Abstract / Summary
Clinical foundation models learn patterns in longitudinal health records that can be reused across prediction tasks. However, the relative strengths of representation-based and generation-based prediction across clinical tasks remain unclear. Using longitudinal electronic health records from 3.77 million patients at a single hospital, we developed FERMAT (Foundation model for Exploring Real-world Multimodal health data using Autoregressive Trajectory modeling), a 65-million-parameter clinical foundation model. We compared predictions from task-specific predictors trained on patient representations with those derived from generated clinical event sequences. Representation-based prediction performed better in the disease-risk comparisons. In detailed analyses of five-year chronic kidney disease, fatty liver, and diabetes risk in a test cohort of 10,000 patients, representation-based predictors exceeded generation-based estimates by 0.098-0.115 in observation-weighted AUROC and had lower probability error. Generation-based prediction, in turn, performed better in predicting diagnoses, prescriptions, and procedures recorded on the same day, a task motivated by the frequent presence of multiple events with the same date in hospital EHRs. Using 50 generated trajectories per patient, it achieved a Recall@10 of 71.0%, compared with 55.7% for representation-based prediction, with a paired improvement of 15.31 percentage points (95% CI, 13.92-16.79; n = 1,862). These findings demonstrate task-dependent strengths of representation-based and generation-based applications within a single clinical foundation model, providing an empirical basis for exploring how the two approaches can be used individually or combined to address clinical prediction needs.