Stronger Baseline Models -- A Key Requirement for Aligning Machine Learning Research with Clinical Utility

Machine Learning (ML) research has increased substantially in recent years, due to the success of predictive modeling across diverse application domains. However, well-known barriers exist when attempting to deploy ML models in high-stakes, clinical settings, including lack of model transparency (or the inability to audit the inference process), large training data requirements with siloed data sources, and complicated metrics for measuring model utility. In this work, we show empirically that including stronger baseline models in healthcare ML evaluations has important downstream effects that aid practitioners in addressing these challenges. Through a series of case studies, we find that the common practice of omitting baselines or comparing against a weak baseline model (e.g. a linear model with no optimization) obscures the value of ML methods proposed in the research literature. Using these insights, we propose some best practices that will enable practitioners to more effectively study and deploy ML models in clinical settings.

PRISM: Patient Records Interpretation for Semantic Clinical Trial Matching using Large Language Models

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.