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.
We implement gradient-based variational inference routines for Wishart and inverse Wishart processes, which we apply as Bayesian models for the dynamic, heteroskedastic covariance matrix of a multivariate time series. The Wishart and inverse Wishart processes are constructed from i.i.d. Gaussian processes, existing variational inference algorithms for which form the basis of our approach. These methods are easy to implement as a black-box and scale favorably with the length of the time series, however, they fail in the case of the Wishart process, an issue we resolve with a simple modification…
Functional data are defined as realizations of random functions (mostly smooth functions) varying over a continuum, which are usually collected with measurement errors on discretized grids. In order to accurately smooth noisy functional observations and deal with the issue of high-dimensional observation grids, we propose a novel Bayesian method based on the Bayesian hierarchical model with a Gaussian-Wishart process prior and basis function representations. We first derive an induced model for the basis-function coefficients of the functional data, and then use this model to conduct posterior…
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…
This paper revisits the Bayesian CMA-ES and provides updates for normal Wishart. It emphasizes the difference between a normal and normal inverse Wishart prior. After some computation, we prove that the only difference relies surprisingly in the expected covariance. We prove that the expected covariance should be lower in the normal Wishart prior model because of the convexity of the inverse. We present a mixture model that generalizes both normal Wishart and normal inverse Wishart model. We finally present various numerical experiments to compare both methods as well as the generalized method…
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…
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-…
Gaussian graphical models have received considerable attention during the past four decades from the statistical and machine learning communities. In Bayesian treatments of this model, the G-Wishart distribution serves as the conjugate prior for inverse covariance matrices satisfying graphical constraints. While it is straightforward to posit the unnormalized densities, the normalizing constants of these distributions have been known only for graphs that are chordal, or decomposable. Up until now, it was unknown whether the normalizing constant for a general graph could be represented explicit…
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…
Analysis of structural and functional connectivity (FC) of human brains is of pivotal importance for diagnosis of cognitive ability. The Human Connectome Project (HCP) provides an excellent source of neural data across different regions of interest (ROIs) of the living human brain. Individual specific data were available from an existing analysis (Dai et al., 2017) in the form of time varying covariance matrices representing the brain activity as the subjects perform a specific task. As a preliminary objective of studying the heterogeneity of brain connectomics across the population, we develo…
The prediction of the variance-covariance matrix of the multivariate normal distribution is important in the multivariate analysis. We investigated Bayesian predictive distributions for Wishart distributions under the Kullback-Leibler divergence. The conditional reducibility of the family of Wishart distributions enables us to decompose the risk of a Bayesian predictive distribution. We considered a recently introduced class of prior distributions, which is called the family of enriched standard conjugate prior distributions, and compared the Bayesian predictive distributions based on these pr…
The estimation of the covariance matrix is an initial step in many multivariate statistical methods such as principal components analysis and factor analysis, but in many practical applications the dimensionality of the sample space is large compared to the number of samples, and the usual maximum likelihood estimate is poor. Typically, improvements are obtained by modelling or regularization. From a practical point of view, these methods are often computationally heavy and rely on approximations. As a fast substitute, we propose an easily calculable maximum a posteriori (MAP) estimator based …
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…
We investigate the Student-t process as an alternative to the Gaussian process as a nonparametric prior over functions. We derive closed form expressions for the marginal likelihood and predictive distribution of a Student-t process, by integrating away an inverse Wishart process prior over the covariance kernel of a Gaussian process model. We show surprising equivalences between different hierarchical Gaussian process models leading to Student-t processes, and derive a new sampling scheme for the inverse Wishart process, which helps elucidate these equivalences. Overall, we show that a Studen…
