Linear shrinkage estimators of a covariance matrix --- defined by a weighted average of the sample covariance matrix and a pre-specified shrinkage target matrix --- are popular when analysing high-throughput molecular data. However, their performance strongly relies on an appropriate choice of target matrix. This paper introduces a more flexible class of linear shrinkage estimators that can accommodate multiple shrinkage target matrices, directly accounting for the uncertainty regarding the target choice. This is done within a conjugate Bayesian framework, which is computationally efficient. Using both simulated and real data, we show that the proposed estimator is less sensitive to target misspecification and can outperform state-of-the-art (nonparametric) single-target linear shrinkage estimators. Using protein expression data from The Cancer Proteome Atlas we illustrate how multiple sources of prior information (obtained from more than 30 different cancer types) can be incorporated into the proposed multi-target linear shrinkage estimator. In particular, it is shown that the target-specific weights can provide insights into the differences and similarities between cancer types. Software for the method is freely available as an R-package at http://github.com/HGray384/TAS.
We address high dimensional covariance estimation for elliptical distributed samples, which are also known as spherically invariant random vectors (SIRV) or compound-Gaussian processes. Specifically we consider shrinkage methods that are suitable for high dimensional problems with a small number of samples (large $p$ small $n$). We start from a classical robust covariance estimator [Tyler(1987)], which is distribution-free within the family of elliptical distribution but inapplicable when $n<p$. Using a shrinkage coefficient, we regularize Tyler's fixed point iterations. We prove that, for all…
Recent literature provides many computational and modeling approaches for covariance matrices estimation in a penalized Gaussian graphical models but relatively little study has been carried out on the choice of the tuning parameter. This paper tries to fill this gap by focusing on the problem of shrinkage parameter selection when estimating sparse precision matrices using the penalized likelihood approach. Previous approaches typically used K-fold cross-validation in this regard. In this paper, we first derived the generalized approximate cross-validation for tuning parameter selection which …
We consider Bayesian shrinkage predictions for the Normal regression problem under the frequentist Kullback-Leibler risk function. Firstly, we consider the multivariate Normal model with an unknown mean and a known covariance. While the unknown mean is fixed, the covariance of future samples can be different from training samples. We show that the Bayesian predictive distribution based on the uniform prior is dominated by that based on a class of priors if the prior distributions for the covariance and future covariance matrices are rotation invariant. Then, we consider a class of priors for t…
We investigate predictive densities for multivariate normal models with unknown mean vectors and known covariance matrices. Bayesian predictive densities based on shrinkage priors often have complex representations, although they are effective in various problems. We consider extended normal models with mean vectors and covariance matrices as parameters, and adopt predictive densities that belong to the extended models including the original normal model. We adopt predictive densities that are optimal with respect to the posterior Bayes risk in the extended models. The proposed predictive dens…
In recent years, shrinkage priors have received much attention in high-dimensional data analysis from a Bayesian perspective. Compared with widely used spike-and-slab priors, shrinkage priors have better computational efficiency. But the theoretical properties, especially posterior contraction rate, which is important in uncertainty quantification, are not established in many cases. In this paper, we apply global-local shrinkage priors to high-dimensional multivariate linear regression with unknown covariance matrix. We show that when the prior is highly concentrated near zero and has heavy ta…
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 study the problem of sparse signal detection on a spatial domain. We propose a novel approach to model continuous signals that are sparse and piecewise smooth as product of independent Gaussian processes (PING) with a smooth covariance kernel. The smoothness of the PING process is ensured by the smoothness of the covariance kernels of Gaussian components in the product, and sparsity is controlled by the number of components. The bivariate kurtosis of the PING process shows more components in the product results in thicker tail and sharper peak at zero. The simulation results demonstrate the…
This study proposes a novel hierarchical prior for inferring possibly low-rank matrices measured with noise. We consider three-component matrix factorization, as in singular value decomposition, and its fully Bayesian inference. The proposed prior is specified by a scale mixture of exponential distributions that has spike and slab components. The weights for the spike/slab parts are inferred using a special prior based on a cumulative shrinkage process. The proposed prior is designed to increasingly aggressively push less important, or essentially redundant, singular values toward zero, leadin…
We develop singular value shrinkage priors for the mean matrix parameters in the matrix-variate normal model with known covariance matrices. Our priors are superharmonic and put more weight on matrices with smaller singular values. They are a natural generalization of the Stein prior. Bayes estimators and Bayesian predictive densities based on our priors are minimax and dominate those based on the uniform prior in finite samples. In particular, our priors work well when the true value of the parameter has low rank.
