Genomics-guided Representation Learning for Pathologic Pan-cancer Tumor Microenvironment Subtype Prediction (MICCAI 2024 oral)
git clone https://github.com/Mengflz/PathoTME.git
cd PathoTME
conda create -n pathotme python==3.7.7
conda activate pathotme
pip install -e .
-
Download TCGA WSIs or prepare your own WSIs.
-
Please refer to HIPT to extract features from WSIs. Store your features in pickle like
data/sample.pkl
. We use 1000 samples extracted from total TCGA datasets as sample.pkl for quick implement. If you would like use entire pancancer dataset, please check HIPT repo and download related TCGA RNA expression data from TCGA website. -
Please refer to MFP to obtain the TME labels of your samples. We also include a TCGA TME label file
data/TCGA_pan_MFP_annotation.tsv
.
# train with 5-fold cross validation and test
python train.py
The results files(e.g. metrics, checkpoints) are under results/
. Feel free to change configs in config/config.yaml
Follow the format of data/label_id.csv
,sample_HIPT_features.pkl
and sample_knowledge_exp
, and put your WSI features and gene expression in data/
.
In label_id.csv
, only HISTOLOGICAL_SUBTYPE, MFP, wsi_name and sample_id columns are necessary.
Please use below to cite this paper if you find our work useful in your research.
@misc{meng2024genomicsguided,
title={Genomics-guided Representation Learning for Pathologic Pan-cancer Tumor Microenvironment Subtype Prediction},
author={Fangliangzi Meng and Hongrun Zhang and Ruodan Yan and Guohui Chuai and Chao Li and Qi Liu},
year={2024},
eprint={2406.06517},
archivePrefix={arXiv},
primaryClass={cs.CV}
}
Please submit an issue or send an email to [email protected]