A Sparse Structured Shrinkage Estimator for Nonparametric Varying-Coefficient Model with an Application in Genomics

Many problems in genomics are related to variable selection where high-dimensional genomic data are treated as covariates. Such genomic covariates often have certain structures and can be represented as vertices of an undirected graph. Biological processes also vary as functions depending upon some biological state, such as time. High-dimensional variable selection where covariates are graph-structured and underlying model is nonparametric presents an important but largely unaddressed statistical challenge. Motivated by the problem of regression-based motif discovery, we consider the problem of variable selection for high-dimensional nonparametric varying-coefficient models and introduce a sparse structured shrinkage (SSS) estimator based on basis function expansions and a novel smoothed penalty function. We present an efficient algorithm for computing the SSS estimator. Results on model selection consistency and estimation bounds are derived. Moreover, finite-sample performances are studied via simulations, and the effects of high-dimensionality and structural information of the covariates are especially highlighted. We apply our method to motif finding problem using a yeast cell-cycle gene expression dataset and word counts in genes' promoter sequences. Our results demonstrate that the proposed method can result in better variable selection and prediction for high-dimensional regression when the underlying model is nonparametric and covariates are structured. Supplemental materials for the article are available online.     

Asymptotic properties of Lasso in high-dimensional partially linear models

We study the properties of the Lasso in the high-dimensional partially linear model where the number of variables in the linear part can be greater than the sample size. We use truncated series expansion based on polynomial splines to approximate the nonparametric component in this model. Under a sparsity assumption on the regression coefficients of the linear component and some regularity conditions, we derive the oracle inequalities for the prediction risk and the estimation error. We also provide sufficient conditions under which the Lasso estimator is selection consistent for the variables in the linear part of the model. In addition, we derive the rate of convergence of the estimator of the nonparametric function. We conduct simulation studies to evaluate the finite sample performance of variable selection and nonparametric function estimation.     

Variable selection and model choice in structured survival models

We aim at modeling the survival time of intensive care patients suffering from severe sepsis. The nature of the problem requires a flexible model that allows to extend the classical Cox-model via the inclusion of time-varying and nonparametric effects. These structured survival models are very flexible but additional difficulties arise when model choice and variable selection are desired. In particular, it has to be decided which covariates should be assigned time-varying effects or whether linear modeling is sufficient for a given covariate. Component-wise boosting provides a means of likelihood-based model fitting that enables simultaneous variable selection and model choice. We introduce a component-wise, likelihood-based boosting algorithm for survival data that permits the inclusion of both parametric and nonparametric time-varying effects as well as nonparametric effects of continuous covariates utilizing penalized splines as the main modeling technique. An empirical evaluation of the methodology precedes the model building for the severe sepsis data. A software implementation is available to the interested reader.     

The rate of convergence for sparse and low-rank quantile trace regression

Trace regression models are widely used in applications involving panel data, images, genomic microarrays, etc., where high-dimensional covariates are often involved. However, the existing research involving high-dimensional covariates focuses mainly on the condition mean model. In this paper, we extend the trace regression model to the quantile trace regression model when the parameter is a matrix of simultaneously low rank and row (column) sparsity. The convergence rate of the penalized estimator is derived under mild conditions. Simulations, as well as a real data application, are also carried out for illustration.     

Marginal quantile regression for varying coefficient models with longitudinal data

In this paper, we investigate the quantile varying coefficient model for longitudinal data, where the unknown nonparametric functions are approximated by polynomial splines and the estimators are obtained by minimizing the quadratic inference function. The theoretical properties of the resulting estimators are established, and they achieve the optimal convergence rate for the nonparametric functions. Since the objective function is non-smooth, an estimation procedure is proposed that uses induced smoothing and we prove that the smoothed estimator is asymptotically equivalent to the original estimator. Moreover, we propose a variable selection procedure based on the regularization method, which can simultaneously estimate and select important nonparametric components and has the asymptotic oracle property. Extensive simulations and a real data analysis show the usefulness of the proposed method.

