Standard approaches for variable selection in linear models are not tailored to deal properly with high-dimensional and incomplete data. Currently, methods dedicated to high-dimensional data handle missing values by ad-hoc strategies, like complete case analysis or single imputation, while methods dedicated to missing values, mainly based on multiple imputation, do not discuss the imputation method to use with high-dimensional data. Consequently, both approaches appear to be limited for many modern applications.
With inspiration from ensemble methods, a new variable selection method is proposed. It extends classical variable selection methods in the case of high-dimensional data with or without missing data. Theoretical properties are studied and the practical interest is demonstrated through a simulation study, as well as through an application to models specification in sequential multiple imputation.
In the low dimensional case, the procedure improves the control of the error risks, especially type I error, even without missing values for stepwise, lasso or knockoff methods. With missing values, the method performs better than reference selection methods based on multiple imputation. Similar performances are obtained in the high-dimensional case with or without missing values.
The regularization approach for variable selection was well developed for a completely observed data set in the past two decades. In the presence of missing values, this approach needs to be tailored to different missing data mechanisms. In this paper, we focus on a flexible and generally applicable missing data mechanism, which contains both ignorable and nonignorable missing data mechanism assumptions. We show how the regularization approach for variable selection can be adapted to the situation under this missing data mechanism. The computational and theoretical properties for variable sele…
For multi-source data, blocks of variable information from certain sources are likely missing. Existing methods for handling missing data do not take structures of block-wise missing data into consideration. In this paper, we propose a Multiple Block-wise Imputation (MBI) approach, which incorporates imputations based on both complete and incomplete observations. Specifically, for a given missing pattern group, the imputations in MBI incorporate more samples from groups with fewer observed variables in addition to the group with complete observations. We propose to construct estimating equatio…
Genomic data arising from a genome-wide association study (GWAS) are often not only of large-scale, but also incomplete. A specific form of their incompleteness is missing values with non-ignorable missingness mechanism. The intrinsic complications of genomic data present significant challenges in developing an unbiased and informative procedure of phenotype-genotype association analysis by a statistical variable selection approach. In this paper we develop a coherent procedure of categorical phenotype-genotype association analysis, in the presence of missing values with non-ignorable missingn…
Smoothed empirical likelihood estimation and automatic variable selection for an expectile high-dimensional model with possibly missing response variable
This paper provides an alternative to penalized estimators for estimation and vari- able selection in high dimensional linear regression models with measurement error or missing covariates. We propose estimation via bias corrected least squares after model selection. We show that by separating model selection and estimation, it is possible to achieve an improved rate of convergence of the L2 estimation error compared to the rate sqrt{s log p/n} achieved by simultaneous estimation and variable selection methods such as L1 penalized corrected least squares. If the correct model is selected with …
We consider the problem of model-based clustering in the presence of many correlated, mixed continuous and discrete variables, some of which may have missing values. Discrete variables are treated with a latent continuous variable approach and the Dirichlet process is used to construct a mixture model with an unknown number of components. Variable selection is also performed to identify the variables that are most influential for determining cluster membership. The work is motivated by the need to cluster patients thought to potentially have autism spectrum disorder (ASD) on the basis of many …
In this article, we advocate the ensemble approach for variable selection. We point out that the stochastic mechanism used to generate the variable-selection ensemble (VSE) must be picked with care. We construct a VSE using a stochastic stepwise algorithm, and compare its performance with numerous state-of-the-art algorithms.
