Dataset Information

Variable selection with multiply-imputed datasets: choosing between stacked and grouped methods.

ABSTRACT: Penalized regression methods are used in many biomedical applications for variable selection and simultaneous coefficient estimation. However, missing data complicates the implementation of these methods, particularly when missingness is handled using multiple imputation. Applying a variable selection algorithm on each imputed dataset will likely lead to different sets of selected predictors. This paper considers a general class of penalized objective functions which, by construction, force selection of the same variables across imputed datasets. By pooling objective functions across imputations, optimization is then performed jointly over all imputed datasets rather than separately for each dataset. We consider two objective function formulations that exist in the literature, which we will refer to as "stacked" and "grouped" objective functions. Building on existing work, we (a) derive and implement efficient cyclic coordinate descent and majorization-minimization optimization algorithms for continuous and binary outcome data, (b) incorporate adaptive shrinkage penalties, (c) compare these methods through simulation, and (d) develop an R package miselect. Simulations demonstrate that the "stacked" approaches are more computationally efficient and have better estimation and selection properties. We apply these methods to data from the University of Michigan ALS Patients Biorepository aiming to identify the association between environmental pollutants and ALS risk. Supplementary materials are available online.

SUBMITTER: Du J

PROVIDER: S-EPMC9838615 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Variable selection with multiply-imputed datasets: choosing between stacked and grouped methods.

Du Jiacong J Boss Jonathan J Han Peisong P Beesley Lauren J LJ Kleinsasser Michael M Goutman Stephen A SA Batterman Stuart S Feldman Eva L EL Mukherjee Bhramar B

Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America 20220328 4

Penalized regression methods are used in many biomedical applications for variable selection and simultaneous coefficient estimation. However, missing data complicates the implementation of these methods, particularly when missingness is handled using multiple imputation. Applying a variable selection algorithm on each imputed dataset will likely lead to different sets of selected predictors. This paper considers a general class of penalized objective functions which, by construction, force sele ...[more]

PMID: 36644406

Similar Datasets

Project description:Background Assessing disparities in injury is crucial for injury prevention and for evaluating injury prevention strategies, but efforts have been hampered by missing data. This study aimed to show the utility and reliability of the injury surveillance system as a trustworthy resource for examining disparities by generating multiple imputed companion datasets. Methods We employed data from the National Electronic Injury Surveillance System-All Injury Program (NEISS-AIP) for the period 2014–2018. A comprehensive simulation study was conducted to identify the appropriate strategy for addressing missing data limitations in NEISS-AIP. To evaluate the imputation performance more quantitatively, a new method based on Brier Skill Score (BSS) was developed to assess the accuracy of predictions by different approaches. We selected the multiple imputations by fully conditional specification (FCS MI) to generate the imputed companion data to NEISS-AIP 2014–2018. We further assessed health disparities systematically in nonfatal assault injuries treated in U.S. hospital emergency departments (EDs) by race and ethnicity, location of injury and sex. Results We found for the first time that significantly higher age-adjusted nonfatal assault injury rates for ED visits per 100,000 population occurred among non-Hispanic Black persons (1306.8, 95% Confidence Interval [CI]: 660.1 – 1953.5), in public settings (286.3, 95% CI: 183.2 – 389.4) and for males (603.5, 95% CI: 409.4 – 797.5). We also observed similar trends in age-adjusted rates (AARs) by different subgroups for non-Hispanic Black persons, injuries occurring in public settings, and for males: AARs of nonfatal assault injury increased significantly from 2014 through 2017, then declined significantly in 2018. Conclusions Nonfatal assault injury imposes significant health care costs and productivity losses for millions of people each year. This study is the first to specifically look at health disparities in nonfatal assault injuries using multiply imputed companion data. Understanding how disparities differ by various groups may lead to the development of more effective initiatives to prevent such injury. Supplementary Information The online version contains supplementary material available at 10.1186/s12939-023-01940-4.

Dataset Information

Variable selection with multiply-imputed datasets: choosing between stacked and grouped methods.

Publications

Variable selection with multiply-imputed datasets: choosing between stacked and grouped methods.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets