Auto-MD-bench: Evaluating Autoresearch Agents for Real-World Medical Tasks

Abstract

Autonomous agents are increasingly capable of developing machine learning (ML) models end to end. In medical practice, however, strong performance on the target metric does not fully characterize how good the models are in real-world use cases. For example, medical ML models should also provide well-calibrated risk estimates and remain robust across patient populations. Yet autonomous model development is typically guided by task objectives that emphasize simple predictive discrimination (e.g. AUROC). This raises a key question: are these objectives sufficient to guide agents toward models that meet the broader requirements of real-world medical use? In this study, we introduce Auto-MD-bench, a benchmark of 15 real-world medical tasks from 10 clinical datasets, spanning survival analysis, classification and sequential prediction, with external validation across cohorts, hospitals and time periods. We evaluate four agents: AIDE, AI Scientist v2, Codex, and Autoresearch. The strongest agents achieve competitive primary scores, yet their predicted risks are less calibrated than those of the simple baseline models, which could lead to severe medical accidents. Moreover, models with nearly identical primary scores can exhibit markedly different calibration, while performance varies substantially across population shifts. These findings show that primary task performance alone is insufficient to assess autonomous clinical modeling and multiple different metrics widely used in healthcare practice need to be taken into consideration.