     

Variable selection for single-index varying-coefficient model

We consider the problem of variable selection for single-index varying-coefficient model, and present a regularized variable selection procedure by combining basis function approximations with SCAD penalty. The proposed procedure simultaneously selects significant covariates with functional coefficients and local significant variables with parametric coefficients. With appropriate selection of the tuning parameters, the consistency of the variable selection procedure and the oracle property of the estimators are established. The proposed method can naturally be applied to deal with pure single-index model and varying-coefficient model. Finite sample performances of the proposed method are illustrated by a simulation study and the real data analysis.     

Robust and efficient variable selection for semiparametric partially linear varying coefficient model based on modal regression

Semiparametric partially linear varying coefficient models (SPLVCM) are frequently used in statistical modeling. With high-dimensional covariates both in parametric and nonparametric part for SPLVCM, sparse modeling is often considered in practice. In this paper, we propose a new estimation and variable selection procedure based on modal regression, where the nonparametric functions are approximated by $B$ -spline basis. The outstanding merit of the proposed variable selection procedure is that it can achieve both robustness and efficiency by introducing an additional tuning parameter (i.e., bandwidth $h$ ). Its oracle property is also established for both the parametric and nonparametric part. Moreover, we give the data-driven bandwidth selection method and propose an EM-type algorithm for the proposed method. Monte Carlo simulation study and real data example are conducted to examine the finite sample performance of the proposed method. Both the simulation results and real data analysis confirm that the newly proposed method works very well.     

高维部分线性模型的变量选择和估计

考虑高维部分线性模型,提出了同时进行变量选择和估计兴趣参数的变量选择方法.将Dantzig变量选择应用到线性部分及非参数部分的各阶导数,从而获得参数和非参数部分的估计,且参数部分的估计具有稀疏性,证明了估计的非渐近理论界.最后,模拟研究了有限样本的性质.     

Robust variable selection for finite mixture regression models

Finite mixture regression (FMR) models are frequently used in statistical modeling, often with many covariates with low significance. Variable selection techniques can be employed to identify the covariates with little influence on the response. The problem of variable selection in FMR models is studied here. Penalized likelihood-based approaches are sensitive to data contamination, and their efficiency may be significantly reduced when the model is slightly misspecified. We propose a new robust variable selection procedure for FMR models. The proposed method is based on minimum-distance techniques, which seem to have some automatic robustness to model misspecification. We show that the proposed estimator has the variable selection consistency and oracle property. The finite-sample breakdown point of the estimator is established to demonstrate its robustness. We examine small-sample and robustness properties of the estimator using a Monte Carlo study. We also analyze a real data set.     

Variable Selection in Varying-Coefficient Models Using P-Splines

In this article, we consider nonparametric smoothing and variable selection in varying-coefficient models. Varying-coefficient models are commonly used for analyzing the time-dependent effects of covariates on responses measured repeatedly (such as longitudinal data). We present the P-spline estimator in this context and show its estimation consistency for a diverging number of knots (or B-spline basis functions). The combination of P-splines with nonnegative garrote (which is a variable selection method) leads to good estimation and variable selection. Moreover, we consider APSO (additive P-spline selection operator), which combines a P-spline penalty with a regularization penalty, and show its estimation and variable selection consistency. The methods are illustrated with a simulation study and real-data examples. The proofs of the theoretical results as well as one of the real-data examples are provided in the online supplementary materials.     

Simultaneous confidence bands for nonparametric regression with missing covariate data

We consider a weighted local linear estimator based on the inverse selection probability for nonparametric regression with missing covariates at random. The asymptotic distribution of the maximal deviation between the estimator and the true regression function is derived and an asymptotically accurate simultaneous confidence band is constructed. The estimator for the regression function is shown to be oracally efficient in the sense that it is uniformly indistinguishable from that when the selection probabilities are known. Finite sample performance is examined via simulation studies which support our asymptotic theory. The proposed method is demonstrated via an analysis of a data set from the Canada 2010/2011 Youth Student Survey.

