The increasing complexity of data requires methods and models that can effectively handle intricate structures, as simplifying them would result in loss of information. While several analytical tools have been developed to work with complex data objects in their original form, these tools are typically limited to single-type variables. In this work, we propose energy trees as a regression and classification model capable of accommodating structured covariates of various types. Energy trees leverage energy statistics to extend the capabilities of conditional inference trees, from which they inherit sound statistical foundations, interpretability, scale invariance, and freedom from distributional assumptions. We specifically focus on functional and graph-structured covariates, while also highlighting the model's flexibility in integrating other variable types. Extensive simulation studies demonstrate the model's competitive performance in terms of variable selection and robustness to overfitting. Finally, we assess the model's predictive ability through two empirical analyses involving human biological data. Energy trees are implemented in the R package etree.
The Graduate University for Advanced Studies, SOKENDAI（综合研究大学院大学）
Robust and sparse estimation of linear regression coefficients is investigated. The situation addressed by the present paper is that covariates and noises are sampled from heavy-tailed distributions, and the covariates and noises are contaminated by malicious outliers. Our estimator can be computed efficiently. Further, the error bound of the estimator is nearly optimal.
We consider the problem of variable selection in regression models. In particular, we are interested in selecting explanatory covariates linked with the response variable and we want to determine which covariates are relevant, that is which covariates are involved in the model. In this framework, we deal with L1-penalised regression models. To handle the choice of the penalty parameter to perform variable selection, we develop a new method based on the knockoffs idea. This revisited knockoffs method is general, suitable for a wide range of regressions with various types of response variables. …
Lasso is a popular and efficient approach to simultaneous estimation and variable selection in high-dimensional regression models. In this paper, a robust LAD-lasso method for multiple outcomes is presented that addresses the challenges of non-normal outcome distributions and outlying observations. Measured covariate data from space or time, or spectral bands or genomic positions often have natural correlation structure arising from measuring distance between the covariates. The proposed multi-outcome approach includes handling of such covariate blocks by a group fusion penalty, which encourag…
Gaussian graphical regression is a powerful means that regresses the precision matrix of a Gaussian graphical model on covariates, permitting the numbers of the response variables and covariates to far exceed the sample size. Model fitting is typically carried out via separate node-wise lasso regressions, ignoring the network-induced structure among these regressions. Consequently, the error rate is high, especially when the number of nodes is large. We propose a multi-task learning estimator for fitting Gaussian graphical regression models; we design a cross-task group sparsity penalty and a …
Sliced inverse regression is a popular tool for sufficient dimension reduction, which replaces covariates with a minimal set of their linear combinations without loss of information on the conditional distribution of the response given the covariates. The estimated linear combinations include all covariates, making results difficult to interpret and perhaps unnecessarily variable, particularly when the number of covariates is large. In this paper, we propose a convex formulation for fitting sparse sliced inverse regression in high dimensions. Our proposal estimates the subspace of the linear c…
Though Gaussian graphical models have been widely used in many scientific fields, relatively limited progress has been made to link graph structures to external covariates. We propose a Gaussian graphical regression model, which regresses both the mean and the precision matrix of a Gaussian graphical model on covariates. In the context of co-expression quantitative trait locus (QTL) studies, our method can determine how genetic variants and clinical conditions modulate the subject-level network structures, and recover both the population-level and subject-level gene networks. Our framework enc…
We propose a new model selection criterion for mixed effects regression models that is computable when the model is fitted with a two-step method, even when the structure and the distribution of the random effects are unknown. The criterion is especially useful in the early stage of the model building process when one needs to decide which covariates should be included in a mixed effects regression model but has no knowledge of the random effect structure. This is particularly relevant in substantive fields where variable selection is guided by information criteria rather than regularization. …
Graphs and networks are common ways of depicting biological information. In biology, many different biological processes are represented by graphs, such as regulatory networks, metabolic pathways and protein--protein interaction networks. This kind of a priori use of graphs is a useful supplement to the standard numerical data such as microarray gene expression data. In this paper we consider the problem of regression analysis and variable selection when the covariates are linked on a graph. We study a graph-constrained regularization procedure and its theoretical properties for regression ana…
École Polytechnique Fédérale de Lausanne（洛桑联邦理工学院）
Data analyses based on linear methods constitute the simplest, most robust, and transparent approaches to the automatic processing of large amounts of data for building supervised or unsupervised machine learning models. Principal covariates regression (PCovR) is an underappreciated method that interpolates between principal component analysis and linear regression, and can be used to conveniently reveal structure-property relations in terms of simple-to-interpret, low-dimensional maps. Here we provide a pedagogic overview of these data analysis schemes, including the use of the kernel trick t…