Covariance estimation and selection for high-dimensional multivariate datasets is a fundamental problem in modern statistics. Gaussian directed acyclic graph (DAG) models are a popular class of models used for this purpose. Gaussian DAG models introduce sparsity in the Cholesky factor of the inverse covariance matrix, and the sparsity pattern in turn corresponds to specific conditional independence assumptions on the underlying variables. A variety of priors have been developed in recent years for Bayesian inference in DAG models, yet crucial convergence and sparsity selection properties for t…
We present an objective Bayes method for covariance selection in Gaussian multivariate regression models whose error term has a covariance structure which is Markov with respect to a Directed Acyclic Graph (DAG). The scope is covariate-adjusted sparse graphical model selection, a topic of growing importance especially in the area of genetical genomics (eQTL analysis). Specifically, we provide a closed-form expression for the marginal likelihood of any DAG (with small parent sets) whose computation virtually requires no subjective elicitation by the user and involves only conjugate matrix norma…
We consider Bayesian inference of sparse covariance matrices and propose a post-processed posterior. This method consists of two steps. In the first step, posterior samples are obtained from the conjugate inverse-Wishart posterior without considering the sparse structural assumption. The posterior samples are transformed in the second step to satisfy the sparse structural assumption through the hard-thresholding function. This non-traditional Bayesian procedure is justified by showing that the post-processed posterior attains the optimal minimax rates. We also investigate the application of th…
We present a Bayesian model for area-level count data that uses Gaussian random effects with a novel type of G-Wishart prior on the inverse variance--covariance matrix. Specifically, we introduce a new distribution called the truncated G-Wishart distribution that has support over precision matrices that lead to positive associations between the random effects of neighboring regions while preserving conditional independence of non-neighboring regions. We describe Markov chain Monte Carlo sampling algorithms for the truncated G-Wishart prior in a disease mapping context and compare our results t…
We consider the five classes of multivariate statistical problems identified by James (1964), which together cover much of classical multivariate analysis, plus a simpler limiting case, symmetric matrix denoising. Each of James' problems involves the eigenvalues of $E^{-1}H$ where $H$ and $E$ are proportional to high dimensional Wishart matrices. Under the null hypothesis, both Wisharts are central with identity covariance. Under the alternative, the non-centrality or the covariance parameter of $H$ has a single eigenvalue, a spike, that stands alone. When the spike is smaller than a case-spec…
This paper presents a hierarchical Bayesian modeling framework for the uncertainty quantification in modal identification of linear dynamical systems using multiple vibration data sets. This novel framework integrates the state-of-the-art Bayesian formulations into a hierarchical setting aiming to capture both the identification precision and the ensemble variability prompted due to modeling errors. Such cutting-edge developments have been absent from the modal identification literature, sustained as a long-standing problem at the research spotlight. Central to this framework is a Gaussian hyp…
This paper introduces a novel theoretically sound approach for the celebrated CMA-ES algorithm. Assuming the parameters of the multi variate normal distribution for the minimum follow a conjugate prior distribution, we derive their optimal update at each iteration step. Not only provides this Bayesian framework a justification for the update of the CMA-ES algorithm but it also gives two new versions of CMA-ES either assuming normal-Wishart or normal-Inverse Wishart priors, depending whether we parametrize the likelihood by its covariance or precision matrix. We support our theoretical findings…
We consider Bayesian inference of banded covariance matrices and propose a post-processed posterior. The post-processing of the posterior consists of two steps. In the first step, posterior samples are obtained from the conjugate inverse-Wishart posterior which does not satisfy any structural restrictions. In the second step, the posterior samples are transformed to satisfy the structural restriction through a post-processing function. The conceptually straightforward procedure of the post-processed posterior makes its computation efficient and can render interval estimators of functionals of …
