A generalization of moderated statistics to data adaptive semiparametric estimation in high-dimensional biology. (March 2023)

• Record Type: Journal Article
• Authors: Hejazi, Nima S; Boileau, Philippe; van der Laan, Mark J; Hubbard, Alan E
• Is Part Of: Statistical methods in medical research. Volume 32:Number 3(2023)
• Page Start: 539
• Page End: 554
• Publication Date: 2023-03
• Subjects: Variance shrinkage -- semiparametric estimation -- nonparametric inference -- efficient estimation -- causal machine learning -- differential expression -- differential methylation; Medicine -- Research -- Statistical methods -- Periodicals; Research -- Periodicals; Review Literature -- Periodicals; Statistics -- methods -- Periodicals; Médecine -- Recherche -- Méthodes statistiques -- Périodiques; 610.727
• DOI: 10.1177/09622802221146313
• Languages: English
• ISSNs: 0962-2802

Abstract

The widespread availability of high-dimensional biological data has made the simultaneous screening of many biological characteristics a central problem in computational and high-dimensional biology. As the dimensionality of datasets continues to grow, so too does the complexity of identifying biomarkers linked to exposure patterns. The statistical analysis of such data often relies upon parametric modeling assumptions motivated by convenience, inviting opportunities for model misspecification. While estimation frameworks incorporating flexible, data adaptive regression strategies can mitigate this, their standard variance estimators are often unstable in high-dimensional settings, resulting in inflated Type-I error even after standard multiple testing corrections. We adapt a shrinkage approach compatible with parametric modeling strategies to semiparametric variance estimators of a family of efficient, asymptotically linear estimators of causal effects, defined by counterfactual exposure contrasts. Augmenting the inferential stability of these estimators in high-dimensional settings yields a data adaptive approach for robustly uncovering stable causal associations, even when sample sizes are limited. Our generalized variance estimator is evaluated against appropriate alternatives in numerical experiments, and an open sourceR /Bioconductor package, biotmle, is introduced. The proposal is demonstrated in an analysis of high-dimensional DNA methylation data from an observational study on the epigenetic effects of tobacco smoking.