Advancing Clinical Trial Outcome Prediction with Domain-Specific Large Language Models

Burak Bakkar, Hana Moalla, Mohamed Salem Jedidi, Haifa Ben Messaoud, Nicolas Lopez Carranza

Clinical trial failures are a major barrier to efficient drug development, incurring substantial costs and delaying patient access to effective therapies. Structured approaches such as the Hierarchical Interaction Network (HINT) predict trial outcomes by explicitly modelling interactions between drugs, diseases and protocols, but make limited use of the free text in trial registrations. We evaluate two domain-specific language models, BioBERT (108M parameters) and BioMistral (7B parameters), for phase-level outcome prediction on the TOP benchmark (12,477 trials), representing each trial as text built from ten ClinicalTrials.gov fields. We compare fine-tuning (full fine-tuning for BioBERT, low-rank adaptation for BioMistral) with probing, in which the pretrained model is frozen and only a lightweight classifier is trained on its embeddings. On the held-out test set of each phase, all four language-model variants achieved higher ROC-AUC (0.613--0.772) and PR-AUC (0.649--0.901) than the published HINT results, corresponding to relative PR-AUC gains of 10--20\%. F1 differences were small and mixed, and no model, including HINT, clearly exceeded the F1 of a trivial classifier that…