Multi-group covariance estimation for matrix-variate data with small within group sample sizes is a key part of many data analysis tasks in modern applications. To obtain accurate group-specific covariance estimates, shrinkage estimation methods which shrink an unstructured, group-specific covariance either across groups towards a pooled covariance or within each group towards a Kronecker structure have been developed. However, in many applications, it is unclear which approach will result in more accurate covariance estimates. In this article, we present a hierarchical prior distribution which flexibly allows for both types of shrinkage. The prior linearly combines shrinkage across groups towards a shared pooled covariance and shrinkage within groups towards a group-specific Kronecker covariance. We illustrate the utility of the proposed prior in speech recognition and an analysis of chemical exposure data.
Since the emergence of genome-wide association studies (GWASs), estimation of the narrow sense heritability explained by common single-nucleotide polymorphisms (SNPs) via linear mixed model approaches became widely used. As in most GWASs, most of the heritability analyses are performed using univariate approaches i.e. considering each phenotype independently. In this study, we propose a Bayesian matrix-variate mixed model that takes into account the genetic correlation between phenotypes in addition to the genetic correlation between individuals which is usually modelled via a relatedness matr…
We undertake Bayesian learning of the high-dimensional functional relationship between a system parameter vector and an observable, that is in general tensor-valued. The ultimate aim is Bayesian inverse prediction of the system parameters, at which test data is recorded. We attempt such learning given hypercuboidally-shaped data that displays strong discontinuities, rendering learning challenging. We model the sought high-dimensional function, with a tensor-variate Gaussian Process (GP), and use three independent ways for learning covariance matrices of the resulting likelihood, which is Tenso…
Tensor-variate Gaussian process regression for efficient emulation of complex systems: comparing regressor and covariance structures in outer product and parallel partial emulators
We present a method for modelling the covariance structure of tensor-variate data, with the ulterior aim of learning an unknown model parameter vector using such data. We express the high-dimensional observable as a function of this sought model parameter vector, and attempt to learn such a high-dimensional function given training data, by modelling it as a realisation from a tensor-variate Gaussian Process (GP). The likelihood of the unknowns given training data, is then tensor-normal. We choose vague priors on the unknown GP parameters (mean tensor and covariance matrices) and write the post…
We illustrate the use of the R-package "rstiefel" for matrix-variate data analysis in the context of two examples. The first example considers estimation of a reduced-rank mean matrix in the presence of normally distributed noise. The second example considers the modeling of a social network of friendships among teenagers. Bayesian estimation for these models requires the ability to simulate from the matrix-variate von Mises-Fisher distributions and the matrix-variate Bingham distributions on the Stiefel manifold.
Bayesian Gaussian Mixture Modeling for Symmetric Matrix Variate Data
University of Washington（华盛顿大学）；Australian National University（澳大利亚国立大学）；Virginia Commonwealth University（弗吉尼亚联邦大学）；William & Mary’s Batten School of Coastal & Marine Sciences, Virginia Institute of Marine Science（威廉玛丽学院巴滕沿海与海洋科学学院，弗吉尼亚海洋科学研究所）；University of Waterloo（滑铁卢大学）
Bayesian model comparison relies upon the model evidence, yet for many models of interest the model evidence is unavailable in closed form and must be approximated. Many of the estimators for evidence that have been proposed in the Monte Carlo literature suffer from high variability. This paper considers the reduction of variance that can be achieved by exploiting control variates in this setting. Our methodology is based on thermodynamic integration and applies whenever the gradient of both the log-likelihood and the log-prior with respect to the parameters can be efficiently evaluated. Resul…
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…
This article introduces an R package to perform statistical analysis for task-based fMRI data at both individual and group levels. The analysis to detect brain activation at the individual level is based on modeling the fMRI signal using Matrix-Variate Dynamic Linear Models (MDLM). Therefore, the analysis for the group stage is based on posterior distributions of the state parameter obtained from the modeling at the individual level. In this way, this package offers several R functions with different algorithms to perform inference on the state parameter to assess brain activation for both ind…
A Bayesian approach is used to estimate the covariance matrix of Gaussian data. Ideas from Gaussian graphical models and model selection are used to construct a prior for the covariance matrix that is a mixture over all decomposable graphs. For this prior the probability of each graph size is specified by the user and graphs of equal size are assigned equal probability. Most previous approaches assume that all graphs are equally probable. We show empirically that the prior that assigns equal probability over graph sizes outperforms the prior that assigns equal probability over all graphs, both…
