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Discovery of sparse, reliable omic biomarkers with Stabl

Hédou, Julien1; Marić, Ivana1; Bellan, Grégoire2; Einhaus, Jakob1; Gaudillière, Brice1

Published Oct 12, 2023 on Dryad. https://doi.org/10.5061/dryad.stqjq2c7d

Data files

Oct 12, 2023 version files 19.91 MB

Abstract

Adoption of high-content omic technologies in clinical studies, coupled with computational methods, have yielded an abundance of candidate biomarkers. However, translating such findings into bona fide clinical biomarkers remains challenging. To facilitate this process, we introduce Stabl, a general machine learning framework that identifies a sparse, reliable set of biomarkers by integrating noise injection and a data-driven signal-to-noise threshold into multivariable predictive modeling. Evaluation of Stabl on synthetic datasets and five independent clinical studies demonstrates improved biomarker sparsity and reliability compared to commonly used sparsity-promoting regularization methods while maintaining predictive performance; it distills datasets containing 1,400 to 35,000 features down to 4 to 34 candidate biomarkers. Stabl extends to multi-omic integration tasks, enabling biological interpretation of complex predictive models, as it hones in on a shortlist of proteomic, metabolomic, and cytometric events predicting labor onset, microbial biomarkers of preterm birth, and a pre-operative immune signature of post-surgical infections.