CF-SimCLR: counterfactual contrastive learning

This repository contains the code for the paper "Counterfactual contrastive learning: robust representations via causal image synthesis".

Overview

The repository is divided in three main parts:

• The causal_model/ folder contains all code related to counterfactual inference model training. It contains its own README, giving you all necessary commands to train a DSCM on EMBED and PadChest.
• The classification/ folder contains all the code related to self-supervised training as well as finetuning for evaluation (see below).
• The data_handling/ folder contains everything you need to define your dataset classes. In particular, it contains all the boilerplate for CF-SimCLR specific data loading.
• The evaluation/ folder contains all the code related to test inference and results plotting for reproducing the plots from the paper.

Prerequisites

Code dependencies

The code is written in PyTorch, with PyTorch Lightning. You can install all our dependencies using our conda enviromnent requirements file environment_gpu.yml.

Datasets

You will need to download the relevant datasets to run our code. All datasets are publicly available and be downloaded at:

• PadChest https://bimcv.cipf.es/bimcv-projects/padchest/, https://www.sciencedirect.com/science/article/pii/S1361841520301614
• RSNA Pneumonia Detection Dataset: https://www.kaggle.com/c/rsna-pneumonia-detection-challenge
• CheXpert https://stanfordaimi.azurewebsites.net/datasets/8cbd9ed4-2eb9-4565-affc-111cf4f7ebe2
• EMBED https://pubs.rsna.org/doi/full/10.1148/ryai.220047, https://github.com/Emory-HITI/EMBED_Open_Data/tree/main
• VinDR Mammo https://vindr.ai/datasets/mammo

Once you have downloaded the datasets, please update the corresponding paths at the top of the mammo.py and xray.py files. Additionally, for EMBED you will need to preprocess the original dataframes with our script data_handling/csv_generation_code/generate_embed_csv.ipynb. Similarly for RSNA please run first data_handling/csv_generation_code/rsna_generate_full_csv.py.

Full workflow example for training and evaluating CF-SimCLR on mammography

Here we'll run through an example to train and evaluate CF-SimCLR on EMBED

1. Train a counterfactual image generation model with

python causal_models/main.py --hps embed

2. Generate and save all counterfactuals from every image in the training set with

python causal_models/save_embed_scanner_cf.py

3. Train the CF-SimCLR model

python classification/train.py experiment=simclr_embed data.use_counterfactuals=True data.counterfactual_contrastive=True

Alternatively to train a SimCLR baseline just run

python classification/train.py experiment=simclr_embed

Or to run the baseline with counterfactuals added to the training set without counterfactual contrastive objective

python classification/train.py experiment=simclr_embed data.use_counterfactuals=True counterfactual_contrastive=False

4. Train classifier with linear finetuning or finetuning

python classification/train.py experiment=base_density trainer.finetune_path=PATH_TO_ENCODER seed=33 trainer.freeze_encoder=True

You can choose the proportion of labelled data to use for finetuning with the flag data.prop_train=1.0

5. Evaluate on the test set by running the notebook evaluation/embed_density.ipynb to run and save inference results on the test set.