggest choices based on prior coverage/asymptotic considerations. In this paper, we consider the fully Bayesian…
University of Torontoland（托伦托兰大学）；Googol ShallowMind；University of Edenborrow（伊登伯勒大学）
Making inferences from data streams is a pervasive problem in many modern data analysis applications. But it requires to address the problem of continuous model updating and adapt to changes or drifts in the underlying data generating distribution. In this paper, we approach these problems from a Bayesian perspective covering general conjugate exponential models. Our proposal makes use of non-conjugate hierarchical priors to explicitly model temporal changes of the model parameters. We also derive a novel variational inference scheme which overcomes the use of non-conjugate priors while mainta…
In recent years, much of the focus in monitoring child mortality has been on assessing changes in the under-five mortality rate (U5MR). However, as the U5MR decreases, the share of neonatal deaths (within the first month) tends to increase, warranting increased efforts in monitoring this indicator in addition to the U5MR. A Bayesian splines regression model is presented for estimating neonatal mortality rates (NMR) for all countries. In the model, the relationship between NMR and U5MR is assessed and used to inform estimates, and spline regression models are used to capture country-specific tr…
Large amounts of labeled data are typically required to train deep learning models. For many real-world problems, however, acquiring additional data can be expensive or even impossible. We present semi-supervised deep kernel learning (SSDKL), a semi-supervised regression model based on minimizing predictive variance in the posterior regularization framework. SSDKL combines the hierarchical representation learning of neural networks with the probabilistic modeling capabilities of Gaussian processes. By leveraging unlabeled data, we show improvements on a diverse set of real-world regression tas…
ETH Zürich（苏黎世联邦理工学院）；Max Planck ETH Center for Learning Systems（马克斯·普朗克-苏黎世联邦理工学院学习系统中心）；Max Planck Institute for Intelligent Systems, Tübingen（图宾根马克斯·普朗克智能系统研究所）
Gaussian processes are an important regression tool with excellent analytic properties which allow for direct integration of derivative observations. However, vanilla GP methods scale cubically in the amount of observations. In this work, we propose a novel approach for scaling GP regression with derivatives based on quadrature Fourier features. We then prove deterministic, non-asymptotic and exponentially fast decaying error bounds which apply for both the approximated kernel as well as the approximated posterior. To furthermore illustrate the practical applicability of our method, we then ap…
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.
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…
This paper is concerned with regularized extensions of hierarchical non-stationary temporal Gaussian processes (NSGPs) in which the parameters (e.g., length-scale) are modeled as GPs. In particular, we consider two commonly used NSGP constructions which are based on explicitly constructed non-stationary covariance functions and stochastic differential equations, respectively. We extend these NSGPs by including $L^1$-regularization on the processes in order to induce sparseness. To solve the resulting regularized NSGP (R-NSGP) regression problem we develop a method based on the alternating dire…
National statistical institutes in many countries are now mandated to produce reliable statistics for important variables such as population, income, unemployment, health outcomes, etc. for small areas, defined by geography and/or demography. Due to small samples from these areas, direct sample-based estimates are often unreliable. Model-based small area estimation is now extensively used to generate reliable statistics by "borrowing strength" from other areas and related variables through suitable models. Outliers adversely influence standard model-based small area estimates. To deal with out…
We investigate the statistical dependence of the peak intrinsic colors of Type Ia supernovae (SN Ia) on their expansion velocities at maximum light, measured from the Si II 6355 spectral feature. We construct a new hierarchical Bayesian regression model, accounting for the random effects of intrinsic scatter, measurement error, and reddening by host galaxy dust, and implement a Gibbs sampler and deviance information criteria to estimate the correlation. The method is applied to the apparent colors from BVRI light curves and Si II velocity data for 79 nearby SNe Ia. The apparent color distribut…
Majorization-minimization (MM) is a standard iterative optimization technique which consists in minimizing a sequence of convex surrogate functionals. MM approaches have been particularly successful to tackle inverse problems and statistical machine learning problems where the regularization term is a sparsity-promoting concave function. However, due to non-convexity, the solution found by MM depends on its initialization. Uniform initialization is the most natural and often employed strategy as it boils down to penalizing all coefficients equally in the first MM iteration. Yet, this arbitrary…
Variable selection techniques have become increasingly popular amongst statisticians due to an increased number of regression and classification applications involving high-dimensional data where we expect some predictors to be unimportant. In this context, Bayesian variable selection techniques involving Markov chain Monte Carlo exploration of the posterior distribution over models can be prohibitively computationally expensive and so there has been attention paid to quasi-Bayesian approaches such as maximum a posteriori (MAP) estimation using priors that induce sparsity in such estimates. We…
In linear regression models, fusion of coefficients is used to identify predictors having similar relationships with a response. This is called variable fusion. This paper presents a novel variable fusion method in terms of Bayesian linear regression models. We focus on hierarchical Bayesian models based on a spike-and-slab prior approach. A spike-and-slab prior is tailored to perform variable fusion. To obtain estimates of the parameters, we develop a Gibbs sampler for the parameters. Simulation studies and a real data analysis show that our proposed method achieves better performance than pr…
We propose a novel spike and slab prior specification with scaled beta prime marginals for the importance parameters of regression coefficients to allow for general effect selection within the class of structured additive distributional regression. This enables us to model effects on all distributional parameters for arbitrary parametric distributions, and to consider various effect types such as non-linear or spatial effects as well as hierarchical regression structures. Our spike and slab prior relies on a parameter expansion that separates blocks of regression coefficients into overall scal…
We investigate two empirical Bayes methods and a hierarchical Bayes method for adapting the scale of a Gaussian process prior in a nonparametric regression model. We show that all methods lead to a posterior contraction rate that adapts to the smoothness of the true regression function. Furthermore, we show that the corresponding credible sets cover the true regression function whenever this function satisfies a certain extrapolation condition. This condition depends on the specific method, but is implied by a condition of self-similarity. The latter condition is shown to be satisfied with pro…
A simple Bayesian approach to nonparametric regression is described using fuzzy sets and membership functions. Membership functions are interpreted as likelihood functions for the unknown regression function, so that with the help of a reference prior they can be transformed to prior density functions. The unknown regression function is decomposed into wavelets and a hierarchical Bayesian approach is employed for making inferences on the resulting wavelet coefficients.
