MuSTMIL

Implementation of MuSTMIL (Multi-Scale Task Multiple Instance Learning).

Reference

If you find this repository useful in your research, please cite:

[1] Multi-Scale Task Multiple Instance Learning for the Classification of Digital Pathology Images with Global Annotations, N. Marini, S. Otálora, F. Ciompi, G. Silvello, S. Marchesin, S. Vatrano, G. Buttafuoco, M. Atzori, H. Müller Proceedings of the MICCAI Workshop on Computational Pathology, PMLR 156:170-181, 2021.

Paper link: https://proceedings.mlr.press/v156/marini21a.html

Requirements

Python==3.6.9, albumentations==0.1.8, numpy==1.17.3, opencv==4.2.0, pandas==0.25.2, pillow==6.1.0, torchvision==0.8.1, pytorch==1.7.0

Pre-Processing

The WSIs are split in 224x224 pixels patches, from magnification 5/10x. The methods used to extract the patches come from Multi_Scale_Tools library

The method is in the /preprocessing folder of the Multi_Scale_Tools library:

• python Patch_Extractor_Dense_Grid.py -m 10 -w 1.25 -p 10 -r True -s 224 -x 0.7 -y 0 -i /PATH/CSV/IMAGES/TO/EXTRACT.csv -t /PATH/TISSUE/MASKS/TO/USE/ -o /FOLDER/WHERE/TO/STORE/THE/PATCHES/

The method to link patches from different magnification levels is in: /classification/Generate_csv_upper_region.py

More info: https://www.frontiersin.org/articles/10.3389/fcomp.2021.684521/full

CSV Input Files:

CSV files are used as input for the scripts. The csvs have the following structures

• For each partition (train, validation, test), the csv file has id_img, cancer, high-grade dysplasia, low-grade dysplasia, hyperplastic polyp, normal glands as column.

Training

Script to train the CNN at WSI-level, using an embedding-based MIL CNN:

Single Scale

• python training_single_scale.py -c resnet34 -b 512 -p att -e 10 -t multilabel -f True -m 10 -i /PATH/WHERE/TO/FIND/THE/CSVS/INCLUDING/THE/PARTITIONS -o /PATH/WHERE/TO/SAVE/THE/MODEL/WEIGHTS -w /PATH/WHERE/TO/FIND/THE/PATCHES
  • -c: CNN backbone to use
  • -b: batch size
  • -p: pooling layer for the MIL CNN
  • -e: number of epochs
  • -t: task (binary/multilabel)
  • -f: if True an embedding layer with 128 nodes is inserted before the output layer
  • -m: magnification level selected
  • -i: path where to find the csvs including the csv files with the partitions
  • -o: path where CNN’s weights will be stored
  • -w: path where the WSIs’ patches are stored.

Multi Scale

• python training_multi_scale.py -c resnet34 -b 512 -p att -e 10 -t multilabel -f True -m 10_5 -i /PATH/WHERE/TO/FIND/THE/CSVS/INCLUDING/THE/PARTITIONS -o /PATH/WHERE/TO/SAVE/THE/MODEL/WEIGHTS -w /PATH/WHERE/TO/FIND/THE/PATCHES
  • -c: CNN backbone to use
  • -b: batch size
  • -p: pooling layer for the MIL CNN
  • -e: number of epochs
  • -t: task (binary/multilabel)
  • -f: if True an embedding layer with 128 nodes is inserted before the output layer
  • -m: magnifications level selected (m1_m2)
  • -i: path where to find the csvs including the csv files with the partitions
  • -a: weight of alpha and beta parameters
  • -o: path where CNN’s weights will be stored
  • -w: path where the WSIs’ patches are stored.

Testing

Single Scale

• python testing_single_scale_WSI.py -c resnet34 -b 512 -p att -t multilabel -f True -w /PATH/TO/MODEL/WEIGHTS.pt -i /PATH/TO/INPUT/CSV.csv -w /PATH/WHERE/TO/FIND/THE/PATCHES

  • -c: CNN backbone to use
  • -b: batch size
  • -p: pooling layer for the MIL CNN
  • -t: task (binary/multilabel)
  • -f: if True an embedding layer with 128 nodes is inserted before the output layer
  • -n: path where CNN’s weights are stored
  • -i: path where to find the csvs including the csv files with the partitions
  • -w: path where the WSIs’ patches are stored

Multi Scale

Multi-scale output of the MuSTMIL CNN

• python testing_multi_scale_WSI.py -c resnet34 -b 512 -p att -t multilabel -f True -w /PATH/TO/MODEL/WEIGHTS.pt -i /PATH/TO/INPUT/CSV.csv -w /PATH/WHERE/TO/FIND/THE/PATCHES -m 10_5. The script evaluates the multi_scale output of the CNN.
  • -c: CNN backbone to use
  • -b: batch size
  • -p: pooling layer for the MIL CNN
  • -t: task (binary/multilabel)
  • -f: if True an embedding layer with 128 nodes is inserted before the output layer
  • -n: path where CNN’s weights are stored
  • -m: magnification to use (m1_m2).
  • -i: path where to find the csvs including the csv files with the partitions
  • -w: path where the WSIs’ patches are stored

Single Scale on Multi-scale branches

Single-scale output of the MuSTMIL CNN

• python testing_multi_scale_on_single_scale_WSI.py -c resnet34 -b 512 -p att -t multilabel -f True -m /PATH/TO/MODEL/WEIGHTS.pt -i /PATH/TO/INPUT/CSV.csv -w /PATH/WHERE/TO/FIND/THE/PATCHES -m 10. The script evaluates the single_scale output branch of the CNN.
  • -c: CNN backbone to use
  • -b: batch size
  • -p: pooling layer for the MIL CNN
  • -t: task (binary/multilabel)
  • -f: if True an embedding layer with 128 nodes is inserted before the output layer
  • -w: path where CNN’s weights are stored
  • -i: path where to find the csvs including the csv files with the partitions
  • -w: path where the WSIs’ patches are stored
  • -m: magnification to use (m1_m2).

Acknoledgements

This project has received funding from the EuropeanUnion’s Horizon 2020 research and innovation programme under grant agree-ment No. 825292 ExaMode. Infrastructure fromthe SURFsara HPC center was used to train the CNN models in parallel.