Fig. 2: Clinical Transformer performance and impact of pretraining.

a Kaplan-Meier (KM) curves of the Clinical Transformer applied to the Chowell et al.³ dataset, using the median survival score to stratify patients into high and low populations. b KM curves of Chowell et al.³ random forest model used in the testing dataset (using Chowell et al. optimal pan-cancer cutoff = 0.238). c KM curves for evaluating TMB score in the Chowell et al.³ dataset (cutoff = 10 mutations per megabase [mut/mb]). P-values for HR in (a–c) reported from a Wald statistical test. d Learning curves of the Clinical Transformer (C-index vs. training epochs), evaluated on the 10 testing splits from the Samstein et al.³³ pan-cancer dataset, with and without using GENIE data for model pretraining. e Learning curves of the Clinical Transformer, evaluated on the 10 testing splits from the MYSTIC dataset, with and without using GENIE data for model pretraining. f Learning curves of the Clinical Transformer, evaluated on the 10 testing splits from the MYSTIC dataset, with and without using the Chowell et al. ³ dataset for model pretraining. Source data are provided in the SourceData file.