CLaDMoP: Learning Transferrable Models from Successful Clinical Trials via LLMs
This work addresses the challenge of false positives/negatives in predicting clinical trial outcomes, offering a more transferable model for drug development, though it is incremental as it builds on existing LLM and fusion methods.
The paper tackled the problem of poor generalizability in clinical trial outcome prediction by introducing CLaDMoP, a pre-training approach with a novel multi-level fusion technique, which achieved up to 10.5% improvement in PR-AUC and 3.6% in ROC-AUC over baselines.
Many existing models for clinical trial outcome prediction are optimized using task-specific loss functions on trial phase-specific data. While this scheme may boost prediction for common diseases and drugs, it can hinder learning of generalizable representations, leading to more false positives/negatives. To address this limitation, we introduce CLaDMoP, a new pre-training approach for clinical trial outcome prediction, alongside the Successful Clinical Trials dataset(SCT), specifically designed for this task. CLaDMoP leverages a Large Language Model-to encode trials' eligibility criteria-linked to a lightweight Drug-Molecule branch through a novel multi-level fusion technique. To efficiently fuse long embeddings across levels, we incorporate a grouping block, drastically reducing computational overhead. CLaDMoP avoids reliance on task-specific objectives by pre-training on a "pair matching" proxy task. Compared to established zero-shot and few-shot baselines, our method significantly improves both PR-AUC and ROC-AUC, especially for phase I and phase II trials. We further evaluate and perform ablation on CLaDMoP after Parameter-Efficient Fine-Tuning, comparing it to state-of-the-art supervised baselines, including MEXA-CTP, on the Trial Outcome Prediction(TOP) benchmark. CLaDMoP achieves up to 10.5% improvement in PR-AUC and 3.6% in ROC-AUC, while attaining comparable F1 score to MEXA-CTP, highlighting its potential for clinical trial outcome prediction. Code and SCT dataset can be downloaded from https://github.com/murai-lab/CLaDMoP.