A Novel Two-Stage Adaptive Method for Estimating Large Covariance and Precision Matrices

High dimensional covariance matrices have attracted much attention of statisticians and econometricians during the past decades. Vast literature is devoted to the research in high dimensional covariance matrices. However, most of them are for constant covariance matrices. In many applications, constant covariance matrices are not appropriate, e.g. in portfolio allocation, dynamic covariance matrices would make much more sense. Simply assuming each entry of a covariance matrix is a function of time to introduce a dynamic structure would not work. In this paper, we are going to introduce a class of high dimensional dynamic covariance matrices in which a kind of additive structure is embedded. We will show the proposed high dimensional dynamic covariance matrices have many advantages in applications. An estimation procedure is also proposed to estimate the proposed high dimensional dynamic covariance matrices. Asymptotic properties are built to justify the proposed estimation procedure. Intensive simulation studies show the proposed estimation procedure works very well when sample size is finite. Finally, we apply the proposed high dimensional dynamic covariance matrices, together with the proposed estimation procedure, to portfolio allocation. The results look very interesting.

Recent advances in shrinkage-based high-dimensional inference

We propose Bayesian methods for Gaussian graphical models that lead to sparse and adaptively shrunk estimators of the precision (inverse covariance) matrix. Our methods are based on lasso-type regularization priors leading to parsimonious parameterization of the precision matrix, which is essential in several applications involving learning relationships among the variables. In this context, we introduce a novel type of selection prior that develops a sparse structure on the precision matrix by making most of the elements exactly zero, in addition to ensuring positive definiteness - thus conducting model selection and estimation simultaneously. More importantly, we extend these methods to analyze clustered data using finite mixtures of Gaussian graphical model and infinite mixtures of Gaussian graphical models. We discuss appropriate posterior simulation schemes to implement posterior inference in the proposed models, including the evaluation of normalizing constants that are functions of parameters of interest, which result from the restriction of positive definiteness on the correlation matrix. We evaluate the operating characteristics of our method via several simulations and demonstrate the application to real data examples in genomics.

Summary The primary purpose of this paper is to propose empirical measures of the structural differences between two communities of plants or animals composed of the same species. Structure is defined to consist of; 1) the species in the community, 2) the pattern of interactions as represented by the covariance or correlation matrix of successive observations on each species, and 3) the mean abundances of each species in each of the two communities. Statistical tests are proposed for testing whether the covariance matrices and the vectors of mean densities for each community are equal and empirical measures of the differences between the covariance matrices and mean vectors are proposed. Given unequal covariance or correlation matrices the factor analysis model is used to derive empirical measures of the degree to which each variable of the ecosystem is responsible for the observed defferences in the pattern of interactions in each community. These tests and measures were applied to data gathered by Hunter (1966) on the abundances of six species of Drosophila censused monthly over a period of approximately two and a half years in two adjacent, but different habitats near Bogota, colombia. The two covariance matrices were significantly different indicating different patterns of interactions in the two Drosophila communities.

Estimation of sparse covariance matrices and their inverse subject to positive definiteness constraints has drawn a lot of attention in recent years. The abundance of high-dimensional data, where the sample size (n) is less than the dimension (d), requires shrinkage estimation methods since the maximum likelihood estimator is not positive definite in this case. Furthermore, when n is larger than d but not sufficiently larger, shrinkage estimation is more stable than maximum likelihood as it reduces the condition number of the precision matrix. Frequentist methods have utilized penalized likelihood methods, whereas Bayesian approaches rely on matrix decompositions or Wishart priors for shrinkage. In this paper we propose a new method, called the Bayesian Covariance Lasso (BCLASSO), for the shrinkage estimation of a precision (covariance) matrix. We consider a class of priors for the precision matrix that leads to the popular frequentist penalties as special cases, develop a Bayes estimator for the precision matrix, and propose an efficient sampling scheme that does not precalculate boundaries for positive definiteness. The proposed method is permutation invariant and performs shrinkage and estimation simultaneously for non-full rank data. Simulations show that the proposed BCLASSO performs similarly as frequentist methods for non-full rank data.