Covariance estimation and selection for multivariate datasets in a high-dimensional regime is a fundamental problem in modern statistics. Gaussian graphical models are a popular class of models used for this purpose. Current Bayesian methods for inverse covariance matrix estimation under Gaussian graphical models require the underlying graph and hence the ordering of variables to be known. However, in practice, such information on the true underlying model is often unavailable. We therefore propose a novel permutation-based Bayesian approach to tackle the unknown variable ordering issue. In pa…
We consider the problem of estimating high-dimensional covariance matrices of a particular structure, which is a summation of low rank and sparse matrices. This covariance structure has a wide range of applications including factor analysis and random effects models. We propose a Bayesian method of estimating the covariance matrices by representing the covariance model in the form of a factor model with unknown number of latent factors. We introduce binary indicators for factor selection and rank estimation for the low rank component combined with a Bayesian lasso method for the sparse compone…
Gaussian process (GP) covariance function is proposed as a matching tool in GPMatch within a full Bayesian framework under relatively weaker causal assumptions. The matching is accomplished by utilizing GP prior covariance function to define matching distance. We show that GPMatch provides a doubly robust estimate of the averaged treatment effect (ATE) much like the G-estimation, the ATE is correctly estimated when either conditions are satisfied: 1) the GP mean function correctly specifies potential outcome \(Y^{(0)}\); or 2) the GP covariance function correctly specifies matching structure. …
In this work we present full Bayesian inference for a new flexible nonseparable class of cross-covariance functions for multivariate spatial data. A Bayesian test is proposed for separability of covariance functions which is much more interpretable than parameters related to separability. Spatial models have been increasingly applied in several areas, such as environmental science, climate science and agriculture. These data are usually available in space, time and possibly for several processes. In this context the modeling of dependence is crucial for correct uncertainty quantification and r…
This paper is considered with joint estimation of state and time-varying noise covariance matrices in non-linear stochastic state space models. We present a variational Bayes and Gaussian filtering based algorithm for efficient computation of the approximate filtering posterior distributions. The Gaussian filtering based formulation of the non-linear state space model computation allows usage of efficient Gaussian integration methods such as unscented transform, cubature integration and Gauss-Hermite integration along with the classical Taylor series approximations. The performance of the algo…
Conditional neural control variates for variance reduction in Bayesian inverse problems
Department of Computer Science University of Central Florida（计算机科学系佛罗里达中央大学）；Department of Physics and Maryland Center for Fundamental Physics University of Maryland College Park（物理系马里兰根本物理中心马里兰大学学院公园分校）
Cluster-weighted models (CWMs) extend finite mixtures of regressions (FMRs) in order to allow the distribution of covariates to contribute to the clustering process. In a matrix-variate framework, the matrix-variate normal CWM has been recently introduced. However, problems may be encountered when data exhibit skewness or other deviations from normality in the responses, covariates or both. Thus, we introduce a family of 24 matrix-variate CWMs which are obtained by allowing both the responses and covariates to be modelled by using one of four existing skewed matrix-variate distributions or the…
In this paper we develop an inverse Bayesian approach to find the value of the unknown model parameter vector that supports the real (or test) data, where the data comprises measurements of a matrix-variate variable. The method is illustrated via the estimation of the unknown Milky Way feature parameter vector, using available test and simulated (training) stellar velocity data matrices. The data is represented as an unknown function of the model parameters, where this high-dimensional function is modelled using a high-dimensional Gaussian Process (${\cal GP}$). The model for this function is …
Covariance matrix estimation arises in multivariate problems including multivariate normal sampling models and regression models where random effects are jointly modeled, e.g. random-intercept, random-slope models. A Bayesian analysis of these problems requires a prior on the covariance matrix. Here we assess, through a simulation study and a real data set, the impact this prior choice has on posterior inference of the covariance matrix. Inverse Wishart distribution is the natural choice for a covariance matrix prior because its conjugacy on normal model and simplicity, is usually available in…
Tensor-valued data are being encountered increasingly more commonly, in the biological, natural as well as the social sciences. The learning of the unknown model parameter vector given such data, involves covariance modelling of such data, though this can be difficult owing to the high-dimensional nature of the data, where the numerical challenge of such modelling can only be compounded by the largeness of the available data set. Assuming such data to be modelled using a correspondingly high-dimensional Gaussian Process (${\cal GP}$), the joint density of a finite set of such data sets is then…