We develop algorithms for performing semiparametric regression analysis in real time, with data processed as it is collected and made immediately available via modern telecommunications technologies. Our definition of semiparametric regression is quite broad and includes, as special cases, generalized linear mixed models, generalized additive models, geostatistical models, wavelet nonparametric regression models and their various combinations. Fast updating of regression fits is achieved by couching semiparametric regression into a Bayesian hierarchical model or, equivalently, graphical model …
Motivation: Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. Wang et al. (Bioinformatics, 2012) have developed an approach for the analysis of imaging genomic studies using penalized multi-task regression with regularization based on a novel group $l_{2,1}$-norm penalty which encourages structured sparsity at both the gene level and SNP level. While incorporating a number of useful features, the proposed method only furnishes a point estimate of the regression coefficients; tec…
We propose a novel Bayesian approach to the problem of variable selection in multiple linear regression models. In particular, we present a hierarchical setting which allows for direct specification of a-priori beliefs about the number of nonzero regression coefficients as well as a specification of beliefs that given coefficients are nonzero. To guarantee numerical stability, we adopt a $g$-prior with an additional ridge parameter for the unknown regression coefficients. In order to simulate from the joint posterior distribution an intelligent random walk Metropolis-Hastings algorithm which i…
We offer a general Bayes theoretic framework to derive posterior contraction rates under a hierarchical prior design: the first-step prior serves to assess the model selection uncertainty, and the second-step prior quantifies the prior belief on the strength of the signals within the model chosen from the first step. In particular, we establish non-asymptotic oracle posterior contraction rates under (i) a local Gaussianity condition on the log likelihood ratio of the statistical experiment, (ii) a local entropy condition on the dimensionality of the models, and (iii) a sufficient mass conditio…
In this study, we present a Bayesian hierarchical framework to model fluid-induced seismicity. The framework is based on a non-homogeneous Poisson process (NHPP) with a fluid-induced seismicity rate proportional to the rate of injected fluid. The fluid-induced seismicity rate model depends upon a set of physically meaningful parameters, and has been validated for six fluid-induced case studies. In line with the vision of hierarchical Bayesian modeling, the rate parameters are considered as random variables. We develop both the Bayesian inference and updating rules, which are used to develop a …
The problem motivating the paper is the quantification of students' preferences regarding teaching/coursework quality, under certain numerical restrictions, in order to build a model for identifying, assessing and monitoring the major components of the overall academic quality. After reviewing the strengths and limitations of conjoint analysis and of the random coefficient regression model used in similar problems in the past, we propose a Bayesian beta regression model with a Dirichlet prior on the model coefficients. This approach not only allows for the incorporation of informative prior wh…
In this paper we propose a new adaptive wavelet denoising methodology using complex wavelets. The method is based on a fully Bayesian hierarchical model in the complex wavelet domain that uses a bivariate mixture prior on the wavelet coefficients. The heart of the procedure is computational, where the posterior mean is computed through Markov chain Monte Carlo (MCMC) simulations. We show that the method has good performance, as demonstrated by simulations on the well-known test functions and by comparison to a well-established complex wavelet-based denoising procedure. An application to real-l…
Statistical modelling of sports data has become more and more popular in the recent years and different types of models have been proposed to achieve a variety of objectives: from identifying the key characteristics which lead a team to win or lose to predicting the outcome of a game or the team rankings in national leagues. Although not as popular as football or basketball, volleyball is a team sport with both national and international level competitions in almost every country. However, there is almost no study investigating the prediction of volleyball game outcomes and team rankings in na…
This paper proposes a novel graph-based regularized regression estimator - the hierarchical feature regression (HFR) -, which mobilizes insights from the domains of machine learning and graph theory to estimate robust parameters for a linear regression. The estimator constructs a supervised feature graph that decomposes parameters along its edges, adjusting first for common variation and successively incorporating idiosyncratic patterns into the fitting process. The graph structure has the effect of shrinking parameters towards group targets, where the extent of shrinkage is governed by a hype…
