Summary   Many contemporary large‐scale applications involve building interpretable models linking a large set of potential covariates to a response in a non‐linear fashion, such as when the response is binary. Although this modelling problem has been extensively studied, it remains unclear how to control the fraction of false discoveries effectively even in high dimensional logistic regression, not to mention general high dimensional non‐linear models. To address such a practical problem, we propose a new framework of ‘model‐X’ knockoffs, which reads from a different perspective the knockoff procedure that was originally designed for controlling the false discovery rate in linear models. Whereas the knockoffs procedure is constrained to homoscedastic linear models with n⩾p, the key innovation here is that model‐X knockoffs provide valid inference from finite samples in settings in which the conditional distribution of the response is arbitrary and completely unknown. Furthermore, this holds no matter the number of covariates. Correct inference in such a broad setting is achieved by constructing knockoff variables probabilistically instead of geometrically. To do this, our approach requires that the covariates are random (independent and identically distributed rows) with a distribution that is known, although we provide preliminary experimental evidence that our procedure is robust to unknown or estimated distributions. To our knowledge, no other procedure solves the controlled variable selection problem in such generality but, in the restricted settings where competitors exist, we demonstrate the superior power of knockoffs through simulations. Finally, we apply our procedure to data from a case–control study of Crohn's disease in the UK, making twice as many discoveries as the original analysis of the same data.

Classification using high-dimensional features arises frequently in many contemporary statistical studies such as tumor classification using microarray or other high-throughput data. The impact of dimensionality on classifications is largely poorly understood. In a seminal paper, Bickel and Levina (2004) show that the Fisher discriminant performs poorly due to diverging spectra and they propose to use the independence rule to overcome the problem. We first demonstrate that even for the independence classification rule, classification using all the features can be as bad as the random guessing due to noise accumulation in estimating population centroids in high-dimensional feature space. In fact, we demonstrate further that almost all linear discriminants can perform as bad as the random guessing. Thus, it is paramountly important to select a subset of important features for highdimensional classification, resulting in Features Annealed Independence Rules (FAIR). The conditions under which all the important features can be selected by the two-sample t-statistic are established. The choice of the optimal number of features, or equivalently, the threshold value of the test statistics are proposed based on an upper bound of the classification error. Simulation studies and real data analysis support our theoretical results and demonstrate convincingly the advantage of our new classification procedure.

The variance-covariance matrix plays a central role in the inferential theories of high-dimensional factor models in finance and economics. Popular regularization methods of directly exploiting sparsity are not directly applicable to many financial problems. Classical methods of estimating the covariance matrices are based on the strict factor models, assuming independent idiosyncratic components. This assumption, however, is restrictive in practical applications. By assuming sparse error covariance matrix, we allow the presence of the cross-sectional correlation even after taking out common factors, and it enables us to combine the merits of both methods. We estimate the sparse covariance using the adaptive thresholding technique as in Cai and Liu [J. Amer. Statist. Assoc. 106 (2011) 672-684], taking into account the fact that direct observations of the idiosyncratic components are unavailable. The impact of high dimensionality on the covariance matrix estimation based on the factor structure is then studied.

Model selection and sparse recovery are two important problems for which many regularization methods have been proposed. We study the properties of regularization methods in both problems under the unified framework of regularized least squares with concave penalties. For model selection, we establish conditions under which a regularized least squares estimator enjoys a nonasymptotic property, called the weak oracle property, where the dimensionality can grow exponentially with sample size. For sparse recovery, we present a sufficient condition that ensures the recoverability of the sparsest solution. In particular, we approach both problems by considering a family of penalties that give a smooth homotopy between L0 and L1 penalties. We also propose the sequentially and iteratively reweighted squares (SIRS) algorithm for sparse recovery. Numerical studies support our theoretical results and demonstrate the advantage of our new methods for model selection and sparse recovery.

Determining how to appropriately select the tuning parameter is essential in penalized likelihood methods for high-dimensional data analysis. We examine this problem in the setting of penalized likelihood methods for generalized linear models, where the dimensionality of covariates p is allowed to increase exponentially with the sample size n. We propose to select the tuning parameter by optimizing the generalized information criterion (GIC) with an appropriate model complexity penalty. To ensure that we consistently identify the true model, a range for the model complexity penalty is identified in GIC. We find that this model complexity penalty should diverge at the rate of some power of $\log p$ depending on the tail probability behavior of the response variables. This reveals that using the AIC or BIC to select the tuning parameter may not be adequate for consistently identifying the true model. Based on our theoretical study, we propose a uniform choice of the model complexity penalty and show that the proposed approach consistently identifies the true model among candidate models with asymptotic probability one. We justify the performance of the proposed procedure by numerical simulations and a gene expression data analysis.Comment: 38 page

This paper is concerned with the selection and estimation of fixed and random effects in linear mixed effects models. We propose a class of nonconcave penalized profile likelihood methods for selecting and estimating important fixed effects. To overcome the difficulty of unknown covariance matrix of random effects, we propose to use a proxy matrix in the penalized profile likelihood. We establish conditions on the choice of the proxy matrix and show that the proposed procedure enjoys the model selection consistency where the number of fixed effects is allowed to grow exponentially with the sample size. We further propose a group variable selection strategy to simultaneously select and estimate important random effects, where the unknown covariance matrix of random effects is replaced with a proxy matrix. We prove that, with the proxy matrix appropriately chosen, the proposed procedure can identify all true random effects with asymptotic probability one, where the dimension of random effects vector is allowed to increase exponentially with the sample size. Monte Carlo simulation studies are conducted to examine the finite-sample performance of the proposed procedures. We further illustrate the proposed procedures via a real data example.

Heavy-tailed high-dimensional data are commonly encountered in various scientific fields and pose great challenges to modern statistical analysis. A natural procedure to address this problem is to use penalized quantile regression with weighted L1-penalty, called weighted robust Lasso (WR-Lasso), in which weights are introduced to ameliorate the bias problem induced by the L1-penalty. In the ultra-high dimensional setting, where the dimensionality can grow exponentially with the sample size, we investigate the model selection oracle property and establish the asymptotic normality of the WR-Lasso. We show that only mild conditions on the model error distribution are needed. Our theoretical results also reveal that adaptive choice of the weight vector is essential for the WR-Lasso to enjoy these nice asymptotic properties. To make the WR-Lasso practically feasible, we propose a two-step procedure, called adaptive robust Lasso (AR-Lasso), in which the weight vector in the second step is constructed based on the L1-penalized quantile regression estimate from the first step. This two-step procedure is justified theoretically to possess the oracle property and the asymptotic normality. Numerical studies demonstrate the favorable finite-sample performance of the AR-Lasso.

We suggest a new method, called Functional Additive Regression, or FAR, for efficiently performing high-dimensional functional regression. FAR extends the usual linear regression model involving a functional predictor, $X(t)$, and a scalar response, $Y$, in two key respects. First, FAR uses a penalized least squares optimization approach to efficiently deal with high-dimensional problems involving a large number of functional predictors. Second, FAR extends beyond the standard linear regression setting to fit general nonlinear additive models. We demonstrate that FAR can be implemented with a wide range of penalty functions using a highly efficient coordinate descent algorithm. Theoretical results are developed which provide motivation for the FAR optimization criterion. Finally, we show through simulations and two real data sets that FAR can significantly outperform competing methods.Comment: Published at http://dx.doi.org/10.1214/15-AOS1346 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org