The missing data issue is ubiquitous in health studies. Variable selection in the presence of both missing covariates and outcomes is an important statistical research topic but has been less studied. Existing literature focuses on parametric regression techniques that provide direct parameter estimates of the regression model. Flexible nonparametric machine learning methods considerably mitigate the reliance on the parametric assumptions, but do not provide as naturally defined variable importance measure as the covariate effect native to parametric models. We investigate a general variable s…
We propose Robust Lasso-Zero, an extension of the Lasso-Zero methodology, initially introduced for sparse linear models, to the sparse corruptions problem. We give theoretical guarantees on the sign recovery of the parameters for a slightly simplified version of the estimator, called Thresholded Justice Pursuit. The use of Robust Lasso-Zero is showcased for variable selection with missing values in the covariates. In addition to not requiring the specification of a model for the covariates, nor estimating their covariance matrix or the noise variance, the method has the great advantage of hand…
Prior work has shown that combining bootstrap imputation with tree-based machine learning variable selection methods can provide good performances achievable on fully observed data when covariate and outcome data are missing at random (MAR). This approach however is computationally expensive, especially on large-scale datasets. We propose an inference-based method, called RR-BART, which leverages the likelihood-based Bayesian machine learning technique, Bayesian additive regression trees, and uses Rubin's rule to combine the estimates and variances of the variable importance measures on multip…
1. Abrupt environmental changes can lead to evolutionary shifts in trait evolution. Identifying these shifts is an important step in understanding the evolutionary history of phenotypes. 2. We propose an ensemble variable selection method (R package ELPASO) for the evolutionary shift detection task and compare it with existing methods (R packages l1ou and PhylogeneticEM) under several scenarios. 3. The performances of methods are highly dependent on the selection criterion. When the signal sizes are small, the methods using the Bayesian information criterion (BIC) have better performances. And…
An exploration of sequential Bayesian variable selection -- A comment on García-Donato et al. (2025). "Model uncertainty and missing data: An objective Bayesian perspective"
Inference and Estimation in Missing Information (MI) scenarios are important topics in Statistical Learning Theory and Machine Learning (ML). In ML literature, attempts have been made to enhance prediction through precise feature selection methods. In sparse linear models, LASSO is well-known in extracting the desired support of the signal and resisting against noisy systems. When sparse models are also suffering from MI, the sparse recovery and inference of the missing models are taken into account simultaneously. In this paper, we will introduce an approach which enjoys sparse regression and…
Xi’an Jiaotong University（西安交通大学）；University of Waterloo（滑铁卢大学）
In the context of variable selection, ensemble learning has gained increasing interest due to its great potential to improve selection accuracy and to reduce false discovery rate. A novel ordering-based selective ensemble learning strategy is designed in this paper to obtain smaller but more accurate ensembles. In particular, a greedy sorting strategy is proposed to rearrange the order by which the members are included into the integration process. Through stopping the fusion process early, a smaller subensemble with higher selection accuracy can be obtained. More importantly, the sequential i…
A Unified Framework for Variable Selection in Model-Based Clustering with Missing Not at Random
Faculty of Mathematics and Computer Science, University of Science, Ho Chi Minh City, Vietnam（越南科技大学数学与计算机科学学院）；Vietnam National University Ho Chi Minh City, Vietnam（越南胡志明市国家大学）；School of Information and Communications Technology, Hanoi University of Science and Technology, Ha Noi, Vietnam（河内科学技术大学信息与通信技术学院）；ARC Centre of Excellence for the Mathematical Analysis of Cellular Systems（细胞系统数学分析卓越中心）；School of Mathematical Sciences, Queensland University of Technology, Brisbane City, Australia（昆士兰科技大学数学科学学院）
ControlBurn is a Python package to construct feature-sparse tree ensembles that support nonlinear feature selection and interpretable machine learning. The algorithms in this package first build large tree ensembles that prioritize basis functions with few features and then select a feature-sparse subset of these basis functions using a weighted lasso optimization criterion. The package includes visualizations to analyze the features selected by the ensemble and their impact on predictions. Hence ControlBurn offers the accuracy and flexibility of tree-ensemble models and the interpretability o…
Texas A&M University（得克萨斯农工大学）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）；ETRI（电子通信研究院）