     

Hierarchical nonparametric survival modeling for demand forecasting with fragmented categorical covariates

This paper addresses the problem of data fragmentation when incorporating imbalanced categorical covariates in nonparametric survival models. The problem arises in an application of demand forecasting where certain categorical covariates are important explanatory factors for the diversity of survival patterns but are severely imbalanced in the sense that a large percentage of data segments defined by these covariates have very small sample sizes. Two general approaches, called the class‐based approach and the fusion‐based approach, are proposed to handle the problem. Both reply on judicious utilization of a data segment hierarchy defined by the covariates. The class‐based approach allows certain segments in the hierarchy to have their private survival functions and aggregates the others to share a common survival function. The fusion‐based approach allows all survival functions to borrow and share information from all segments based on their positions in the hierarchy. A nonparametric Bayesian estimator with Dirichlet process priors provides the data‐sharing mechanism in the fusion‐based approach. The hyperparameters in the priors are treated as fixed quantities and learned from data by taking advantage of the data segment hierarchy. The proposed methods are motivated and validated by a case study with real‐world data from an operation of software development service.     

Post selection shrinkage estimation for high‐dimensional data analysis

In high‐dimensional data settings where p  ? n , many penalized regularization approaches were studied for simultaneous variable selection and estimation. However, with the existence of covariates with weak effect, many existing variable selection methods, including Lasso and its generations, cannot distinguish covariates with weak and no contribution. Thus, prediction based on a subset model of selected covariates only can be inefficient. In this paper, we propose a post selection shrinkage estimation strategy to improve the prediction performance of a selected subset model. Such a post selection shrinkage estimator (PSE) is data adaptive and constructed by shrinking a post selection weighted ridge estimator in the direction of a selected candidate subset. Under an asymptotic distributional quadratic risk criterion, its prediction performance is explored analytically. We show that the proposed post selection PSE performs better than the post selection weighted ridge estimator. More importantly, it improves the prediction performance of any candidate subset model selected from most existing Lasso‐type variable selection methods significantly. The relative performance of the post selection PSE is demonstrated by both simulation studies and real‐data analysis. Copyright © 2016 John Wiley & Sons, Ltd.     

Nonlinear logistic discrimination via regularized radial basis functions for classifying high-dimensional data

A flexible nonparametric method is proposed for classifying high- dimensional data with a complex structure. The proposed method can be regarded as an extended version of linear logistic discriminant procedures, in which the linear predictor is replaced by a radial-basis-expansion predictor. Radial basis functions with a hyperparameter are used to take the information on covariates and class labels into account; this was nearly impossible within the previously proposed hybrid learning framework. The penalized maximum likelihood estimation procedure is employed to obtain stable parameter estimates. A crucial issue in the model-construction process is the choice of a suitable model from candidates. This issue is examined from information-theoretic and Bayesian viewpoints and we employed Ando et al. (Japanese Journal of Applied Statistics, 31, 123–139, 2002)’s model evaluation criteria. The proposed method is available not only for the high-dimensional data but also for the variable selection problem. Real data analysis and Monte Carlo experiments show that our proposed method performs well in classifying future observations in practical situations. The simulation results also show that the use of the hyperparameter in the basis functions improves the prediction performance.     

