A compound decision approach to covariance matrix estimation

Huiqin Xin, Sihai Dave Zhao

Research output: Contribution to journalArticlepeer-review


Covariance matrix estimation is a fundamental statistical task in many applications, but the sample covariance matrix is suboptimal when the sample size is comparable to or less than the number of features. Such high-dimensional settings are common in modern genomics, where covariance matrix estimation is frequently employed as a method for inferring gene networks. To achieve estimation accuracy in these settings, existing methods typically either assume that the population covariance matrix has some particular structure, for example, sparsity, or apply shrinkage to better estimate the population eigenvalues. In this paper, we study a new approach to estimating high-dimensional covariance matrices. We first frame covariance matrix estimation as a compound decision problem. This motivates defining a class of decision rules and using a nonparametric empirical Bayes g-modeling approach to estimate the optimal rule in the class. Simulation results and gene network inference in an RNA-seq experiment in mouse show that our approach is comparable to or can outperform a number of state-of-the-art proposals.

Original languageEnglish (US)
Pages (from-to)1201-1212
Number of pages12
Issue number2
StatePublished - Jun 2023


  • compound decision theory
  • g-modeling
  • nonparametric maximum likelihood
  • separable decision rule

ASJC Scopus subject areas

  • General Immunology and Microbiology
  • Applied Mathematics
  • General Biochemistry, Genetics and Molecular Biology
  • General Agricultural and Biological Sciences
  • Statistics and Probability


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