Gary Gao

Liwen Sun, Hao-Ren Yao, Gary Gao et al.

Cancer screening, leading to early detection, saves lives. Unfortunately, existing screening techniques require expensive and intrusive medical procedures, not globally available, resulting in too many lost would-be-saved lives. We present CATCH-FM, CATch Cancer early with Healthcare Foundation Models, a cancer pre-screening methodology that identifies high-risk patients for further screening solely based on their historical medical records. With millions of electronic healthcare records (EHR), we establish the scaling law of EHR foundation models pretrained on medical code sequences, pretrain compute-optimal foundation models of up to 2.4 billion parameters, and finetune them on clinician-curated cancer risk prediction cohorts. In our retrospective evaluation comprising of thirty thousand patients, CATCH-FM achieves strong efficacy, with 50% sensitivity in predicting first cancer risks at 99% specificity cutoff, and outperforming feature-based tree models and both general and medical LLMs by up to 20% AUPRC. Despite significant demographic, healthcare system, and EHR coding differences, CATCH-FM achieves state-of-the-art pancreatic cancer risk prediction on the EHRSHOT few-shot leaderboard, outperforming EHR foundation models pretrained using on-site patient data. Our analysis demonstrates the robustness of CATCH-FM in various patient distributions, the benefits of operating in the ICD code space, and its ability to capture non-trivial cancer risk factors. Our code will be open-sourced.

Cathy Jiao, Gary Gao, Aditi Raghunathan et al.

Data attribution methods are used to measure the contribution of training data towards model outputs, and have several important applications in areas such as dataset curation and model interpretability. However, many standard data attribution methods, such as influence functions, utilize model gradients and are computationally expensive. In our paper, we show in-context probing (ICP) -- prompting a LLM -- can serve as a fast proxy for gradient-based data attribution for data selection under conditions contingent on data similarity. We study this connection empirically on standard NLP tasks, and show that ICP and gradient-based data attribution are well-correlated in identifying influential training data for tasks that share similar task type and content as the training data. Additionally, fine-tuning models on influential data selected by both methods achieves comparable downstream performance, further emphasizing their similarities. We also examine the connection between ICP and gradient-based data attribution using synthetic data on linear regression tasks. Our synthetic data experiments show similar results with those from NLP tasks, suggesting that this connection can be isolated in simpler settings, which offers a pathway to bridging their differences.