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…
We derive an optimal shrinkage sample covariance matrix (SCM) estimator which is suitable for high dimensional problems and when sampling from an unspecified elliptically symmetric distribution. Specifically, we derive the optimal (oracle) shrinkage parameters that obtain the minimum mean-squared error (MMSE) between the shrinkage SCM and the true covariance matrix when sampling from an elliptical distribution. Subsequently, we show how the oracle shrinkage parameters can be consistently estimated under the random matrix theory regime. Simulations show the advantage of the proposed estimator o…
Estimating a covariance matrix is an important task in applications where the number of variables is larger than the number of observations. Shrinkage approaches for estimating a high-dimensional covariance matrix are often employed to circumvent the limitations of the sample covariance matrix. A new family of nonparametric Stein-type shrinkage covariance estimators is proposed whose members are written as a convex linear combination of the sample covariance matrix and of a predefined invertible target matrix. Under the Frobenius norm criterion, the optimal shrinkage intensity that defines the…
The accurate computation of the covariance matrix of fitted model parameters is a somewhat neglected task in Statistics. Algorithms are given for computing accurate covariance matrices derived from computing the Hessian matrix by numerical differentiation, and also for the covariance matrix of the posterior distribution of model parameters. Evaluations on two datasets where the Hessian could be computed analytically show that the numerical differentiation algorithm is very accurate.
In this paper, a shrinkage estimator for the population mean is proposed under known quadratic loss functions with unknown covariance matrices. The new estimator is non-parametric in the sense that it does not assume a specific parametric distribution for the data and it does not require the prior information on the population covariance matrix. Analytical results on the improvement of the proposed shrinkage estimator are provided and some corresponding asymptotic properties are also derived. Finally, we demonstrate the practical improvement of the proposed method over existing methods through…
Tuning-Free Covariance-Aware Sequential Shrinkage for Multi-Source Estimation
College of Business, City University of Hong Kong（香港城市大学商学院）；Stern School of Business, New York University（纽约大学斯特恩商学院）；Department of IEOR and Data Science Institute, Columbia University（哥伦比亚大学工业工程与运筹学系及数据科学研究所）；Daniels School of Business, Purdue University（普渡大学丹尼尔斯商学院）
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 …
Analyzing large samples of high-dimensional data under dependence is a challenging statistical problem as long time series may have change points, most importantly in the mean and the marginal covariances, for which one needs valid tests. Inference for large covariance matrices is especially difficult due to noise accumulation, resulting in singular estimates and poor power of related tests. The singularity of the sample covariance matrix in high dimensions can be overcome by considering a linear combination with a regular, more structured target matrix. This approach is known as shrinkage, an…
This paper considers the problem of estimating a high-dimensional (HD) covariance matrix when the sample size is smaller, or not much larger, than the dimensionality of the data, which could potentially be very large. We develop a regularized sample covariance matrix (RSCM) estimator which can be applied in commonly occurring sparse data problems. The proposed RSCM estimator is based on estimators of the unknown optimal (oracle) shrinkage parameters that yield the minimum mean squared error (MMSE) between the RSCM and the true covariance matrix when the data is sampled from an unspecified elli…
The Ensemble Kalman Filters (EnKF) employ a Monte-Carlo approach to represent covariance information, and are affected by sampling errors in operational settings where the number of model realizations is much smaller than the model state dimension. To alleviate the effects of these errors EnKF relies on model-specific heuristics such as covariance localization, which takes advantage of the spatial locality of correlations among the model variables. This work proposes an approach to alleviate sampling errors that utilizes a locally averaged-in-time dynamics of the model, described in terms of a…
Statistical inference for sparse covariance matrices is crucial to reveal dependence structure of large multivariate data sets, but lacks scalable and theoretically supported Bayesian methods. In this paper, we propose beta-mixture shrinkage prior, computationally more efficient than the spike and slab prior, for sparse covariance matrices and establish its minimax optimality in high-dimensional settings. The proposed prior consists of beta-mixture shrinkage and gamma priors for off-diagonal and diagonal entries, respectively. To ensure positive definiteness of the resulting covariance matrix,…