While variable selection is essential to optimize the learning complexity by prioritizing features, automating the selection process is preferred since it requires laborious efforts with intensive analysis otherwise. However, it is not an easy task to enable the automation due to several reasons. First, selection techniques often need a condition to terminate the reduction process, for example, by using a threshold or the number of features to stop, and searching an adequate stopping condition is highly challenging. Second, it is uncertain that the reduced variable set would work well; our pre…
Hyperparameters tuning and model selection are important steps in machine learning. Unfortunately, classical hyperparameter calibration and model selection procedures are sensitive to outliers and heavy-tailed data. In this work, we construct a selection procedure which can be seen as a robust alternative to cross-validation and is based on a median-of-means principle. Using this procedure, we also build an ensemble method which, trained with algorithms and corrupted heavy-tailed data, selects an algorithm, trains it with a large uncorrupted subsample and automatically tune its hyperparameters…
The standard quantile regression model assumes a linear relationship at the quantile of interest and that all variables are observed. We relax these assumptions by considering a partial linear model while allowing for missing linear covariates. To handle the potential bias caused by missing data we propose a weighted objective function using inverse probability weighting. Our work examines estimators using parametric and nonparametric estimates of the missing probability. For variable selection of the linear terms in the presence of missing data we consider a penalized and weighted objective f…
Longitudinal data are common in clinical trials and observational studies, where missing outcomes due to dropouts are always encountered. Under such context with the assumption of missing at random, the weighted generalized estimating equations (WGEE) approach is widely adopted for marginal analysis. Model selection on marginal mean regression is a crucial aspect of data analysis, and identifying an appropriate correlation structure for model fitting may also be of interest and importance. However, the existing information criteria for model selection in WGEE have limitations, such as separate…
Propensity score weighting is widely used to improve the representativeness and correct the selection bias in the voluntary sample. The propensity score is often developed using a model for the sampling probability, which can be subject to model misspecification. In this paper, we consider an alternative approach of estimating the inverse of the propensity scores using the density ratio function satisfying the self-efficiency condition. The smoothed density ratio function is obtained by the solution to the information projection onto the space satisfying the moment conditions on the balancing …
Logistic regression is a common classification method in supervised learning. Surprisingly, there are very few solutions for performing logistic regression with missing values in the covariates. We suggest a complete approach based on a stochastic approximation version of the EM algorithm to do statistical inference with missing values including the estimation of the parameters and their variance, derivation of confidence intervals and a model selection procedure. We also tackle the problem of prediction for new observations (on a test set) with missing covariate data. The methodology is compu…
Missing data is a common problem in medical research, and is commonly addressed using multiple imputation. Although traditional imputation methods allow for valid statistical inference when data are missing at random (MAR), their implementation is problematic when the presence of missingness depends on unobserved variables, i.e. the data are missing not at random (MNAR). Unfortunately, this MNAR situation is rather common, in observational studies, registries and other sources of real-world data. While several imputation methods have been proposed for addressing individual studies when data ar…
We derive an information criterion to select a parametric model of complete-data distribution when only incomplete or partially observed data is available. Compared with AIC, our new criterion has an additional penalty term for missing data, which is expressed by the Fisher information matrices of complete data and incomplete data. We prove that our criterion is an asymptotically unbiased estimator of complete-data divergence, namely, the expected Kullback-Leibler divergence between the true distribution and the estimated distribution for complete data, whereas AIC is that for the incomplete d…
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…
Missing data are a concern in many real world data sets and imputation methods are often needed to estimate the values of missing data, but data sets with excessive missingness and high dimensionality challenge most approaches to imputation. Here we show that appropriate feature selection can be an effective preprocessing step for imputation, allowing for more accurate imputation and subsequent model predictions. The key feature of this preprocessing is that it incorporates uncertainty: by accounting for uncertainty due to missingness when selecting features we can reduce the degree of missing…
This paper is concerned with the estimating problem of response quantile with high dimensional covariates when response is missing at random. Some existing methods define root-n consistent estimators for the response quantile. But these methods require correct specifications of both the conditional distribution of response given covariates and the selection probability function. In this paper, a debiased method is proposed by solving a convex programming. The estimator obtained by the proposed method is asymptotically normal given a correctly specified parametric model for the condition distri…
In this paper, we propose Ensemble Learning models to identify factors contributing to preterm birth. Our work leverages a rich dataset collected by a NIEHS P42 Center that is trying to identify the dominant factors responsible for the high rate of premature births in northern Puerto Rico. We investigate analytical models addressing two major challenges present in the dataset: 1) the significant amount of incomplete data in the dataset, and 2) class imbalance in the dataset. First, we leverage and compare two types of missing data imputation methods: 1) mean-based and 2) similarity-based, incr…
This paper proposes a simple and efficient estimation procedure for the model with non-ignorable missing data studied by Morikawa and Kim (2016). Their semiparametrically efficient estimator requires explicit nonparametric estimation and so suffers from the curse of dimensionality and requires a bandwidth selection. We propose an estimation method based on the Generalized Method of Moments (hereafter GMM). Our method is consistent and asymptotically normal regardless of the number of moments chosen. Furthermore, if the number of moments increases appropriately our estimator can achieve the sem…
We study the Bayesian approach to variable selection in the context of linear regression. Motivated by a recent work by Rockova and George (2014), we propose an EM algorithm that returns the MAP estimate of the set of relevant variables. Due to its particular updating scheme, our algorithm can be implemented efficiently without inverting a large matrix in each iteration and therefore can scale up with big data. We also show that the MAP estimate returned by our EM algorithm achieves variable selection consistency even when $p$ diverges with $n$. In practice, our algorithm could get stuck with …
Feature selection represents a measure to reduce the complexity of high-dimensional datasets and gain insights into the systematic variation in the data. This aspect is of specific importance in domains that rely on model interpretability, such as life sciences. We propose UBayFS, an ensemble feature selection technique embedded in a Bayesian statistical framework. Our approach considers two sources of information: data and domain knowledge. We build a meta-model from an ensemble of elementary feature selectors and aggregate this information in a multinomial likelihood. The user guides UBayFS …
We consider the problem of variable selection in high-dimensional settings with missing observations among the covariates. To address this relatively understudied problem, we propose a new synergistic procedure -- adaptive Bayesian SLOPE -- which effectively combines the SLOPE method (sorted $l_1$ regularization) together with the Spike-and-Slab LASSO method. We position our approach within a Bayesian framework which allows for simultaneous variable selection and parameter estimation, despite the missing values. As with the Spike-and-Slab LASSO, the coefficients are regarded as arising from a …
IIn recent years, there has been a growing interest in applying data assimilation (DA) methods, originally designed for state estimation, to the model selection problem. In this setting, Carrassi et al. (2017) introduced the contextual formulation of model evidence (CME) and showed that CME can be efficiently computed using a hierarchy of ensemble-based DA procedures. Although Carrassi et al. (2017) analyzed the DA methods most commonly used for operational atmospheric and oceanic prediction worldwide, they did not study these methods in conjunction with localization to a specific domain. Yet …
Unsupervised learning, and more specifically clustering, suffers from the need for expertise in the field to be of use. Researchers must make careful and informed decisions on which algorithm to use with which set of hyperparameters for a given dataset. Additionally, researchers may need to determine the number of clusters in the dataset, which is unfortunately itself an input to most clustering algorithms. All of this before embarking on their actual subject matter work. After quantifying the impact of algorithm and hyperparameter selection, we propose an ensemble clustering framework which c…
We develop a distribution-free, unsupervised anomaly detection method called ECAD, which wraps around any regression algorithm and sequentially detects anomalies. Rooted in conformal prediction, ECAD does not require data exchangeability but approximately controls the Type-I error when data are normal. Computationally, it involves no data-splitting and efficiently trains ensemble predictors to increase statistical power. We demonstrate the superior performance of ECAD on detecting anomalous spatio-temporal traffic flow.