This paper investigates the high-dimensional linear regression with highly correlated covariates. In this setup, the traditional sparsity assumption on the regression coefficients often fails to hold, and consequently many model selection procedures do not work. To address this challenge, we model the variations of covariates by a factor structure. Specifically, strong correlations among covariates are explained by common factors and the remaining variations are interpreted as idiosyncratic components of each covariate. This leads to a factor-adjusted regression model with both common factors …
Given data $y$ and $k$ covariates $x$ one problem in linear regression is to decide which in any of the covariates to include when regressing $y$ on the $x$. If $k$ is small it is possible to evaluate each subset of the $x$. If however $k$ is large then some other procedure must be use. Stepwise regression and the lasso are two such procedures but they both assume a linear model with error term. A different approach is taken here which does not assume a model. A covariate is included if it is better than random noise. This defines a procedure which is simple both conceptually and algorithmical…
This paper presents tests to formally choose between regression models using different derivatives of a functional covariate in scalar-on-function regression. We demonstrate that for linear regression, models using different derivatives can be nested within a model that includes point-impact effects at the end-points of the observed functions. Contrasts can then be employed to test the specification of different derivatives. When nonlinear regression models are defined, we apply a $J$ test to determine the statistical significance of the nonlinear structure between a functional covariate and a…
In clinical or epidemiological follow-up studies, methods based on time scale indicators such as the restricted mean survival time (RMST) have been developed to some extent. Compared with traditional hazard rate indicator system methods, the RMST is easier to interpret and does not require the proportional hazard assumption. To date, regression models based on the RMST are indirect or direct models of the RMST and baseline covariates. However, time-dependent covariates are becoming increasingly common in follow-up studies. Based on the inverse probability of censoring weighting (IPCW) method, …
Classical penalized likelihood regression problems deal with the case that the independent variables data are known exactly. In practice, however, it is common to observe data with incomplete covariate information. We are concerned with a fundamentally important case where some of the observations do not represent the exact covariate information, but only a probability distribution. In this case, the maximum penalized likelihood method can be still applied to estimating the regression function. We first show that the maximum penalized likelihood estimate exists under a mild condition. In the c…
Quantile regression is a very important tool to explore the relationship between the response variable and its covariates. Motivated by mean regression with LASSO for compositional covariates proposed by Lin et al. (2014), we consider quantile regression with no-penalty and penalty function. We develop the computational algorithms based on linear programming. Numerical studies indicate that our methods provides the better alternative than mean regression under many settings, particularly for heavy-tailed or skewed distribution of the error term. Finally, we study the fat data using the propose…
The amount of data collected from patients involved in clinical trials is continuously growing. All patient characteristics are potential covariates that could be used to improve clinical trial analysis and power. However, the restricted number of patients in phases I and II studies limits the possible number of covariates included in the analyses. In this paper, we investigate the cost/benefit ratio of including covariates in the analysis of clinical trials. Within this context, we address the long-running question "What is the optimum number of covariates to include in a clinical trial?" To …
Since survival data occur over time, often important covariates that we wish to consider also change over time. Such covariates are referred as time-dependent covariates. Quantile regression offers flexible modeling of survival data by allowing the covariates to vary with quantiles. This paper provides a novel quantile regression model accommodating time-dependent covariates, for analyzing survival data subject to right censoring. Our simple estimation technique assumes the existence of instrumental variables. In addition, we present a doubly-robust estimator in the sense of Robins and Rotnitz…
In a regression analysis, suppose we suspect that there are several heterogeneous groups in the population that a sample represents. Mixture regression models have been applied to address such problems. By modeling the conditional distribution of the response given the covariate as a mixture, the sample can be clustered into groups and the individual regression models for the groups can be estimated simultaneously. This approach treats the covariate as deterministic so that the covariate carries no information as to which group the subject is likely to belong to. Although this assumption may b…
In this paper, we propose an empirical likelihood-based weighted estimator of regression parameter in quantile regression model with nonignorable missing covariates. The proposed estimator is computationally simple and achieves semiparametric efficiency if the probability of missingness on the fully observed variables is correctly specified. The efficiency gain of the proposed estimator over the complete-case-analysis estimator is quantified theoretically and illustrated via simulation and a real data application.
Logistic regression has been widely applied in the field of biomedical research for a long time. In some applications, covariates of interest have a natural structure, such as being a matrix, at the time of collection. The rows and columns of the covariate matrix then have certain physical meanings, and they must contain useful information regarding the response. If we simply stack the covariate matrix as a vector and fit the conventional logistic regression model, relevant information can be lost, and the problem of inefficiency will arise. Motivated from these reasons, we propose in this pap…
We study regression discontinuity designs when covariates are included in the estimation. We examine local polynomial estimators that include discrete or continuous covariates in an additive separable way, but without imposing any parametric restrictions on the underlying population regression functions. We recommend a covariate-adjustment approach that retains consistency under intuitive conditions, and characterize the potential for estimation and inference improvements. We also present new covariate-adjusted mean squared error expansions and robust bias-corrected inference procedures, with …
In regional economics research, a problem of interest is to detect similarities between regions, and estimate their shared coefficients in economics models. In this article, we propose a mixture of finite mixtures (MFM) clustered regression model with auxiliary covariates that account for similarities in demographic or economic characteristics over a spatial domain. Our Bayesian construction provides both inference for number of clusters and clustering configurations, and estimation for parameters for each cluster. Empirical performance of the proposed model is illustrated through simulation e…
We consider generalized linear regression analysis with left-censored covariate due to the lower limit of detection. Complete case analysis by eliminating observations with values below limit of detection yields valid estimates for regression coefficients, but loses efficiency; substitution methods are biased; maximum likelihood method relies on parametric models for the unobservable tail probability distribution of such covariate, thus may suffer from model misspecification. To obtain robust and more efficient results, we propose a semiparametric likelihood-based approach for the estimation o…
Many biological high-throughput data sets, such as targeted amplicon-based and metagenomic sequencing data, are compositional in nature. A common exploratory data analysis task is to infer statistical associations between the high-dimensional microbial compositions and habitat- or host-related covariates. We propose a general robust statistical regression framework, RobRegCC (Robust Regression with Compositional Covariates), which extends the linear log-contrast model by a mean shift formulation for capturing outliers. RobRegCC includes sparsity-promoting convex and non-convex penalties for pa…
In this paper we give a completely new approach to the problem of covariate selection in linear regression. A covariate or a set of covariates is included only if it is better in the sense of least squares than the same number of Gaussian covariates consisting of i.i.d. $N(0,1)$ random variables. The Gaussian P-value is defined as the probability that the Gaussian covariates are better. It is given in terms of the Beta distribution, it is exact and it holds for all data. The covariate selection procedures based on this require only a cut-off value $α$ for the Gaussian P-value: the default valu…
The Regression Discontinuity (RD) design is a widely used non-experimental method for causal inference and program evaluation. While its canonical formulation only requires a score and an outcome variable, it is common in empirical work to encounter RD analyses where additional variables are used for adjustment. This practice has led to misconceptions about the role of covariate adjustment in RD analysis, from both methodological and empirical perspectives. In this chapter, we review the different roles of covariate adjustment in RD designs, and offer methodological guidance for its correct us…
We consider the situation of estimating Cox regression in which some covariates are subject to missing, and there exists additional information (including observed event time, censoring indicator and fully observed covariates) which may be predictive of the missing covariates. We propose to use two working regression models: one for predicting the missing covariates and the other for predicting the missing probabilities. For each missing covariate observation, these two working models are used to define a nearest neighbor imputing set. This set is then used to nonparametrically impute covariat…