When shrinking a covariance matrix towards (a multiple) of the identity matrix, the trace of the covariance matrix arises naturally as the optimal scaling factor for the identity target. The trace also appears in other context, for example when measuring the size of a matrix or the amount of uncertainty. Of particular interest is the case when the dimension of the covariance matrix is large. Then the problem arises that the sample covariance matrix is singular if the dimension is larger than the sample size. Another issue is that usually the estimation has to based on correlated time series da…
Portfolio optimization requires sophisticated covariance estimators that are able to filter out estimation noise. Non-linear shrinkage is a popular estimator based on how the Oracle eigenvalues can be computed using only data from the calibration window. Contrary to common belief, NLS is not optimal for portfolio optimization because it does not minimize the right cost function when the asset dependence structure is non-stationary. We instead derive the optimal target. Using historical data, we quantify by how much NLS can be improved. Our findings reopen the question of how to build the covar…
In this work, we study the positive definiteness (PDness) problem in covariance matrix estimation. For high dimensional data, many regularized estimators are proposed under structural assumptions on the true covariance matrix including sparsity. They are shown to be asymptotically consistent and rate-optimal in estimating the true covariance matrix and its structure. However, many of them do not take into account the PDness of the estimator and produce a non-PD estimate. To achieve the PDness, researchers consider additional regularizations (or constraints) on eigenvalues, which make both the …
A highly popular regularized (shrinkage) covariance matrix estimator is the shrinkage sample covariance matrix (SCM) which shares the same set of eigenvectors as the SCM but shrinks its eigenvalues toward the grand mean of the eigenvalues of the SCM. In this paper, a more general approach is considered in which the SCM is replaced by an M-estimator of scatter matrix and a fully automatic data adaptive method to compute the optimal shrinkage parameter with minimum mean squared error is proposed. Our approach permits the use of any weight function such as Gaussian, Huber's, Tyler's, or t-weight …
We address covariance estimation in the sense of minimum mean-squared error (MMSE) for Gaussian samples. Specifically, we consider shrinkage methods which are suitable for high dimensional problems with a small number of samples (large p small n). First, we improve on the Ledoit-Wolf (LW) method by conditioning on a sufficient statistic. By the Rao-Blackwell theorem, this yields a new estimator called RBLW, whose mean-squared error dominates that of LW for Gaussian variables. Second, to further reduce the estimation error, we propose an iterative approach which approximates the clairvoyant shr…
We propose a flexible class of models based on scale mixture of uniform distributions to construct shrinkage priors for covariance matrix estimation. This new class of priors enjoys a number of advantages over the traditional scale mixture of normal priors, including its simplicity and flexibility in characterizing the prior density. We also exhibit a simple, easy to implement Gibbs sampler for posterior simulation which leads to efficient estimation in high dimensional problems. We first discuss the theory and computational details of this new approach and then extend the basic model to a new…
One of the major challenges in multivariate analysis is the estimation of population covariance matrix from sample covariance matrix (SCM). Most recent covariance matrix estimators use either shrinkage transformations or asymptotic results from Random Matrix Theory (RMT). Shrinkage techniques help in pulling extreme correlation values towards certain target values whereas tools from RMT help in removing noisy eigenvalues of SCM. Both of these techniques use different approaches to achieve a similar goal which is to remove noisy correlations and add structure to SCM to overcome the bias-varianc…
Linear discriminant analysis (LDA) is a typical method for classification problems with large dimensions and small samples. There are various types of LDA methods that are based on the different types of estimators for the covariance matrices and mean vectors. In this paper, we consider shrinkage methods based on a non-parametric approach. For the precision matrix, methods based on the sparsity structure or data splitting are examined. Regarding the estimation of mean vectors, Non-parametric Empirical Bayes (NPEB) methods and Non-parametric Maximum Likelihood Estimation (NPMLE) methods, also k…
