README.md

---
license: cc-by-4.0
language:
- en
size_categories:
- 10K<n<100K
---

# AbdCTBench: Data + Code + Checkpoints

AbdCTBench is a public benchmark for comorbidity prediction from abdominal CT scans.
This repository contains:

- `AbdCTBench_dataset/`: split CSVs + image data archive + 3D stl meshes
- `code/`: training and evaluation pipeline
- `models/`: released pretrained checkpoints (`.safetensors`) with configs
- `code/dicom_stl_png_pipeline/`: DICOM -> STL -> PNG conversion scripts

## Quick Start

From `code/`:

```bash
pip install -r requirements.txt
```

Use dataset in this same repo:

```bash
cd code
python test.py \
  --data_dir ../AbdCTBench_dataset \
  --checkpoint_path ../models/mi_only/ResNet-18_lr1e-05_bs16/best_checkpoint.safetensors \
  --biomarker_config ../models/mi_only/ResNet-18_lr1e-05_bs16/biomarker_config.json \
  --output_dir ./test_results
```

## Training

```bash
cd code
python train.py \
  --model "ResNet-18" \
  --data_dir ../AbdCTBench_dataset \
  --biomarker_config ./config/biomarker_config_multitask_example.yaml \
  --output_dir ./outputs
```

Reproducibility controls:

- `--seed` (default `42`)
- `--deterministic` (slower but more deterministic backend behavior)

## Checkpoint Format

Each released model folder under `models/` contains:

- `best_checkpoint.safetensors`
- `config.json`
- `biomarker_config.json`

`test.py` supports both `.safetensors` and `.pth` checkpoints.

## Expected Data Layout

`--data_dir` should contain:

- `train.csv`, `val.csv`, `test.csv`
- `data/` with PNG files named by `FILE` column values

## Citation

If you use AbdCTBench, please cite:

```bibtex
@inproceedings{
chaudhry2026abdctbench,
title={Abd{CTB}ench: Learning Clinical Biomarker Representations from Abdominal Surface Geometry},
author={Muhammad Ahmed Chaudhry and Suhana Bedi and Pola Lydia Lagari and Brian T Layden and William Galanter and Ayis Pyrros and Sanmi Koyejo},
booktitle={The Fourteenth International Conference on Learning Representations},
year={2026},
url={https://openreview.net/forum?id=dKRAo0a9Gm}
}
```

---

For detailed internals and full argument descriptions, see `code/README.md`.