Evaluating Pretrained Language Semantics for Structured EHR Prediction Tasks

Structured Electronic Health Records (EHR) models typically treat each clinical concept as a dataset-specific token, discarding the natural-language semantics associated with the event. As a result, relationships between concepts must largely be learned from EHR co-occurrence, without directly exploiting any prior semantic knowledge. We investigate how pretrained causal language models can be adapted for longitudinal EHR prediction by developing tEHR. Here, we represent events with their natural language description and use this text stream to apply EHR-adaptive continued pretraining, followed by task-specific discriminative fine-tuning using LoRA, utilising the LLM as a longitudinal patient-encoder. We evaluate this approach across four prediction tasks on MIMIC-IV and pancreatic cancer prediction in CPRD at 1–12 month horizons, with tEHR using the Mistral-7B-v0.3 backbone achieving the strongest overall performance. Ablations show that performance declines when clinical descriptions are removed or misaligned, when numerical values are omitted, and when either stage of adaptation is removed, while explicit elapsed-time descriptions provide little additional benefit. Analysis of the learned patient representations further reveals clinically coherent structure associated with distinct patterns of disease risk and clinical history.