README.md

---
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},
}
```