Regression-based optimal fingerprinting techniques for climate change detection and attribution require the estimation of the forced signal as well as the internal variability covariance matrix in order to distinguish between their influences in the observational record. While previously developed approaches have taken into account the uncertainty linked to the estimation of the forced signal, there has been less focus on uncertainty in the covariance matrix describing natural variability, despite the fact that the specification of this covariance matrix is known to meaningfully impact the res…
Transposable data represents interactions among two sets of entities, and are typically represented as a matrix containing the known interaction values. Additional side information may consist of feature vectors specific to entities corresponding to the rows and/or columns of such a matrix. Further information may also be available in the form of interactions or hierarchies among entities along the same mode (axis). We propose a novel approach for modeling transposable data with missing interactions given additional side information. The interactions are modeled as noisy observations from a la…
Diffusion tensor imaging (DTI) is a popular magnetic resonance imaging technique used to characterize microstructural changes in the brain. DTI studies quantify the diffusion of water molecules in a voxel using an estimated 3x3 symmetric positive definite diffusion tensor matrix. Statistical analysis of DTI data is challenging because the data are positive definite matrices. Matrix-variate information is often summarized by a univariate quantity, such as the fractional anisotropy (FA), leading to a loss of information. Furthermore, DTI analyses often ignore the spatial association of neighbori…
Modeling correlation (and covariance) matrices can be challenging due to the positive-definiteness constraint and potential high-dimensionality. Our approach is to decompose the covariance matrix into the correlation and variance matrices and propose a novel Bayesian framework based on modeling the correlations as products of unit vectors. By specifying a wide range of distributions on a sphere (e.g. the squared-Dirichlet distribution), the proposed approach induces flexible prior distributions for covariance matrices (that go beyond the commonly used inverse-Wishart prior). For modeling real-…
This paper deals with the problem of estimating predictive densities of a matrix-variate normal distribution with known covariance matrix. Our main aim is to establish some Bayesian predictive densities related to matricial shrinkage estimators of the normal mean matrix. The Kullback-Leibler loss is used for evaluating decision-theoretical optimality of predictive densities. It is shown that a proper hierarchical prior yields an admissible and minimax predictive density. Also, superharmonicity of prior densities is paid attention to for finding out a minimax predictive density with good numeri…
This paper focuses on Bayesian shrinkage for covariance matrix estimation. We examine posterior properties and frequentist risks of Bayesian estimators based on new hierarchical inverse-Wishart priors. More precisely, we give the existence conditions of the posterior distributions. Advantages in terms of numerical simulations of posteriors are shown. A simulation study illustrates the performance of the estimation procedures under three loss functions for relevant sample sizes and various covariance structures.
Functional data, with basic observational units being functions (e.g., curves, surfaces) varying over a continuum, are frequently encountered in various applications. While many statistical tools have been developed for functional data analysis, the issue of smoothing all functional observations simultaneously is less studied. Existing methods often focus on smoothing each individual function separately, at the risk of removing important systematic patterns common across functions. We propose a nonparametric Bayesian approach to smooth all functional observations simultaneously and nonparametr…
In this work, we propose a modeling procedure for fMRI data analysis using a Bayesian Matrix-Variate Dynamic Linear Model (MVDLM). With this type of model, less complex than the more traditional temporal-spatial models, we are able to take into account the temporal and -- at least locally -- the spatial structures that are usually present in this type of data. Despite employing a voxel-wise approach, every voxel in the brain is jointly modeled with its nearest neighbors, which are defined through a euclidian metric. MVDLM's have been widely used in applications where the interest lies in to pe…
A separable covariance model for a random matrix provides a parsimonious description of the covariances among the rows and among the columns of the matrix, and permits likelihood-based inference with a very small sample size. However, in many applications the assumption of exact separability is unlikely to be met, and data analysis with a separable model may overlook or misrepresent important dependence patterns in the data. In this article, we propose a compromise between separable and unstructured covariance estimation. We show how the set of covariance matrices may be uniquely parametrized …
Gaussian graphical models are used for determining conditional relationships between variables. This is accomplished by identifying off-diagonal elements in the inverse-covariance matrix that are non-zero. When the ratio of variables (p) to observations (n) approaches one, the maximum likelihood estimator of the covariance matrix becomes unstable and requires shrinkage estimation. Whereas several classical (frequentist) methods have been introduced to address this issue, fully Bayesian methods remain relatively uncommon in practice and methodological literatures. Here we introduce a Bayesian m…