Most HMM-based speech recognition systems use Gaussian mixtures as observation probability density functions. An important goal in all such systems is to improve parsimony. One method is to adjust the type of covariance matrices used. In this work, factored sparse inverse covariance matrices are introduced. Based on U'DU factorization, the inverse covariance matrix can be represented using linear regressive coefficients which 1) correspond to sparse patterns in the inverse covariance matrix (and therefore represent conditional independence properties of the Gaussian), and 2), result in a method of partial tying of the covariance matrices without requiring non-linear EM update equations. Results show that the performance of full-covariance Gaussians can be matched by factored sparse inverse covariance Gaussians having significantly fewer parameters.

In many engineering applications, estimation of covariance and precision matrices is of great importance, helping researchers understand the dependency and conditional dependency between variables of interest. Among various matrix estimation methods, the modified Cholesky decomposition is a commonly used technique. It has the advantage of transforming the matrix estimation task into solving a sequence of regression models. Moreover, the sparsity on the regression coefficients implies certain sparse structure on the covariance and precision matrices. In this chapter, we first overview the Cholesky-based covariance and precision matrices estimation. It is known that the Cholesky-based matrix estimation depends on a prespecified ordering of variables, which is often not available in practice. To address this issue, we then introduce several techniques to enhance the Cholesky-based estimation of covariance and precision matrices. These approaches are able to ensure the positive definiteness of the matrix estimate and applicable in general situations without specifying the ordering of variables. The advantage of Cholesky-based estimation is illustrated by numerical studies and several real-case applications.

The smoothness of subdiagonals of the Cholesky factor of large covariance matrices is closely related to the degree of nonstationarity of autoregressive models for time series data. Heuristically, one expects for nearly stationary covariance matrix entries in each subdiagonal of the Cholesky factor of its inverse to be approximately the same in the sense that the sum of the absolute values of successive differences is small. Statistically, such smoothness is achieved by regularizing each subdiagonal using fused-type lasso penalties. We rely on the standard Cholesky factor as the new parameter within a regularized normal likelihood setup which guarantees: (a) joint convexity of the likelihood function, (b) strict convexity of the likelihood function restricted to each subdiagonal even when n < p, and (c) positive-definiteness of the estimated covariance matrix. A block coordinate descent algorithm, where each block is a subdiagonal, is proposed, and its convergence is established under mild conditions. Lack of decoupling of the penalized likelihood function into a sum of functions involving individual subdiagonals gives rise to some computational challenges and advantages relative to two recent algorithms for sparse estimation of the Cholesky factor, which decouple row-wise. Simulation results and real data analysis show the scope and good performance of the proposed methodology. Software for our method is freely available in R language. Supplementary materials for this article are available online.

Estimation of the high-dimensional banded covariance matrix is widely used in multivariate statistical analysis. To ensure the validity of estimation, we aim to test the hypothesis that the covariance matrix is banded with a certain bandwidth under the high-dimensional framework. Though several testing methods have been proposed in the literature, the existing tests are only powerful for some alternatives with certain sparsity levels, whereas they may not be powerful for alternatives with other sparsity structures. The goal of this paper is to propose a new test for the bandedness of high-dimensional covariance matrix, which is powerful for alternatives with various sparsity levels. The proposed new test also be used for testing the banded structure of covariance matrices of error vectors in high-dimensional factor models. Based on these statistics, a consistent bandwidth estimator is also introduced for a banded high dimensional covariance matrix. Extensive simulation studies and an application to a prostate cancer dataset from protein mass spectroscopy are conducted for evaluating the effectiveness of the proposed adaptive tests blue and bandwidth estimator for the banded covariance matrix.

