Awesome

GLoRIA: A Multimodal Global-Local Representation Learning Framework for Label-efficient Medical Image Recognition

GLoRIA (Global-Local Representations for Images using Attenion) is a multimodal representation learning framework for label-efficient medical image recognition. Our results demonstrate high-performance and label-efficiency for image-text retrieval, classification (finetuning and zeros-shot settings), and segmentation on different medical imaging datasets.

GLoRIA Manuscript
Shih-Cheng Huang (Mars), Liyue Shen, Matthew P. Lungren, Serena Yeung <br> Stanford University <br> Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV), 2021 <br>

Approach

GLoRIA

Usage

Start by installing PyTorch 1.7.1 with the right CUDA version, then clone this repository and install the dependencies.

$ conda install pytorch==1.7.1 torchvision==0.8.2 torchaudio==0.7.2 cudatoolkit=10.1 -c pytorch
$ pip install git@github.com:marshuang80/gloria.git
$ conda env create -f environment.yml

Make sure to download the pretrained weights from here and place it in the ./pretrained folder.

Load GLoRIA pretrained models

import torch
import gloria

# get device
device = "cuda" if torch.cuda.is_available() else "cpu"

# load classifier
num_class = 5   # 5 class classification
freeze = True   # freeze encoder and only train linear classifier (less likely to overfit when training data is limited)
model = gloria.load_img_classification_model(num_cls=num_class, freeze_encoder=freeze, device=device)

# load segmentation model (UNet)
seg_model = gloria.load_img_segmentation_model(device=device)

Zeroshot classification for CheXpert5x200

import torch
import gloria
import pandas as pd 

df = pd.read_csv(gloria.constants.CHEXPERT_5x200)

# load model
device = "cuda" if torch.cuda.is_available() else "cpu"
gloria_model = gloria.load_gloria(device=device)

# generate class prompt
# cls_promts = {
#    'Atelectasis': ['minimal residual atelectasis ', 'mild atelectasis' ...]
#    'Cardiomegaly': ['cardiomegaly unchanged', 'cardiac silhouette enlarged' ...] 
# ...
# } 
cls_prompts = gloria.generate_chexpert_class_prompts()

# process input images and class prompts 
processed_txt = gloria_model.process_class_prompts(cls_prompts, device)
processed_imgs = gloria_model.process_img(df['Path'].tolist(), device)

# zero-shot classification on 1000 images
similarities = gloria.zero_shot_classification(
    gloria_model, processed_imgs, processed_txt)

print(similarities)
#      Atelectasis  Cardiomegaly  Consolidation     Edema  Pleural Effusion
# 0       1.371477     -0.416303      -1.023546 -1.460464          0.145969
# 1       1.550474      0.277534       1.743613  0.187523          1.166638
# ..           ...           ...            ...       ...               ...

Training

This codebase has been developed with python version 3.7, PyTorch version 1.7.1, CUDA 10.2 and pytorch-lightning 1.1.4. Example configurations for pretraining and downstream classification can be found in the ./configs. All training and testing are done using the run.py script. For more documentation, please run:

python run.py --help

The preprocessing steps for each dataset can be found in ./gloria/datasets/preprocess_datasets.py

Representation Learning

Train the representation learning model with the following command:

python run.py -c ./configs/chexpert_pretrain_config.yaml --train

Please note that the CheXpert radiology reports are still under PHI review for HIPPA compliency, and not publicly availible yet.

Classification

Fine-tune the GLoRIA pretrained image model for classification with the following command:

# chexpert
python run.py -c ./configs/chexpert_classification_config.yaml --train --test --train_pct 0.01
# pneumonia
python run.py -c ./configs/pneumonia_classification_config.yaml --train --test --train_pct 0.01

The train_pct flag randomly selects a percentage of the dataset to fine-tune the model. This is use to determine the performance of the model under low data regime.

Segmentation

Fine-tune the GLoRIA pretrained image model for segmentation with the following command:

# chexpert
python run.py -c ./configs/pneumothorax_segmentation_config.yaml --train --test --train_pct 0.01

Citation

@inproceedings{huang2021gloria,
  title={GLoRIA: A Multimodal Global-Local Representation Learning Framework for Label-Efficient Medical Image Recognition},
  author={Huang, Shih-Cheng and Shen, Liyue and Lungren, Matthew P and Yeung, Serena},
  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision},
  pages={3942--3951},
  year={2021}
}

Acknowledgements

This codebase is adapted from ControlGAN