FIGURE 1:

Model selection and optimization overview. The top panel highlights the five different studies (NHS, ALTS, CVT, Biop and D Biop; see Table 1, Supp. Table 1, and Supp. Methods for detailed description and breakdown of the studies by ground truth) used to generate the final dataset on the middle panel, which is subsequently used to generate a train and validation set, as well as two separate test sets. The intersections of model selection choices on the bottom panel are used to generate a compendium of models trained using the corresponding train and validation sets and evaluated on Test Set 1, optimizing for repeatability, classification performance, reduced extreme misclassifications and combined risk-stratification with high-risk human papillomavirus (HPV) types. Test Set 2 is utilized to verify the performance of top candidates that emerge from evaluation on Test Set 1. SWT: Swin Transformer; QWK: quadratic weighted kappa; CORAL: CORAL (consistent rank logits) loss, as described in the METHODS section.