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This is the implementation of the CDGPT2 model mentioned in our paper 'Automated Radiology Report Generation using Conditioned Transformers'

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GPT2-Chest-X-Ray-Report-Generation (CDGPT2)

This is the implementation of the CDGPT2 model mentioned in our paper 'Automated Radiology Report Generation using Conditioned Transformers'.

Paper link here.

Thesis link here.

We automatically generate full radiology reports given chest X-ray images from the IU-X-Ray dataset by conditioning a pre-trained GPT2 model on the visual and semantic features of the image.

Model checkpoint here. chest overall dpi

Sample Predictions

image

Installation & Usage

The project was tested on a virtual environment of python 3.7, pip 23.2.1, and MacOS

  • pip install -r full_requirements.txt (or pip install -r requirements.txt if there are errors because of using a different operating system, as requirements.txt only contains the main dependencies and pip will fetch the compatible sub-dependencies, but it will be slower)
  • nlg-eval --setup
  • python get_iu_xray.py (to download the dataset)
  • python train.py

Related Repositories

  • VSGRU repository here.
  • Finetuned Chexnet repository here.

Citation

To cite this paper, please use:

@article{ALFARGHALY2021100557,
title = {Automated radiology report generation using conditioned transformers},
journal = {Informatics in Medicine Unlocked},
volume = {24},
pages = {100557},
year = {2021},
issn = {2352-9148},
doi = {https://doi.org/10.1016/j.imu.2021.100557},
url = {https://www.sciencedirect.com/science/article/pii/S2352914821000472},
author = {Omar Alfarghaly and Rana Khaled and Abeer Elkorany and Maha Helal and Aly Fahmy}
}

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This is the implementation of the CDGPT2 model mentioned in our paper 'Automated Radiology Report Generation using Conditioned Transformers'

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