Selection of 51 predictors from 13,782 candidate multimodal features using machine learning improves coronary artery disease prediction

Abstract

Current cardiovascular risk assessment tools use a small number of predictors. Here, we study how machine learning might: (1) enable principled selection from a large multimodal set of candidate variables and (2) improve prediction of incident coronary artery disease (CAD) events. An elastic net-based Cox model (ML4H_EN-COX) trained and evaluated in 173,274 UK Biobank participants selected 51 predictors from 13,782 candidates. Beyond most traditional risk factors, ML4H_EN-COX selected a polygenic score, waist circumference, socioeconomic deprivation, and several hematologic indices. A more than 30-fold gradient in 10-year risk estimates was noted across ML4H_EN-COX quintiles, ranging from 0.25% to 7.8%. ML4H_EN-COX improved discrimination of incident CAD (C-statistic = 0.796) compared with the Framingham risk score, pooled cohort equations, and QRISK3 (range 0.754-0.761). This approach to variable selection and model assessment is readily generalizable to a broad range of complex datasets and disease endpoints.