A Efficient Graph-based Framework for Multi-Organ Histology Image Classification

Code of Paper: A Efficient Graph-based Framework for Multi-Organ Histology Image Classification

Extended version of our BMVC 2021 paper: HAT-Net: A Hierarchical Transformer Graph Neural Network for Grading of Colorectal Cancer Histology Images

Our code is partially inspired by CGC-Net, shout out to them.

Requirements

Some of our installed packages:

• torch-geometric 1.7.2
• torch 1.8.2
• scikit-image 0.17.2
• scikit-learn 1.0
• opencv-python 4.5.3.56
• numpy 1.20.3
• matplotlib 3.4.2

Datasets:

4 public histlogy image classification dataset:

• CRC dataset: a colorectal cancer grading dataset:
• Extended CRC dataset: a colorectal cancer grading dataset.
• UZH dataset: a prostate cancer grading dataset.
• BACH dataset: a breast cancer classification dataset.

Train the model

python -u train_GIN_Hierarchical.py  --norm_adj --batch-size=20 --step_size=15 --jk  --cv 3  --num_eval 5 --visualization --epochs 20   --stage 2 3 --depth 6

tested:

python -u train_GIN_Hierarchical.py  --norm_adj --batch-size=20 --step_size=15 --jk  --cv 3  --num_eval 5 --visualization --lr 0.0003 --epochs 20   --gamma 0.33 --stage 2 3 --depth 1 --load_data_list

or(has not been tested):

python -u train_GIN_Hierarchical.py  --norm_adj --batch-size=20 --step_size=15 --jk  --cv 3  --num_eval 5 --visualization --lr 0.0003 --epochs 20   --gamma 0.33 --stage 2 3 --depth 1

eval:

python -u eval.py  --norm_adj --batch-size=10 --step_size=10 --jk  --depth 1  --stage  2 3 --cv 1  --weight_file /data/by/tmp/HGIN/output/result/nuclei_soft-assign_l3x1_ar10_h20_o20_fca_%1fuse_adj0.4_sr1_d0.2_jkknn_cv2/Monday_24_May_2021_09h_50m_38s/model_best.pth.tar

visulization:

python -u train_GIN_Hierarchical.py  --norm_adj --batch-size=20 --step_size=15 --jk  --cv 3  --num_eval 5 --visualization --lr 0.0003 --epochs 20   --gamma 0.33 --stage 2 3 --depth 1

Citation

If you used our code for your research, please cite:

@inproceedings{su2021,
  title="HAT-Net: A Hierarchical Transformer Graph Neural Network for Grading of Colorectal Cancer Histology Images",
  author={Yihan {Su} and Yu {Bai} and Bo {Zhang} and Zheng {Zhang} and Wendong {Wang}},
  booktitle={The British Machine Vision Conference (BMVC)},
  year={2021}
}