All analyses employed five-fold cross-validation stratified by lithium response. We did this to ensure that model performance is measured out of sample, thus minimizing the possibility of over fitting. By definition, the predict-one-site-out analysis validation phase is conducted out of sample.

Performance measures included accuracy, area under the receiver operator characteristic curve (AUC), sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), F-1 score (F1), and Cohen’s kappa. Our primary outcome measure of interest was Cohen’s kappa, which is generally more conservative under class imbalance.

For the Cohen’s kappa metric, we simulated p values that represented the probability p that a “trivial” or “null” classifier applied to a data set with the same proportion of positive examples would achieve greater performance. For the experiments in which we perform a stratified k-fold cross-validation, we combine the results from each testing set before applying this technique. Mathematical details for this procedure are provided in the Appendix.

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