Statistical inference for high-dimensional data is increasingly essential due to the prevalence of big data. While recent advancements have improved testing linear hypotheses for high-dimensional mean vectors, exploration of testing linear hypotheses for high-dimensional covariance matrices remains limited. This article focuses on a general linear hypothesis testing (GLHT) problem for high-dimensional covariance matrices, encompassing various specific cases such as testing the equality of variances, testing for a given covariance matrix, assessing the homogeneity of covariance matrices, and examining linear combinations of covariance matrices. We propose and study a new test statistic for the GLHT problem on high-dimensional covariance matrices. Under certain regularity conditions and the null hypothesis, we demonstrate that the test statistic shares the same limiting distribution as a Chi-squared-type mixture. This mixture’s distribution can be accurately approximated using a three-cumulant matched Chi-squared-approximation approach. Additionally, we establish the asymptotic power of the proposed test against some local alternatives. Simulation studies and a real-world financial data analysis demonstrate that the proposed test outperforms several competitors in terms of size control.

The determination of the covariance matrix and its inverse, the precision matrix, is critical in the statistical analysis of cosmological measurements. The covariance matrix is typically estimated with a limited number of simulations at great computational cost before inversion into the precision matrix; therefore, it can be ill-conditioned and overly noisy when the sample size n used for estimation is not much larger than the data vector dimension. In this work, we consider a class of methods known as shrinkage estimation for the precision matrix, which combines an empirical estimate with a target that is either analytical or stochastic. These methods include linear and non-linear shrinkage applied to the covariance matrix (the latter represented by the so-called NERCOME estimator), and the direct linear shrinkage estimation of the precision matrix which we introduce in a cosmological setting. By performing Bayesian parameter inference and using metrics like matrix loss functions, the Kullback–Leibler divergence and the eigenvalue spectrum, we compare their performance against the standard sample estimator with varying sample size n. We have found the shrinkage estimators to significantly improve the posterior distribution at low n, especially for the linear shrinkage estimators either inverted from the covariance matrix or applied directly to the precision matrix, with an empirical target constructed from the sample estimate. Our results are particularly relevant to the analyses of Stage-IV spectroscopic galaxy surveys such as the Dark Energy Spectroscopic Instrument and Euclid, whose statistical power can be limited by the computational cost of obtaining an accurate precision matrix estimate.

Inferences in panel data with interactive effects using large covariance matrices

The covariance matrix (or its inverse, the precision matrix) is central to many chemometric techniques. Traditional sample estimators perform poorly for high‐dimensional data such as metabolomics data. Because of this, many traditional inference techniques break down or produce unreliable results. In this paper, we selectively review several modern estimators of the covariance and precision matrix that improve upon the traditional sample estimator. We focus on 3 general techniques: eigenvalue‐shrinkage estimation, ridge‐type estimation, and structured estimation. These methods rely on different assumptions regarding the structure of the covariance or precision matrix. Various examples, in particular using metabolomics data, are used to compare these techniques and to demonstrate that in concert with, eg, principal component analysis, multivariate analysis of variance, and Gaussian graphical models, better results are obtained.

Covariance matrices play an important role in many multivariate techniques and hence a good covariance estimation is crucial in this kind of analysis. In many applications a sparse covariance matrix is expected due to the nature of the data or for simple interpretation. Hard thresholding, soft thresholding, and generalized thresholding were therefore developed to this end. However, these estimators do not always yield well-conditioned covariance estimates. To have sparse and well-conditioned estimates, we propose doubly shrinkage estimators: shrinking small covariances towards zero and then shrinking covariance matrix towards a diagonal matrix. Additionally, a richness index is defined to evaluate how rich a covariance matrix is. According to our simulations, the richness index serves as a good indicator to choose relevant covariance estimator.

We study the accuracy of estimating the covariance and the precision matrix of a $D$-variate sub-Gaussian distribution along a prescribed subspace or direction using the finite sample covariance. Our results show that the estimation accuracy depends almost exclusively on the components of the distribution that correspond to desired subspaces or directions. This is relevant and important for problems where the behavior of data along a lower-dimensional space is of specific interest, such as dimension reduction or structured regression problems. We also show that estimation of precision matrices is almost independent of the condition number of the covariance matrix. The presented applications include direction-sensitive eigenspace perturbation bounds, relative bounds for the smallest eigenvalue, and the estimation of the single-index model. For the latter, a new estimator, derived from the analysis, with strong theoretical guarantees and superior numerical performance is proposed.