dasun07 / setmil_repro

Spatial Encoding Transformer-based Multiple Instance Learning for Pathological Image Analysis

Code for paper titled "SETMIL: Spatial Encoding Transformer-based Multiple Instance Learning for Pathological Image Analysis" submitted to MICCAI2022. The basic method and applications are introduced as follows:

The overall framework of the proposed spatial encoding transformer-based MIL (SETMIL). It consists of three main stages including (1) position-preserving encoding (PPE) to transform huge-size WSI to a small-size position encoded feature map, (2) transformer-based pyramid multi-scale fusion (TPMF) aiming at modifying the feature map and enriching representation with multi-scale context information, and (3) spatial encoding transformer (SET)-based bag embedding, which generates a high-level bag representation comprehensively considering all instance representations in a fully trainable way and leverages a joint absolute-relative position encoding mechanism to encode the position and context information.

Sub-figure (A) illustrates the transformer-based pyramid multi-scale fusion module, which consists of three tokens-to-token (T2T) modules \cite{yuan2021tokens} working in a pyramid arrangement to modify the feature map and enrich a representation (token) with multi-scale context information. Each tokens-to-token module has a soft-split and reshape process together with a transformer layer\cite{vaswani2017attention}. Sub-figure (B) shows a example heatmap for model interpretability. Colors reflect the prediction contribution of each local patch.

Dependencies

python==3.7.11
torch==1.7.0
torchvision==0.8.1+cu110
rich==10.16.1
yacs==0.1.8
einops==0.3.2
openslide-python==1.1.2
opencv-python==4.5.4.60
setuptools==58.0.4
matplotlib==3.5.1
Pillow==8.4.0
scikit-image==0.19.1
scikit-learn==1.0.1
scipy==1.7.3
cffi==1.15.0
numpy==1.20.3
pandas==1.3.5
pkgconfig==1.5.1
pycparser==2.20
python-dateutil==2.8.1
pytz==2020.1
pyvips==2.1.12
six==1.16.0

Pathological Image Analysis

This code uses the centralized configs. Before using this code, a config file needs to be edited to assign necessary parameters. A sample config file named 'default.yaml' is provided as the reference.

./main/configs/default.yaml

1、First, in order to split the WSI into patches, execute the following script.

python ./data_prepare/WSI_cropping.py  \
  --dataset path_to_data_folder  \
  --output path_to_output_folder  \
  --scale 20 --patch_size 1120 --num_threads 16

2、Then, extract features from each patch. a pre-trained feature extractor can be utilized here (e.g. EfficientNet-B0 trained on the ImageNet).

python ./data_prepare/extract_feature.py --cfg configs/default.yaml

3、Next, combine features of one WSI.

python ./data_prepare/merge_patch_feat.py --cfg configs/default.yaml

4、Finally, we can use the model with preprocessed data

python ./main/main.py --cfg ./configs/default.yaml --task LUAD_GM

# or 

python ./main/main.py --cfg ./configs/default.yaml --task EC_LNM

Acknowledgement

This repo partially uses code from Deformable DETR, T2T-ViT and [iRPE] (https://github.com/microsoft/Cream.git).