Our article considers a Gaussian variational approximation of the posterior density in a high-dimensional state space model. The variational parameters to be optimized are the mean vector and the covariance matrix of the approximation. The number of parameters in the covariance matrix grows as the square of the number of model parameters, so it is necessary to find simple yet effective parameterizations of the covariance structure when the number of model parameters is large. We approximate the joint posterior distribution over the high-dimensional state vectors by a dynamic factor model, havi…
Kernel Renormalization in Bayesian Deep Neural Networks: the Equivalent Wishart Ansatz in the Proportional Regime
INFN, Sezione di Milano Bicocca（意大利国家研究所（INFN），米兰Bicocca分所）；INFN, Gruppo Collegato di Parma（意大利国家研究所（INFN），帕尔马联合小组）；Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma（帕尔马大学数学、物理和信息科学系）；Istituto dei Materiali per l’Elettronica ed il Magnetismo (IMEM-CNR), Parco Area delle Scienze（电子与磁性材料研究所（IMEM-CNR），帕尔马科技园区）
This paper develops on-line inference for the multivariate local level model, with the focus being placed on covariance estimation of the innovations. We assess the application of the inverse Wishart prior distribution in this context and find it too restrictive since the serial correlation structure of the observation and state innovations is forced to be the same. We generalize the inverse Wishart distribution to allow for a more convenient correlation structure, but still retaining approximate conjugacy. We prove some relevant results for the new distribution and we develop approximate Baye…
Positive-definite matrix-variate data is becoming popular in computer vision. The computer vision data descriptors in the form of Region Covariance Descriptors (RCD) are positive definite matrices, which extract the key features of the images. The RCDs are extensively used in image set classification. Some classification methods treating RCDs as Wishart distributed random matrices are being proposed. However, the majority of the current methods preclude the potential correlation among the RCDs caused by the so-called non-voxel information (e.g., subjects' ages and nose widths, etc). Modeling c…
We provide a MATLAB toolbox, BFDA, that implements a Bayesian hierarchical model to smooth multiple functional data with the assumptions of the same underlying Gaussian process distribution, a Gaussian process prior for the mean function, and an Inverse-Wishart process prior for the covariance function. This model-based approach can borrow strength from all functional data to increase the smoothing accuracy, as well as estimate the mean-covariance functions simultaneously. An option of approximating the Bayesian inference process using cubic B-spline basis functions is integrated in BFDA, whic…
We consider the joint sparse estimation of regression coefficients and the covariance matrix for covariates in a high-dimensional regression model, where the predictors are both relevant to a response variable of interest and functionally related to one another via a Gaussian directed acyclic graph (DAG) model. Gaussian DAG models introduce sparsity in the Cholesky factor of the inverse covariance matrix, and the sparsity pattern in turn corresponds to specific conditional independence assumptions on the underlying predictors. A variety of methods have been developed in recent years for Bayesi…
University of Electronic Science and Technology of China（电子科技大学）；China Academy of Engineering Physics（中国工程物理研究院）
In this paper, we consider the problem of low-rank phase retrieval whose objective is to estimate a complex low-rank matrix from magnitude-only measurements. We propose a hierarchical prior model for low-rank phase retrieval, in which a Gaussian-Wishart hierarchical prior is placed on the underlying low-rank matrix to promote the low-rankness of the matrix. Based on the proposed hierarchical model, a variational expectation-maximization (EM) algorithm is developed. The proposed method is less sensitive to the choice of the initialization point and works well with random initialization. Simulat…
Let $X_1, \ldots, X_n$ be i.i.d. sample in $\mathbb{R}^p$ with zero mean and the covariance matrix $\mathbf{Σ^*}$. The classical PCA approach recovers the projector $\mathbf{P^*_{\mathcal{J}}}$ onto the principal eigenspace of $\mathbf{Σ^*}$ by its empirical counterpart $\mathbf{\widehat{P}_{\mathcal{J}}}$. Recent paper [Koltchinskii, Lounici (2017)] investigated the asymptotic distribution of the Frobenius distance between the projectors $\| \mathbf{\widehat{P}_{\mathcal{J}}} - \mathbf{P^*_{\mathcal{J}}} \|_2$, while [Naumov et al. (2017)] offered a bootstrap procedure to measure uncertainty …
We investigate the geometry of the maximal a posteriori (MAP) partition in the Bayesian Mixture Model where the component and the base distributions are chosen from conjugate exponential families. We prove that in this case the clusters are separated by the contour lines of a linear functional of the sufficient statistic. As a particular example, we describe Bayesian Mixture of Normals with Normal-inverse-Wishart prior on the component mean and covariance, in which the clusters in any MAP partition are separated by a quadratic surface. In connection with results of Rajkowski (2018), where the …
