ISPY2 Dataset Curation for Breast Cancer pCR Prediction

Implementation of the ISPY2 dataset curation pipeline for breast cancer pathologic complete response (pCR) prediction from our publication "Graph Representation Learning of Longitudinal Medical Imaging Trajectories for Treatment Response Prediction".

Example Usage

from ISPY2_pCR_dataset import download_data, preprocess_data

download_dir = "path/to/output/directory"
manifest_file_path = "path/to/tcia/manifest/xlsx/file" # can be found at https://github.com/hannesk95/ISPY2-pCR-dataset/tree/main/data
clinical_file_path = "path/to/clinical_xlsx/file" # can be found at https://github.com/hannesk95/ISPY2-pCR-dataset/tree/main/data

download_data(download_dir=download_dir,
              manifest_file_path=manifest_file_path)

preprocess_data(download_dir=download_dir,
                clinical_file_path=clinical_file_path)

Citation

@article{kiechle2026graph,
title={Graph Representation Learning of Longitudinal Medical Imaging Trajectories for Treatment Response Prediction},
author={Kiechle, Johannes and Osuala, Richard and Lang, Daniel M and Fischer, Stefan M and Jan{\'\i}{\v{c}}kov{\'a}, Ivana and Lekadir, Karim and Schnabel, Julia A and Peeken, Jan C},
journal={arXiv preprint arXiv:2607.04912},
year={2026}
}