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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. Bayesian sparse multiple regression for simultaneous rank reduction and variable selection

   https://doi.org/10.1093/biomet/asz056  

   Chakraborty, Antik ; Bhattacharya, Anirban ; Mallick, Bani K ( November 2019 , Biometrika)

   Summary We develop a Bayesian methodology aimed at simultaneously estimating low-rank and row-sparse matrices in a high-dimensional multiple-response linear regression model. We consider a carefully devised shrinkage prior on the matrix of regression coefficients which obviates the need to specify a prior on the rank, and shrinks the regression matrix towards low-rank and row-sparse structures. We provide theoretical support to the proposed methodology by proving minimax optimality of the posterior mean under the prediction risk in ultra-high-dimensional settings where the number of predictors can grow subexponentially relative to the sample size. A one-step post-processing scheme induced by group lasso penalties on the rows of the estimated coefficient matrix is proposed for variable selection, with default choices of tuning parameters. We additionally provide an estimate of the rank using a novel optimization function achieving dimension reduction in the covariate space. We exhibit the performance of the proposed methodology in an extensive simulation study and a real data example. 

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3. Covariance-Regularized Regression and Classification for high Dimensional Problems

   https://doi.org/10.1111/j.1467-9868.2009.00699.x  

   Witten, Daniela M. ; Tibshirani, Robert ( February 2009 , Journal of the Royal Statistical Society Series B: Statistical Methodology)

   We propose covariance-regularized regression, a family of methods for prediction in high dimensional settings that uses a shrunken estimate of the inverse covariance matrix of the features to achieve superior prediction. An estimate of the inverse covariance matrix is obtained by maximizing the log-likelihood of the data, under a multivariate normal model, subject to a penalty; it is then used to estimate coefficients for the regression of the response onto the features. We show that ridge regression, the lasso and the elastic net are special cases of covariance-regularized regression, and we demonstrate that certain previously unexplored forms of covariance-regularized regression can outperform existing methods in a range of situations. The covariance-regularized regression framework is extended to generalized linear models and linear discriminant analysis, and is used to analyse gene expression data sets with multiple class and survival outcomes.

    

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4. Quantile Regression for Nonignorable Missing Data with Its Application of Analyzing Electronic Medical Records

   https://doi.org/10.1111/biom.13723  

   Yu, Aiai ; Zhong, Yujie ; Feng, Xingdong ; Wei, Ying ( July 2022 , Biometrics)

   Over the past decade, there has been growing enthusiasm for using electronic medical records (EMRs) for biomedical research. Quantile regression estimates distributional associations, providing unique insights into the intricacies and heterogeneity of the EMR data. However, the widespread nonignorable missing observations in EMR often obscure the true associations and challenge its potential for robust biomedical discoveries. We propose a novel method to estimate the covariate effects in the presence of nonignorable missing responses under quantile regression. This method imposes no parametric specifications on response distributions, which subtly uses implicit distributions induced by the corresponding quantile regression models. We show that the proposed estimator is consistent and asymptotically normal. We also provide an efficient algorithm to obtain the proposed estimate and a randomly weighted bootstrap approach for statistical inferences. Numerical studies, including an empirical analysis of real-world EMR data, are used to assess the proposed method's finite-sample performance compared to existing literature.

    

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5. An approach of Bayesian variable selection for ultrahigh‐dimensional multivariate regression

   https://doi.org/10.1002/sta4.476  

   Dai, Xiaotian ; Fu, Guifang ; Reese, Randall ; Zhao, Shaofei ; Shang, Zuofeng ( October 2022 , Stat)

   In many practices, scientists are particularly interested in detecting which of the predictors are truly associated with a multivariate response. It is more accurate to model multiple responses as one vector rather than separating each component one by one. This is particularly true for complex traits having multiple correlated components. A Bayesian multivariate variable selection (BMVS) approach is proposed to select important predictors influencing the multivariate response from a candidate pool with ultrahigh dimension. By applying the sample‐size‐dependent spike and slab priors, the BMVS approach satisfies the strong selection consistency property under certain conditions, which represents the advantages of BMVS over other existing Bayesian multivariate regression‐based approaches. The proposed approach considers the covariance structure of multiple responses without assuming independence and integrates the estimation of covariance‐related parameters together with all regression parameters into one framework through a fast‐updating Markov chain Monte Carlo (MCMC) procedure. It is demonstrated through simulations that the BMVS approach outperforms some other relevant frequentist and Bayesian approaches. The proposed BMVS approach possesses a flexibility of wide applications, including genome‐wide association studies with multiple correlated phenotypes and a large scale of genetic variants and/or environmental variables, as demonstrated in the real data analyses section. The computer code and test data of the proposed method are available as an R package.

    

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