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1. Estimation of the Number of Spiked Eigenvalues in a Covariance Matrix by Bulk Eigenvalue Matching Analysis

   https://doi.org/10.1080/01621459.2021.1933497  

   Ke, Zheng Tracy; Ma, Yucong; Lin, Xihong (July 2021, Journal of the American Statistical Association)

   null (Ed.)

   The spiked covariance model has gained increasing popularity in high-dimensional data analysis. A fundamental problem is determination of the number of spiked eigenvalues, K. For estimation of K, most attention has focused on the use of top eigenvalues of sample covariance matrix, and there is little investigation into proper ways of using bulk eigenvalues to estimate K. We propose a principled approach to incorporating bulk eigenvalues in the estimation of K. Our method imposes a working model on the residual covariance matrix, which is assumed to be a diagonal matrix whose entries are drawn from a gamma distribution. Under this model, the bulk eigenvalues are asymptotically close to the quantiles of a fixed parametric distribution. This motivates us to propose a two-step method: the first step uses bulk eigenvalues to estimate parameters of this distribution, and the second step leverages these parameters to assist the estimation of K. The resulting estimator Kˆ aggregates information in a large number of bulk eigenvalues. We show the consistency of Kˆ under a standard spiked covariance model. We also propose a confidence interval estimate for K. Our extensive simulation studies show that the proposed method is robust and outperforms the existing methods in a range of scenarios. We apply the proposed method to analysis of a lung cancer microarray dataset and the 1000 Genomes dataset. 

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2. Scad-Penalized Complex Gaussian Graphical Model Selection

   https://doi.org/10.1109/MLSP49062.2020.9231821  

   Tugnait, Jitendra K. (September 2020, 2020 IEEE 30th International Workshop on Machine Learning for Signal Processing (MLSP))

   null (Ed.)

   We consider the problem of estimating the conditional independence graph (CIG) of a sparse, high-dimensional proper complex-valued Gaussian graphical model (CGGM). For CGGMs, the problem reduces to estimation of the inverse covariance matrix with more unknowns than the sample size. We consider a smoothly clipped absolute deviation (SCAD) penalty instead of the ℓ 1 -penalty to regularize the problem, and analyze a SCAD-penalized log-likelihood based objective function to establish consistency and sparsistency of a local estimator of inverse covariance in a neighborhood of the true value. A numerical example is presented to illustrate the advantage of SCAD-penalty over the usual ℓ 1 -penalty. 

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3. Ensemble-based estimates of eigenvector error for empirical covariance matrices

   https://doi.org/10.1093/imaiai/iay010  

   Taylor, Dane; Restrepo, Juan G; Meyer, François G (July 2018, Information and Inference: A Journal of the IMA)

   Abstract Covariance matrices are fundamental to the analysis and forecast of economic, physical and biological systems. Although the eigenvalues $$\{\lambda _i\}$$ and eigenvectors $$\{\boldsymbol{u}_i\}$$ of a covariance matrix are central to such endeavours, in practice one must inevitably approximate the covariance matrix based on data with finite sample size $$n$$ to obtain empirical eigenvalues $$\{\tilde{\lambda }_i\}$$ and eigenvectors $$\{\tilde{\boldsymbol{u}}_i\}$$, and therefore understanding the error so introduced is of central importance. We analyse eigenvector error $$\|\boldsymbol{u}_i - \tilde{\boldsymbol{u}}_i \|^2$$ while leveraging the assumption that the true covariance matrix having size $$p$$ is drawn from a matrix ensemble with known spectral properties—particularly, we assume the distribution of population eigenvalues weakly converges as $$p\to \infty $$ to a spectral density $$\rho (\lambda )$$ and that the spacing between population eigenvalues is similar to that for the Gaussian orthogonal ensemble. Our approach complements previous analyses of eigenvector error that require the full set of eigenvalues to be known, which can be computationally infeasible when $$p$$ is large. To provide a scalable approach for uncertainty quantification of eigenvector error, we consider a fixed eigenvalue $$\lambda $$ and approximate the distribution of the expected square error $$r= \mathbb{E}\left [\| \boldsymbol{u}_i - \tilde{\boldsymbol{u}}_i \|^2\right ]$$ across the matrix ensemble for all $$\boldsymbol{u}_i$$ associated with $$\lambda _i=\lambda $$. We find, for example, that for sufficiently large matrix size $$p$$ and sample size $n> p$, the probability density of $$r$$ scales as $1/nr^2$. This power-law scaling implies that the eigenvector error is extremely heterogeneous—even if $$r$$ is very small for most eigenvectors, it can be large for others with non-negligible probability. We support this and further results with numerical experiments. 