Functional-coefficient partially linear regression model

In this paper, the functional-coefficient partially linear regression (FCPLR) model is proposed by combining nonparametric and functional-coefficient regression (FCR) model. It includes the FCR model and the nonparametric regression (NPR) model as its special cases. It is also a generalization of the partially linear regression (PLR) model obtained by replacing the parameters in the PLR model with some functions of the covariates. The local linear technique and the integrated method are employed to give initial estimators of all functions in the FCPLR model. These initial estimators are asymptotically normal. The initial estimator of the constant part function shares the same bias as the local linear estimator of this function in the univariate nonparametric model, but the variance of the former is bigger than that of the latter. Similarly, initial estimators of every coefficient function share the same bias as the local linear estimates in the univariate FCR model, but the variance of the former is bigger than that of the latter. To decrease the variance of the initial estimates, a one-step back-fitting technique is used to obtain the improved estimators of all functions. The improved estimator of the constant part function has the same asymptotic normality property as the local linear nonparametric regression for univariate data. The improved estimators of the coefficient functions have the same asymptotic normality properties as the local linear estimates in FCR model. The bandwidths and the smoothing variables are selected by a data-driven method. Both simulated and real data examples related to nonlinear time series modeling are used to illustrate the applications of the FCPLR model.     

Nonparametric variable selection and its application to additive models

Variable selection for multivariate nonparametric regression models usually involves parameterized approximation for nonparametric functions in the objective function. However, this parameterized approximation often increases the number of parameters significantly, leading to the “curse of dimensionality” and inaccurate estimation. In this paper, we propose a novel and easily implemented approach to do variable selection in nonparametric models without parameterized approximation, enabling selection consistency to be achieved. The proposed method is applied to do variable selection for additive models. A two-stage procedure with selection and adaptive estimation is proposed, and the properties of this method are investigated. This two-stage algorithm is adaptive to the smoothness of the underlying components, and the estimation consistency can reach a parametric rate if the underlying model is really parametric. Simulation studies are conducted to examine the performance of the proposed method. Furthermore, a real data example is analyzed for illustration.

     

基于条件分布函数的高维回归模型的变量选择方法

高维回归分析的变量选择问题是目前统计学研究的一个热点和难点问题.提出了一个基于条件分布函数的相关性度量准则,并在此基础上提出三种变量选择方法.与现有的方法相比,提出的方法不依赖于统计模型,可以适用于线性模型和非参数可加模型.数值模拟结果表明,即使协变量之间存在一定的相关性,方法也有较为满意的表现.     

Estimation of additive quantile regression

We consider the nonparametric estimation problem of conditional regression quantiles with high-dimensional covariates. For the additive quantile regression model, we propose a new procedure such that the estimated marginal effects of additive conditional quantile curves do not cross. The method is based on a combination of the marginal integration technique and non-increasing rearrangements, which were recently introduced in the context of estimating a monotone regression function. Asymptotic normality of the estimates is established with a one-dimensional rate of convergence and the finite sample properties are studied by means of a simulation study and a data example.     

Variable selection for semiparametric varying coefficient partially linear errors-in-variables models

This paper focuses on the variable selections for semiparametric varying coefficient partially linear models when the covariates in the parametric and nonparametric components are all measured with errors. A bias-corrected variable selection procedure is proposed by combining basis function approximations with shrinkage estimations. With appropriate selection of the tuning parameters, the consistency of the variable selection procedure and the oracle property of the regularized estimators are established. A simulation study and a real data application are undertaken to evaluate the finite sample performance of the proposed method.     

Oracle inequality for conditional density estimation and an actuarial example

Conditional density estimation in a parametric regression setting, where the problem is to estimate a parametric density of the response given the predictor, is a classical and prominent topic in regression analysis. This article explores this problem in a nonparametric setting where no assumption about shape of an underlying conditional density is made. For the first time in the literature, it is proved that there exists a nonparametric data-driven estimator that matches performance of an oracle which: (i) knows the underlying conditional density, (ii) adapts to an unknown design of predictors, (iii) performs a dimension reduction if the response does not depend on the predictor, (iv) is minimax over a vast set of anisotropic bivariate function classes. All these results are established via an oracle inequality which is on par with ones known in the univariate density estimation literature. Further, the asymptotically optimal estimator is tested on an interesting actuarial example which explores a relationship between credit scoring and premium for basic auto-insurance for 54 undergraduate college students.