ReX-MLE: The Autonomous Agent Benchmark for Medical Imaging Challenges

Roshan Kenia, Xiaoman Zhang, Pranav Rajpurkar

Keywords: Autonomous Coding Agents, Medical Imaging, Benchmarking

Abstract: Autonomous coding agents built on large language models (LLMs) can now solve many general software and machine learning tasks, but they remain ineffective on complex, domain-specific scientific problems. Medical imaging is a particularly demanding domain, requiring long training cycles, high-dimensional data handling, and specialized preprocessing and validation pipelines, capabilities not fully measured in existing agent benchmarks. To address this gap, we introduce ReX-MLE, a benchmark of 20 challenges derived from high-impact medical imaging competitions spanning diverse modalities and task types. Unlike prior ML-agent benchmarks, ReX-MLE evaluates full end-to-end workflows, requiring agents to independently manage data preprocessing, model training, and submission under realistic compute and time constraints. Evaluating state-of-the-art agents (AIDE, ML-Master, R&D-Agent) with different LLM backends (GPT-5, Gemini, Claude), we observe a severe performance gap: most submissions rank in the 0th percentile compared to human experts. Failures stem from domain-knowledge and engineering limitations. ReX-MLE exposes these bottlenecks and provides a foundation for developing domain-aware autonomous AI systems.

Primary Subject Area: Generative Models

Secondary Subject Area: Application: Radiology

Registration Requirement: Yes

Reproducibility: https://github.com/rajpurkarlab/ReX-MLE

Read CFP & Author Instructions: Yes

Originality Policy: Yes

Single-blind & Not Under Review Elsewhere: Yes

LLM Policy: Yes

Midl Latex Submission Checklist: Ensure no LaTeX errors during compilation., Replace NNN with your OpenReview submission ID., Includes \documentclass{midl}, \jmlryear{2026}, \jmlrworkshop, \jmlrvolume, \editors, and correct \bibliography command., Did not override options of the hyperref package., Did not use the times package., Use the correct spelling and format, avoid Unicode characters, and use LaTeX equivalents instead., Any math in the title and abstract must be enclosed within $...$., Did not override the bibliography style defined in midl.cls and did not use \begin{thebibliography} directly to insert references., Avoid using \scalebox; use \resizebox when needed., Included all necessary figures and removed *unused* files in the zip archive., Removed special formatting, visual annotations, and highlights used during rebuttal., All special characters in the paper and .bib file use LaTeX commands (e.g., \'e for é)., No separate supplementary PDF uploads., Acknowledgements, references, and appendix must start after the main content.

Submission Number: 20