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4. Tracy–Widom distribution for the edge eigenvalues of elliptical model

   https://doi.org/10.1093/imaiai/iaaf004  

   Ding, Xiucai; Xie, Jiahui (March 2025, Information and Inference: A Journal of the IMA)

   Abstract In this paper, we study the largest eigenvalues of sample covariance matrices with elliptically distributed data. We consider the sample covariance matrix $$Q=YY^{*},$$ where the data matrix $$Y \in \mathbb{R}^{p \times n}$$ contains i.i.d. $$p$$-dimensional observations $$\textbf{y}_{i}=\xi _{i}T\textbf{u}_{i},\;i=1,\dots ,n.$$ Here $$\textbf{u}_{i}$$ is distributed on the unit sphere, $$\xi _{i} \sim \xi $$ is some random variable that is independent of $$\textbf{u}_{i}$$ and $$T^{*}T=\varSigma $$ is some deterministic positive definite matrix. Under some mild regularity assumptions on $$\varSigma ,$$ assuming $$\xi ^{2}$$ has bounded support and certain decay behaviour near its edge so that the limiting spectral distribution of $$Q$$ has a square root decay behaviour near the spectral edge, we prove that the Tracy–Widom law holds for the largest eigenvalues of $$Q$$ when $$p$$ and $$n$$ are comparably large. Based on our results, we further construct some useful statistics to detect the signals when they are corrupted by high dimensional elliptically distributed noise. 

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5. On Information Rank Deficiency in Phenotypic Covariance Matrices

   https://doi.org/10.1093/sysbio/syab088  

   O’Keefe, F Robin; Meachen, Julie A; Polly, P David (November 2021, Systematic Biology)

   Esposito, Lauren (Ed.)

   Abstract This article investigates a form of rank deficiency in phenotypic covariance matrices derived from geometric morphometric data, and its impact on measures of phenotypic integration. We first define a type of rank deficiency based on information theory then demonstrate that this deficiency impairs the performance of phenotypic integration metrics in a model system. Lastly, we propose methods to treat for this information rank deficiency. Our first goal is to establish how the rank of a typical geometric morphometric covariance matrix relates to the information entropy of its eigenvalue spectrum. This requires clear definitions of matrix rank, of which we define three: the full matrix rank (equal to the number of input variables), the mathematical rank (the number of nonzero eigenvalues), and the information rank or “effective rank” (equal to the number of nonredundant eigenvalues). We demonstrate that effective rank deficiency arises from a combination of methodological factors—Generalized Procrustes analysis, use of the correlation matrix, and insufficient sample size—as well as phenotypic covariance. Secondly, we use dire wolf jaws to document how differences in effective rank deficiency bias two metrics used to measure phenotypic integration. The eigenvalue variance characterizes the integration change incorrectly, and the standardized generalized variance lacks the sensitivity needed to detect subtle changes in integration. Both metrics are impacted by the inclusion of many small, but nonzero, eigenvalues arising from a lack of information in the covariance matrix, a problem that usually becomes more pronounced as the number of landmarks increases. We propose a new metric for phenotypic integration that combines the standardized generalized variance with information entropy. This metric is equivalent to the standardized generalized variance but calculated only from those eigenvalues that carry nonredundant information. It is the standardized generalized variance scaled to the effective rank of the eigenvalue spectrum. We demonstrate that this metric successfully detects the shift of integration in our dire wolf sample. Our third goal is to generalize the new metric to compare data sets with different sample sizes and numbers of variables. We develop a standardization for matrix information based on data permutation then demonstrate that Smilodon jaws are more integrated than dire wolf jaws. Finally, we describe how our information entropy-based measure allows phenotypic integration to be compared in dense semilandmark data sets without bias, allowing characterization of the information content of any given shape, a quantity we term “latent dispersion”. [Canis dirus; Dire wolf; effective dispersion; effective rank; geometric morphometrics; information entropy; latent dispersion; modularity and integration; phenotypic integration; relative dispersion.] 

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