The University of Electro-Communications（电气通信大学）；National Police Agency Info-Communications Bureau（警察厅信息通信局）
In this paper, we propose a Bayesian Graphical LASSO for correlated countable data and apply it to spatial crime data. In the proposed model, we assume a Gaussian Graphical Model for the latent variables which dominate the potential risks of crimes. To evaluate the proposed model, we determine optimal hyperparameters which represent samples better. We apply the proposed model for estimation of the sparse inverse covariance of the latent variable and evaluate the partial correlation coefficients. Finally, we illustrate the results on crime spots data and consider the estimated latent variables …
We consider a statistical model for pairs of traded assets, based on a Cointegrated Vector Auto Regression (CVAR) Model. We extend standard CVAR models to incorporate estimation of model parameters in the presence of price series level shifts which are not accurately modeled in the standard Gaussian error correction model (ECM) framework. This involves developing a novel matrix variate Bayesian CVAR mixture model comprised of Gaussian errors intra-day and Alpha-stable errors inter-day in the ECM framework. To achieve this we derive a novel conjugate posterior model for the Scaled Mixtures of N…
The paper addresses joint sparsity selection in the regression coefficient matrix and the error precision (inverse covariance) matrix for high-dimensional multivariate regression models in the Bayesian paradigm. The selected sparsity patterns are crucial to help understand the network of relationships between the predictor and response variables, as well as the conditional relationships among the latter. While Bayesian methods have the advantage of providing natural uncertainty quantification through posterior inclusion probabilities and credible intervals, current Bayesian approaches either r…
We propose a novel hierarchical model for multitask bipartite ranking. The proposed approach combines a matrix-variate Gaussian process with a generative model for task-wise bipartite ranking. In addition, we employ a novel trace constrained variational inference approach to impose low rank structure on the posterior matrix-variate Gaussian process. The resulting posterior covariance function is derived in closed form, and the posterior mean function is the solution to a matrix-variate regression with a novel spectral elastic net regularizer. Further, we show that variational inference for the…
Although there is a rich literature on methods for allowing the variance in a univariate regression model to vary with predictors, time and other factors, relatively little has been done in the multivariate case. Our focus is on developing a class of nonparametric covariance regression models, which allow an unknown p x p covariance matrix to change flexibly with predictors. The proposed modeling framework induces a prior on a collection of covariance matrices indexed by predictors through priors for predictor-dependent loadings matrices in a factor model. In particular, the predictor-dependen…
University of Toronto（多伦多大学）；Vector Institute（向量研究所）
Variational Bayesian neural networks combine the flexibility of deep learning with Bayesian uncertainty estimation. However, inference procedures for flexible variational posteriors are computationally expensive. A recently proposed method, noisy natural gradient, is a surprisingly simple method to fit expressive posteriors by adding weight noise to regular natural gradient updates. Noisy K-FAC is an instance of noisy natural gradient that fits a matrix-variate Gaussian posterior with minor changes to ordinary K-FAC. Nevertheless, a matrix-variate Gaussian posterior does not capture an accurat…
This paper proposes a Bayesian framework for localization of multiple sources in the event of accidental hazardous contaminant release. The framework assimilates sensor measurements of the contaminant concentration with an integrated multizone computational fluid dynamics (multizone-CFD) based contaminant fate and transport model. To ensure online tractability, the framework uses deep Gaussian process (DGP) based emulator of the multizone-CFD model. To effectively represent the transient response of the multizone-CFD model, the DGP emulator is reformulated using a matrix-variate Gaussian proce…
We obtain the optimal Bayesian minimax rate for the unconstrained large covariance matrix of multivariate normal sample with mean zero, when both the sample size, n, and the dimension, p, of the covariance matrix tend to infinity. Traditionally the posterior convergence rate is used to compare the frequentist asymptotic performance of priors, but defining the optimality with it is elusive. We propose a new decision theoretic framework for prior selection and define Bayesian minimax rate. Under the proposed framework, we obtain the optimal Bayesian minimax rate for the spectral norm for all rat…
The paper presents a novel approach to direct covariance function learning for Bayesian optimisation, with particular emphasis on experimental design problems where an existing corpus of condensed knowledge is present. The method presented borrows techniques from reproducing kernel Banach space theory (specifically m-kernels) and leverages them to convert (or re-weight) existing covariance functions into new, problem-specific covariance functions. The key advantage of this approach is that rather than relying on the user to manually select (with some hyperparameter tuning and experimentation) …
