Mamba-based-MIL

Usage

Setup

• pip install torch==1.13.0 torchvision==0.14.0 torchaudio==0.13.0 --extra-index-url https://download.pytorch.org/whl/cu117
• pip install packaging
• pip install timm==0.4.12
• pip install pytest chardet yacs termcolor
• pip install submitit tensorboardX
• pip install triton==2.0.0
• pip install causal_conv1d==1.0.0 # causal_conv1d-1.0.0+cu118torch1.13cxx11abiFALSE-cp38-cp38-linux_x86_64.whl
• pip install mamba_ssm==1.0.1 # mmamba_ssm-1.0.1+cu118torch1.13cxx11abiFALSE-cp38-cp38-linux_x86_64.whl
• pip install scikit-learn matplotlib thop h5py SimpleITK scikit-image medpy yacs

Datasets

./                           # parent directory
├── ./positives              # positive images of training data
├── ./positives_t            # positive images of validating data
├── ./negatives              # negative images of training data
├── ./negatives_t            # negative images of validating data
├── ./RGB                    # all images

Dataset preprocessing

python 1_preprocess.py

Model training

python 2_train.py

Model inference

python 3_probmap.py

Output evaluation indicators

python 4_report.py

Output probmap and heatmap

python 4_heatmap.py

Acknowledgement

Thanks MedMamba. for serving as building blocks of our codes.