The Black-Litterman model combines investors' personal views with historical data and gives optimal portfolio weights. In this paper we will introduce the original Black-Litterman model (section 1), we will modify the model such that it fits in a Bayesian framework by considering the investors' personal views to be a direct prior on the means of the returns and by adding a typical Inverse Wishart prior on the covariance matrix of the returns (section 2). Lastly, we will use Leonard and Hsu's (1992) idea of adding a prior on the logarithm of the covariance matrix (section 3). Sensitivity simula…
We show that rate-adaptive multivariate density estimation can be performed using Bayesian methods based on Dirichlet mixtures of normal kernels with a prior distribution on the kernel's covariance matrix parameter. We derive sufficient conditions on the prior specification that guarantee convergence to a true density at a rate that is optimal minimax for the smoothness class to which the true density belongs. No prior knowledge of smoothness is assumed. The sufficient conditions are shown to hold for the Dirichlet location mixture of normals prior with a Gaussian base measure and an inverse-W…
Analysis of brain connectivity is important for understanding how information is processed by the brain. We propose a novel Bayesian vector autoregression (VAR) hierarchical model for analyzing brain connectivity in a resting-state fMRI data set with autism spectrum disorder (ASD) patients and healthy controls. Our approach models functional and effective connectivity simultaneously, which is new in the VAR literature for brain connectivity, and allows for both group- and single-subject inference as well as group comparisons. We combine analytical marginalization with Hamiltonian Monte Carlo (…
We introduce a stochastic process with Wishart marginals: the generalised Wishart process (GWP). It is a collection of positive semi-definite random matrices indexed by any arbitrary dependent variable. We use it to model dynamic (e.g. time varying) covariance matrices. Unlike existing models, it can capture a diverse class of covariance structures, it can easily handle missing data, the dependent variable can readily include covariates other than time, and it scales well with dimension; there is no need for free parameters, and optional parameters are easy to interpret. We describe how to con…
In this paper, we consider high-dimensional Gaussian graphical models where the true underlying graph is decomposable. A hierarchical $G$-Wishart prior is proposed to conduct a Bayesian inference for the precision matrix and its graph structure. Although the posterior asymptotics using the $G$-Wishart prior has received increasing attention in recent years, most of results assume moderate high-dimensional settings, where the number of variables $p$ is smaller than the sample size $n$. However, this assumption might not hold in many real applications such as genomics, speech recognition and cli…
A new multivariate stochastic volatility estimation procedure for financial time series is proposed. A Wishart autoregressive process is considered for the volatility precision covariance matrix, for the estimation of which a two step procedure is adopted. The first step is the conditional inference on the autoregressive parameters and the second step is the unconditional inference, based on a Newton-Raphson iterative algorithm. The proposed methodology, which is mostly Bayesian, is suitable for medium dimensional data and it bridges the gap between closed-form estimation and simulation-based …
This paper reviews minimax best equivariant estimation in these invariant estimation problems: a location parameter, a scale parameter and a (Wishart) covariance matrix. We briefly review development of the best equivariant estimator as a generalized Bayes estimator relative to right invariant Haar measure in each case. Then we prove minimaxity of the best equivariant procedure by giving a least favorable prior sequence based on non-truncated Gaussian distributions. The results in this paper are all known, but we bring a fresh and somewhat unified approach by using, in contrast to most proofs …
While a set of covariance matrices corresponding to different populations are unlikely to be exactly equal they can still exhibit a high degree of similarity. For example, some pairs of variables may be positively correlated across most groups, while the correlation between other pairs may be consistently negative. In such cases much of the similarity across covariance matrices can be described by similarities in their principal axes, the axes defined by the eigenvectors of the covariance matrices. Estimating the degree of across-population eigenvector heterogeneity can be helpful for a variet…
