Extended Data Fig. 6: Coefficients of LOSO LASSO logistic regression models compared to models trained on individual studies.
a, The mean coefficients (feature weights) from LASSO cross-validation models trained on single studies (color-coded) are plotted against the single-feature AUROC for each species feature. The horizontal lines highlight the microbial species that are—for at least one study—selected in more than 50% of the models in cross-validation and account for more than 10% of the absolute model weight in at least 10% of the cross-validation models. b, Similarly, b shows the same for the models trained in the LOSO setting (see Methods). The colors indicate which study has been left out of the training set (and is used for validation). The weights of the LOSO models are spread across more species; thus, generally, lower species are highlighted by the horizontal lines if their weights explain more than 2.5% of the absolute model in at least 10% of cross-validation models and they have been selected in more than 50% of models in cross-validation. c, The inset shows the distribution of the number of non-zero coefficients across all cross-validation models. d, The bar height indicates the number of non-zero coefficients that are shared between the mean models for each study or left-out study, respectively. e, The study-to-study difference (computed as the median of all pairwise differences between model weights for a single species across the mean models) for cross-validation single-study models are plotted against the same measure for the LOSO models. Species with a study-to-study difference of more than 0.02 in the cross-validation models are highlighted and annotated, showing much larger variability between models trained on single studies compared to LOSO models. Country codes as in Fig. 1b.
