DAViT: A domain-adapted vision transformer for automated pneumonia detection and explanation using chest X-ray images
(Replication Package)

DAViT

Detecting and explaining pneumonia types using chest X-ray images

Table of contents

1. How to reproduce
   • Environment Setup
   • Reproduction of Experiments
2. Citation

How to reproduce

Environment Setup

First of all, clone this repository to your local machine and access the main dir via the following command:

git clone https://github.com/awsm-research/DAViT.git
cd DAViT

Then, install the Python dependencies via the following command:

pip install -r requirements.txt

• We highly recommend you check out this installation guide for the "torch" library so you can install the appropriate version on your device.

• To utilize GPU (optional), you also need to install the CUDA library, you may want to check out this installation guide.

• Python 3.12.7 is recommended, which has been fully tested without issues.

Reproduction of Experiments

Download the necessary data and unzip via the following command:

cd data
sh download_data.sh 
cd ..

Reproduce Experimental Results

• DAViT (proposed approach)

  • Download Pre-Trained Models

  cd davit/saved_models/checkpoint-best-f1
  sh download_models.sh
  cd ../..
  

  • Training + Inference (Pneumonia Detection)

  sh train_detection.sh
  cd ..
  

  • Training + Inference (Pneumonia Explanation)

  sh train_type.sh
  cd ..
  

  Simply remove "do_train" in the shell script if you only want to do inference with pre-trained models

• Baselines

  To reproduce baseline approaches, please follow the instructions below:

  • Step 1: cd to the specific baseline folder you wish to reproduce, e.g., "inception_v3"
  • Step 2: cd to the models folder, e.g., "saved_models/checkpoint-best-f1"
  • Step 3: download the models via "sh download_models.sh" and "cd ../.."
  • Step 4: find the shell script named as "train_detection.sh" for pneumonia detection and "train_type.sh" for pneumonia explanation

  Simply remove "do_train" in the shell script if you only want to do inference with pre-trained models

  A concrete example is provided as follows:

  • Inception V3

    • Download Pre-Trained Models

    cd inception_v3/saved_models/checkpoint-best-f1
    sh download_models.sh
    cd ../..
    

    • Training + Inference (Pneumonia Detection)

    sh train_detection.sh
    cd ..
    

    • Training + Inference (Pneumonia Explanation)

    sh train_type.sh
    cd ..
    

Citation

under review at PLOS ONE