dazhangyu123 / acmil

WSI classification

Attention-Challenging Multiple Instance Learning for Whole Slide Image Classification

This is the Pytorch implementation of our "Attention-Challenging Multiple Instance Learning for Whole Slide Image Classification". This code is based on the CLAM.

Dataset Preparation

We provide a part of the extracted features to reimplement our results.

Extracted patch features using ImageNet supervised ResNet18 on Camelyon16 at 20× magnification: https://pan.quark.cn/s/dd77e6a476a0

Extracted patch features using SSL ViT-S/16 on Camelyon16 at 20× magnification: https://pan.quark.cn/s/6ea54bfa0e72

Extracted patch features using ImageNet supervised ResNet18 on Bracs at 10× magnification: https://pan.quark.cn/s/7cf21bbe46a7

Extracted patch features using SSL ViT-S/16 on Bracs at 10× magnification: https://pan.quark.cn/s/f2f9c93cd5e1

Extracted patch features using ImageNet supervised ResNet18 on Bracs at 20× magnification: https://pan.quark.cn/s/cbe4e1d0e68c

Extracted patch features using SSL ViT-S/16 on Bracs at 20× magnification: https://pan.quark.cn/s/3c8c1ffce517

For your own dataset, you can modify and run Step1_create_patches_fp.py and Step2_feature_extract.py. More details about this file can refer CLAM. Note that we recommend extracting features using SSL pretrained method. Our code using the checkpoints provided by Benchmarking Self-Supervised Learning on Diverse Pathology Datasets

Training

For the ABMIL (baseline), you can run Step3_WSI_classification_ACMIL.py and set n_token=1 n_masked_patch=0 mask_drop=0

CUDA_VISIBLE_DEVICES=2 python Step3_WSI_classification_ACMIL.py --seed 4 --wandb_mode online --arch ga --n_token 1 --n_masked_patch 0 --mask_drop 0 --config config/bracs_natural_supervised_config.yml

For our ACMIL, you can run Step3_WSI_classification_ACMIL.py and set n_token=5 n_masked_patch=10 mask_drop=0.6

CUDA_VISIBLE_DEVICES=2 python Step3_WSI_classification_ACMIL.py --seed 4 --wandb_mode online --arch ga --n_token 5 --n_masked_patch 10 --mask_drop 0.6 --config config/bracs_natural_supervised_config.yml

For CLAM, DAMIL, and TransMIL, you run Step3_WSI_classification.py

CUDA_VISIBLE_DEVICES=2 python Step3_WSI_classification.py --seed 4 --wandb_mode online --arch clam_sb/clam_mb/transmil/dsmil --config config/bracs_natural_supervised_config.yml

For DTFD-MIL, you run Step3_WSI_classification_DTFD.py

CUDA_VISIBLE_DEVICES=2 python Step3_WSI_classification_DTFD.py --seed 4 --wandb_mode online --config config/bracs_natural_supervised_config.yml

BibTeX

If you find our work useful for your project, please consider citing the following paper.

@misc{zhang2023attentionchallenging,
      title={Attention-Challenging Multiple Instance Learning for Whole Slide Image Classification}, 
      author={Yunlong Zhang and Honglin Li and Yuxuan Sun and Sunyi Zheng and Chenglu Zhu and Lin Yang},
      year={2023},
      eprint={2311.07125},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}