Linear regression is arguably the most fundamental statistical model; however, the validity of its use in randomized clinical trials, despite being common practice, has never been crystal clear, particularly when stratified or covariate-adaptive randomization is used. In this paper, we investigate several of the most intuitive and commonly used regression models for estimating and inferring the treatment effect in randomized clinical trials. By allowing the regression model to be arbitrarily misspecified, we demonstrate that all these regression-based estimators robustly estimate the treatment…
In this paper, 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 st…
Doubly robust target inference for generalized linear regression with completely missing covariates
School of Mathematics and Statistics, Huazhong University of Science and Technology（华中科技大学数学与统计学院）；Department of Statistics and Data Science, Tsinghua University（清华大学统计与数据科学系）
Datasets from field experiments with covariate-adaptive randomizations (CARs) usually contain extra covariates in addition to the strata indicators. We propose to incorporate these additional covariates via auxiliary regressions in the estimation and inference of unconditional quantile treatment effects (QTEs) under CARs. We establish the consistency and limit distribution of the regression-adjusted QTE estimator and prove that the use of multiplier bootstrap inference is non-conservative under CARs. The auxiliary regression may be estimated parametrically, nonparametrically, or via regulariza…
Recently the shape-restricted inference has gained popularity in statistical and econometric literature in order to relax the linear or quadratic covariate effect in regression analyses. The typical shape-restricted covariate effect includes monotonic increasing, decreasing, convexity or concavity. In this paper, we introduce the shape-restricted inference to the celebrated Cox regression model (SR-Cox), in which the covariate response is modeled as shape-restricted additive functions. The SR-Cox regression approximates the shape-restricted functions using a spline basis expansion with data dr…
Gaussian process (GP) regression is a flexible, nonparametric approach to regression that naturally quantifies uncertainty. In many applications, the number of responses and covariates are both large, and a goal is to select covariates that are related to the response. For this setting, we propose a novel, scalable algorithm, coined VGPR, which optimizes a penalized GP log-likelihood based on the Vecchia GP approximation, an ordered conditional approximation from spatial statistics that implies a sparse Cholesky factor of the precision matrix. We traverse the regularization path from strong to…
Given data y(n) and p(n)covariates x(n) one problem in linear regression is to decide which if any of the covariates to include. There are many articles on this problem but all are based on a stochastic model for the data. This paper gives what seems to be a new approach which does not require any form of model. It is conceptually and algorithmically simple and consistency results can be proved under appropriate assumptions.
In many applications, survey data are collected from different survey centers in different regions. It happens that in some circumstances, response variables are completely observed while the covariates have missing values. In this paper, we propose a joint spatial regression model for the response variable and missing covariates via a sequence of one-dimensional conditional spatial regression models. We further construct a joint spatial model for missing covariate data mechanisms. The properties of the proposed models are examined and a Markov chain Monte Carlo sampling algorithm is used to s…
A prevalent feature of high-dimensional data is the dependence among covariates, and model selection is known to be challenging when covariates are highly correlated. To perform model selection for the high-dimensional Cox proportional hazards model in presence of correlated covariates with factor structure, we propose a new model, Factor-Augmented Regularized Model for Hazard Regression (FarmHazard), which builds upon latent factors that drive covariate dependence and extends Cox's model. This new model generates procedures that operate in two steps by learning factors and idiosyncratic compo…