In this paper, a new ridge-type shrinkage estimator for the precision matrix has been proposed. The asymptotic optimal shrinkage coefficients and the theoretical loss were derived. Data-driven estimators for the shrinkage coefficients were also conducted based on the asymptotic results deriving from random matrix theories. The new estimator which has a simple explicit formula is distribution-free and applicable to situation where the dimension of observation is greater than the sample size. Further, no assumptions are required on the structure of the population covariance matrix or the precisi…
A popular regularized (shrinkage) covariance estimator is the shrinkage sample covariance matrix (SCM) which shares the same set of eigenvectors as the SCM but shrinks its eigenvalues toward its grand mean. In this paper, a more general approach is considered in which the SCM is replaced by an M-estimator of scatter matrix and a fully automatic data adaptive method to compute the optimal shrinkage parameter with minimum mean squared error is proposed. Our approach permits the use of any weight function such as Gaussian, Huber's, or $t$ weight functions, all of which are commonly used in M-esti…
Stein showed that the multivariate sample mean is outperformed by "shrinking" to a constant target vector. Ledoit and Wolf extended this approach to the sample covariance matrix and proposed a multiple of the identity as shrinkage target. In a general framework, independent of a specific estimator, we extend the shrinkage concept by allowing simultaneous shrinkage to a set of targets. Application scenarios include settings with (A) additional data sets from potentially similar distributions, (B) non-stationarity, (C) a natural grouping of the data or (D) multiple alternative estimators which c…
Covariance matrix tapers have a long history in signal processing and related fields. Examples of applications include autoregressive models (promoting a banded structure) or beamforming (widening the spectral null width associated with an interferer). In this paper, the focus is on high-dimensional setting where the dimension $p$ is high, while the data aspect ratio $n/p$ is low. We propose an estimator called Tabasco (TApered or BAnded Shrinkage COvariance matrix) that shrinks the tapered sample covariance matrix towards a scaled identity matrix. We derive optimal and estimated (data adaptiv…
This manuscript presents an approach to perform generalized linear regression with multiple high dimensional covariance matrices as the outcome. Model parameters are proposed to be estimated by maximizing a pseudo-likelihood. When the data are high dimensional, the normal likelihood function is ill-posed as the sample covariance matrix is rank-deficient. Thus, a well-conditioned linear shrinkage estimator of the covariance matrix is introduced. With multiple covariance matrices, the shrinkage coefficients are proposed to be common across matrices. Theoretical studies demonstrate that the propo…
In this work we consider the estimation of spatio-temporal covariance matrices in the low sample non-Gaussian regime. We impose covariance structure in the form of a sum of Kronecker products decomposition (Tsiligkaridis et al. 2013, Greenewald et al. 2013) with diagonal correction (Greenewald et al.), which we refer to as DC-KronPCA, in the estimation of multiframe covariance matrices. This paper extends the approaches of (Tsiligkaridis et al.) in two directions. First, we modify the diagonally corrected method of (Greenewald et al.) to include a block Toeplitz constraint imposing temporal st…
This paper addresses the task of estimating a covariance matrix under a patternless sparsity assumption. In contrast to existing approaches based on thresholding or shrinkage penalties, we propose a likelihood-based method that regularizes the distance from the covariance estimate to a symmetric sparsity set. This formulation avoids unwanted shrinkage induced by more common norm penalties and enables optimization of the resulting non-convex objective by solving a sequence of smooth, unconstrained subproblems. These subproblems are generated and solved via the proximal distance version of the m…
Bayesian DAG Structure Learning with Simultaneous Shrinkage Covariance Estimation under Scale-Mixture Error Distributions in the Proportional High-Dimensional Regime
Ferdowsi University of Mashhad（马什哈德 Ferdowsi 大学）；North Carolina Agricultural and Technical State University（北卡罗来纳农业与技术州立大学）
The main theme of this paper is a modification of the likelihood ratio test (LRT) for testing high dimensional covariance matrix. Recently, the correct asymptotic distribution of the LRT for a large-dimensional case (the case $p/n$ approaches to a constant $γ\in (0,1]$) is specified by researchers. The correct procedure is named as corrected LRT. Despite of its correction, the corrected LRT is a function of sample eigenvalues that are suffered from redundant variability from high dimensionality and, subsequently, still does not have full power in differentiating hypotheses on the covariance ma…
