Rethinking Pre-trained Feature Extractor Selection in Multiple Instance Learning for Whole Slide Image Classification

Under Submission Review for ISBI 2025

Environments

• Linux Ubuntu 20.04.6
• 2 NVIDIA A100 GPUs (40GB each)
• CUDA version: 12.2
• Python version: 3.9.18

Installation

Install Anaconda
Create a new environment and activate it

conda create --name mil_feat_ext python=3.9.18
conda activate mil_feat_ext

Install all required packages

pip install -r requirements.txt
pip install torch==1.13.1+cu117 torchvision==0.14.1+cu117 --extra-index-url https://download.pytorch.org/whl/cu117
pip install timm-0.5.4.tar

Dataset Preparation

A. TCGA-NSCLC (Lung Cancer) → Provided by DSMIL, it can be download directly in both 2.5x and 10x magnifications from the following link

B. Camelyon16 → The HS2P project, build on CLAM is utilized for standardized tissue patch extraction. Following default configuration file config/extraction/default.yaml from the HS2P, below are the most important configurations to note:

• spacing: 0.5 µm/px (~20x magnification)
• tissue_thresh: 0.1
• patch_size: 256
• save_patches_to_disk: True

We follow the official train/test split on the Camelyon16 dataset and take the first 836 entries in datasets_csv/tcga-nsclc.csv for training and the remaining 210 entries for testing

Below is the example of the TCGA-NSCLC dataset structure after splitting into classes and train/test:

Folder structure

<datasets>/
├── data_tcga_lung_tree/
    ├── train/
        ├── LUAD/
            ├── TCGA-4B-A93V-01Z-00-DX1/
                ├── x1_y1
                    ├── x11_y11.png
                    ├── x12_y12.png
                ├── x2_y2.png
                ├── x3_y3.png
                ├── ...
            ├── ...
        
        ├── LUSC/
            ├── TCGA-18-3408-01Z-00-DX1/
                ├── x4_y4
                    ├── x41_y41.png
                    ├── x42_y42.png
                ├── x5_y5.png
                ├── x6_y6.png
                ├── ...
            ├── ...
        
    ├── test/
        ├── ...
                

Feature Extraction

Create a config file under feature_extraction/configs/ with the name as follows: [name of backbone]-[name of pre-training method]-[name of pre-training dataset].yaml. Below are the examples of config file names:

• resnet50-supervised-imagenet1k (Timm)
• swin_base-supervised-imagenet21k (Timm)
• vit_small16-ssl-dino-imagenet1k (PyTorch Hub)
• resnet50-lunit-ssl-barlow_twins-tcga-tulip (Benchmark SSL Pathology)

A good starting point is to follow the config file below (e.g., resnet50-supervised-imagenet1k.yaml), making changes only to the sections marked with '#CHANGE' comments (see feature_extraction/configs/ for more details)

Config File

gpu_id: 0 # CHANGE

# Output settings
output_dir_path: 'outputs'
feature_extractor: 'resnet50-supervised-imagenet1k-transform' # CHANGE
resume: False # CHANGE

# Dataset settings
dataset:
  name: 'tcga-nsclc' # CHANGE: ['tcga-nsclc', 'camelyon16']
  patch_size: 224 # CHANGE
  base_folder_path: '../../feature_extractor_MIL_study/datasets/data_tcga_lung_tree'  # CHANGE
  slide_data_path: 'slide_data/${dataset.name}.csv'
  extracted_summary_path: '../datasets_csv/${dataset.name}/${feature_extractor}.csv'
  slide_missing_path: 'slide_missing/${dataset.name}.csv'
  subsets:
  - train
  - test
  classes: # CHANGE
  - LUAD
  - LUSC
  
# Model settings
model:
  backbone: 'resnet50' # CHANGE
  feats_dim: 1024 # CHANGE
  kernel_size:
  trained_path:

# Feature Extraction settings
feature_extraction:
  save_patch_features: False # CHANGE
  normalization: 'imagenet' # CHANGE: ['imagenet', 'lunit']
  stain_norm_macenko: False
 

To kick off the feature extraction process using resnet50-supervised-imagenet1k features

cd feature_extraction/
python extract_features.py --config-name resnet50-supervised-imagenet1k

This will result in the slide features being stored under feature_extraction/outputs/tcga-nsclc/resnet50-supervised-imagenet1k/

MIL Aggregator Training

Below are the useful arguments to train MIL models

seed                # Seed to reproduce experiments
device              # Which GPU for training
num_classes         # Depends on the number of positive classes (e.g., camelyon16: 1, tcga-nsclc: 2)
feature_extractor   # Name of the feature extractor used
feats_size          # Dimension of the feature vector
model               # Which MIL model to use ['abmil', 'dsmil', 'transmil', 'DTFD']
distill             # Only Used for DTFD-MIL ['MaxMinS', 'MaxS', 'AFS']

To train all four SOTA MIL models with 3 times running (e.g., seed 0, 5, 10) using the previously extracted features (e.g., resnet50-supervised-pretrained-imagenet-1k) is as below (refer to train.sh):

cd ..

python train_abmil_dsmil.py --seed 0 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model abmil
python train_abmil_dsmil.py --seed 0 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model dsmil
python train_transmil.py --seed 0 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model transmil
python train_dtfdmil.py --seed 0 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model DTFD --distill MaxMinS

python train_abmil_dsmil.py --seed 5 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model abmil
python train_abmil_dsmil.py --seed 5 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model dsmil
python train_transmil.py --seed 5 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model transmil
python train_dtfdmil.py --seed 5 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model DTFD --distill MaxMinS

python train_abmil_dsmil.py --seed 10 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model abmil
python train_abmil_dsmil.py --seed 10 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model dsmil
python train_transmil.py --seed 10 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model transmil
python train_dtfdmil.py --seed 10 --device cuda:0 --num_classes 2 --dataset tcga-nsclc --feature_extractor resnet50-supervised-imagenet1k --feats_size 1024 --model DTFD --distill MaxMinS

Acknowledgement

Our code is mainly built from these amazing works IBMIL, ABMIL, DSMIL, TransMIL, DTFD-MIL, HS2P, Re-implementation HIPT