| --- |
| pretty_name: Auto-MD-bench |
| license: other |
| license_name: mixed |
| license_link: LICENSE |
| language: |
| - en |
| tags: |
| - medical |
| - clinical-prediction |
| - survival-analysis |
| - benchmark |
| - agents |
| task_categories: |
| - tabular-classification |
| size_categories: |
| - 1M<n<10M |
| viewer: false |
| --- |
| |
| # Auto-MD-bench: task packages |
|
|
| Auto-MD-bench evaluates autoresearch agents that build prediction models for medical tasks. An agent |
| receives a task description and labeled training data, develops a model on its own within a fixed |
| time budget, and submits predictions for a hidden test set. Submissions are scored on the task's |
| primary metric, on risk calibration and on performance under population shift. |
|
|
| This repository holds the ready-built packages of the 10 benchmark tasks that use public data, plus |
| the two objective variants of `uci_diabetes` used in the calibration experiment. The other 5 tasks use |
| MIMIC-IV, eICU-CRD and SEER, which cannot be redistributed; build them from the scripts in the code |
| repository after obtaining access. |
|
|
| Paper: https://arxiv.org/abs/2610.25069 |
|
|
| Code, agents, grader and paper results: https://github.com/Edwin0080/Auto-MD-bench |
|
|
| ## Tasks in this repository |
|
|
| | Task | Data | Outcome | Validation | Primary metric | Train / test | |
| |---|---|---|---|---|---| |
| | `support` | SUPPORT | Death | Internal | C<sup>td</sup> | 7,098 / 1,775 | |
| | `metabric` | METABRIC | Death | Internal | C<sup>td</sup> | 1,523 / 381 | |
| | `rotterdam` | Rotterdam | Recurrence or death | Internal | C<sup>td</sup> | 2,385 / 597 | |
| | `rotterdam_gbsg` | Rotterdam → GBSG | Recurrence or death | External (cohort) | C<sup>td</sup> | 2,982 / 686 | |
| | `nhanes` | NHANES | Death | Internal | C<sup>td</sup> | 11,639 / 2,910 | |
| | `uci_diabetes` | UCI Diabetes, 130 US hospitals | 30-day readmission | Internal | AUROC | 81,347 / 20,419 encounters | |
| | `physionet2012` | PhysioNet/CinC 2012, ICU | In-hospital death | Internal | min(Se, PPV) | 4,000 / 8,000 stays | |
| | `sepsis` | PhysioNet/CinC 2019, ICU | Sepsis onset | Internal | Utility | 32,268 / 8,068 | |
| | `sepsis_new_hospital` | PhysioNet/CinC 2019, ICU | Sepsis onset | External (hospital) | Utility | 20,336 / 4,000 | |
| | `sepsis_500_labels` | PhysioNet/CinC 2019, ICU | Sepsis onset | External (hospital) | Utility | 20,336 + 500 / 4,000 | |
|
|
| `uci_diabetes_brier` and `uci_diabetes_ece` have the same data as `uci_diabetes`; only the stated |
| objective in `description.md` differs (Brier score; AUROC and ECE). |
|
|
| Not here (build locally): `seer`, `seer_later_period` (SEER Research Data Agreement), `mimiciv`, `eicu`, |
| `eicu_new_hospitals` (PhysioNet credentialed access). |
|
|
| ## Layout |
|
|
| ``` |
| <task>/ |
| public/ what the agent sees: description.md, training data, test features, |
| sample_submission.csv, validate.py (format checker) |
| private/ hidden test labels, used only by the grader |
| ``` |
|
|
| Give an agent only `public/`. The data are the same as in the paper's experiments. |
|
|
| ## Usage |
|
|
| ```bash |
| pip install -U huggingface_hub |
| git clone https://github.com/Edwin0080/Auto-MD-bench && cd Auto-MD-bench |
| pip install -e . |
| hf download Edwin0080/Auto-MD-bench --repo-type dataset --local-dir packages |
| python -m automdbench.grade support packages/support/public/sample_submission.csv |
| ``` |
|
|
| See the code repository for running agents and for the scoring protocol. |
|
|
| ## Data sources and licenses |
|
|
| Each task keeps the license of its source data. Cite the sources below when you use the tasks. |
|
|
| | Tasks | Source | License or terms | |
| |---|---|---| |
| | `support` | SUPPORT (Knaus et al., 1995), as processed by DeepSurv (Katzman et al., 2018) from the Vanderbilt Biostatistics data repository | "Permission is granted to anyone wishing to use the data sets"; data obtained from https://hbiostat.org/data courtesy of the Vanderbilt University Department of Biostatistics | |
| | `metabric` | METABRIC (Curtis et al., 2012; Pereira et al., 2016; Rueda et al., 2019), as processed by DeepSurv; the same values are in cBioPortal `brca_metabric` | ODC Open Database License (ODbL) 1.0, as distributed by cBioPortal | |
| | `rotterdam`, `rotterdam_gbsg` | Rotterdam tumour bank and GBSG trial (Royston and Altman, 2013), as distributed in the R package `survival` | LGPL (≥ 2), the license of the `survival` package | |
| | `nhanes` | NHANES 2011–2016 and NCHS public-use linked mortality files | U.S. public-use data; NCHS data use restrictions apply (no attempt to identify individuals) | |
| | `uci_diabetes*` | Diabetes 130-US Hospitals for Years 1999–2008, UCI Machine Learning Repository (Strack et al., 2014) | CC BY 4.0 | |
| | `physionet2012` | PhysioNet/CinC Challenge 2012 (Silva et al., 2012; Goldberger et al., 2000) | Open Data Commons Attribution License 1.0 | |
| | `sepsis*` | PhysioNet/CinC Challenge 2019 (Reyna et al., 2020; Goldberger et al., 2000) | CC BY 4.0 | |
|
|
| The `sepsis*` packages include `utility_score.py`, the official PhysioNet/CinC Challenge 2019 scoring |
| functions (BSD 2-Clause). The `validate.py` format checkers are part of the benchmark code (MIT). |
|
|
| ## Citation |
|
|
| ```bibtex |
| @misc{zhou2026automdbenchevaluatingautoresearchagents, |
| title={Auto-MD-bench: Evaluating Autoresearch Agents for Real-World Medical Tasks}, |
| author={Shenqi Zhou and Qiran Zou and Wenhao Zhao and Zhenyu Liao and Dianbo Liu}, |
| year={2026}, |
| eprint={2610.25069}, |
| archivePrefix={arXiv}, |
| primaryClass={cs.LG}, |
| url={https://arxiv.org/abs/2610.25069}, |
| } |
| ``` |
|
|
