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Background  Social-environmental data obtained from the US Census is an important resource for understanding health disparities, but rarely is the full dataset utilized for analysis. A barrier to incorporating the full data is a lack of solid recommendations for variable selection, with researchers often hand-selecting a few variables. Thus, we evaluated the ability of empirical machine learning approaches to identify social-environmental factors having a true association with a health outcome.    Methods  We compared several popular machine learning methods, including penalized regressions (e.g. lasso, elastic net), and tree ensemble methods. Via simulation, we assessed the methods’ ability to identify census variables truly associated with binary and continuous outcomes while minimizing false positive results (10 true associations, 1000 total variables). We applied the most promising method to the full census data ( p  = 14,663 variables) linked to prostate cancer registry data ( n  = 76,186 cases) to identify social-environmental factors associated with advanced prostate cancer.    Results  In simulations, we found that elastic net identified many true-positive variables, while lasso provided good control of false positives. Using a combined measure of accuracy, hierarchical clustering based on Spearman’s correlation with sparse group lasso regression performed the best overall. Bayesian Adaptive Regression Trees outperformed other tree ensemble methods, but not the sparse group lasso. In the full dataset, the sparse group lasso successfully identified a subset of variables, three of which replicated earlier findings.    Conclusions  This analysis demonstrated the potential of empirical machine learning approaches to identify a small subset of census variables having a true association with the outcome, and that replicate across empiric methods. Sparse clustered regression models performed best, as they identified many true positive variables while controlling false positive discoveries.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12874-020-01183-9.

Variable selection in social-environmental data: sparse regression and tree ensemble machine learning approaches