Comparing large covariance matrices under weak conditions on the dependence structure and its application to gene clustering

Comparing large covariance matrices has important applications in modern genomics, where scientists are often interested in understanding whether relationships (e.g., dependencies or co-regulations) among a large number of genes vary between different biological states. We propose a computationally fast procedure for testing the equality of two large covariance matrices when the dimensions of the covariance matrices are much larger than the sample sizes. A distinguishing feature of the new procedure is that it imposes no structural assumptions on the unknown covariance matrices. Hence the test is robust with respect to various complex dependence structures that frequently arise in genomics. We prove that the proposed procedure is asymptotically valid under weak moment conditions. As an interesting application, we derive a new gene clustering algorithm which shares the same nice property of avoiding restrictive structural assumptions for high-dimensional genomics data. Using an asthma gene expression dataset, we illustrate how the new test helps compare the covariance matrices of the genes across different gene sets/pathways between the disease group and the control group, and how the gene clustering algorithm provides new insights on the way gene clustering patterns differ between the two groups. The proposed methods have been implemented in an R-package HDtest and is available on CRAN.Comment: The original title dated back to May 2015 is "Bootstrap Tests on High Dimensional Covariance Matrices with Applications to Understanding Gene Clustering

Simulation-Based Hypothesis Testing of High Dimensional Means Under Covariance Heterogeneity

In this paper, we study the problem of testing the mean vectors of high dimensional data in both one-sample and two-sample cases. The proposed testing procedures employ maximum-type statistics and the parametric bootstrap techniques to compute the critical values. Different from the existing tests that heavily rely on the structural conditions on the unknown covariance matrices, the proposed tests allow general covariance structures of the data and therefore enjoy wide scope of applicability in practice. To enhance powers of the tests against sparse alternatives, we further propose two-step procedures with a preliminary feature screening step. Theoretical properties of the proposed tests are investigated. Through extensive numerical experiments on synthetic datasets and an human acute lymphoblastic leukemia gene expression dataset, we illustrate the performance of the new tests and how they may provide assistance on detecting disease-associated gene-sets. The proposed methods have been implemented in an R-package HDtest and are available on CRAN.Comment: 34 pages, 10 figures; Accepted for biometric

Matrix Completion via Max-Norm Constrained Optimization

Matrix completion has been well studied under the uniform sampling model and the trace-norm regularized methods perform well both theoretically and numerically in such a setting. However, the uniform sampling model is unrealistic for a range of applications and the standard trace-norm relaxation can behave very poorly when the underlying sampling scheme is non-uniform. In this paper we propose and analyze a max-norm constrained empirical risk minimization method for noisy matrix completion under a general sampling model. The optimal rate of convergence is established under the Frobenius norm loss in the context of approximately low-rank matrix reconstruction. It is shown that the max-norm constrained method is minimax rate-optimal and yields a unified and robust approximate recovery guarantee, with respect to the sampling distributions. The computational effectiveness of this method is also discussed, based on first-order algorithms for solving convex optimizations involving max-norm regularization.Comment: 33 page

A Max-Norm Constrained Minimization Approach to 1-Bit Matrix Completion

We consider in this paper the problem of noisy 1-bit matrix completion under a general non-uniform sampling distribution using the max-norm as a convex relaxation for the rank. A max-norm constrained maximum likelihood estimate is introduced and studied. The rate of convergence for the estimate is obtained. Information-theoretical methods are used to establish a minimax lower bound under the general sampling model. The minimax upper and lower bounds together yield the optimal rate of convergence for the Frobenius norm loss. Computational algorithms and numerical performance are also discussed.Comment: 33 pages, 3 figure

Cram\'er type moderate deviation theorems for self-normalized processes

Cram\'er type moderate deviation theorems quantify the accuracy of the relative error of the normal approximation and provide theoretical justifications for many commonly used methods in statistics. In this paper, we develop a new randomized concentration inequality and establish a Cram\'er type moderate deviation theorem for general self-normalized processes which include many well-known Studentized nonlinear statistics. In particular, a sharp moderate deviation theorem under optimal moment conditions is established for Studentized $U$-statistics.Comment: Published at http://dx.doi.org/10.3150/15-BEJ719 in the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm

Nonparametric covariate-adjusted regression

We consider nonparametric estimation of a regression curve when the data are observed with multiplicative distortion which depends on an observed confounding variable. We suggest several estimators, ranging from a relatively simple one that relies on restrictive assumptions usually made in the literature, to a sophisticated piecewise approach that involves reconstructing a smooth curve from an estimator of a constant multiple of its absolute value, and which can be applied in much more general scenarios. We show that, although our nonparametric estimators are constructed from predictors of the unobserved undistorted data, they have the same first order asymptotic properties as the standard estimators that could be computed if the undistorted data were available. We illustrate the good numerical performance of our methods on both simulated and real datasets.Comment: 32 pages, 4 figure

On Gaussian Comparison Inequality and Its Application to Spectral Analysis of Large Random Matrices

Recently, Chernozhukov, Chetverikov, and Kato [Ann. Statist. 42 (2014) 1564--1597] developed a new Gaussian comparison inequality for approximating the suprema of empirical processes. This paper exploits this technique to devise sharp inference on spectra of large random matrices. In particular, we show that two long-standing problems in random matrix theory can be solved: (i) simple bootstrap inference on sample eigenvalues when true eigenvalues are tied; (ii) conducting two-sample Roy's covariance test in high dimensions. To establish the asymptotic results, a generalized $\epsilon$-net argument regarding the matrix rescaled spectral norm and several new empirical process bounds are developed and of independent interest.Comment: to appear in Bernoull

Are Discoveries Spurious? Distributions of Maximum Spurious Correlations and Their Applications

Over the last two decades, many exciting variable selection methods have been developed for finding a small group of covariates that are associated with the response from a large pool. Can the discoveries from these data mining approaches be spurious due to high dimensionality and limited sample size? Can our fundamental assumptions about the exogeneity of the covariates needed for such variable selection be validated with the data? To answer these questions, we need to derive the distributions of the maximum spurious correlations given a certain number of predictors, namely, the distribution of the correlation of a response variable $Y$ with the best $s$ linear combinations of $p$ covariates $\mathbf{X}$, even when $\mathbf{X}$ and $Y$ are independent. When the covariance matrix of $\mathbf{X}$ possesses the restricted eigenvalue property, we derive such distributions for both a finite $s$ and a diverging $s$, using Gaussian approximation and empirical process techniques. However, such a distribution depends on the unknown covariance matrix of $\mathbf{X}$. Hence, we use the multiplier bootstrap procedure to approximate the unknown distributions and establish the consistency of such a simple bootstrap approach. The results are further extended to the situation where the residuals are from regularized fits. Our approach is then used to construct the upper confidence limit for the maximum spurious correlation and to test the exogeneity of the covariates. The former provides a baseline for guarding against false discoveries and the latter tests whether our fundamental assumptions for high-dimensional model selection are statistically valid. Our techniques and results are illustrated with both numerical examples and real data analysis