A calibration method for non-positive definite covariance matrix in multivariate data analysis

Covariance matrices that fail to be positive definite arise often in covariance estimation. Approaches addressing this problem exist, but are not well supported theoretically. In this paper, we propose a unified statistical and numerical matrix calibration, finding the optimal positive definite surrogate in the sense of Frobenius norm. The proposed algorithm can be directly applied to any estimated covariance matrix. Numerical results show that the calibrated matrix is typically closer to the true covariance, while making only limited changes to the original covariance structure

A nonparametric empirical Bayes approach to covariance matrix estimation

We propose an empirical Bayes method to estimate high-dimensional covariance matrices. Our procedure centers on vectorizing the covariance matrix and treating matrix estimation as a vector estimation problem. Drawing from the compound decision theory literature, we introduce a new class of decision rules that generalizes several existing procedures. We then use a nonparametric empirical Bayes g-modeling approach to estimate the oracle optimal rule in that class. This allows us to let the data itself determine how best to shrink the estimator, rather than shrinking in a pre-determined direction such as toward a diagonal matrix. Simulation results and a gene expression network analysis shows that our approach can outperform a number of state-of-the-art proposals in a wide range of settings, sometimes substantially.Comment: 20 pages, 4 figure