Awesome
Multi-site COVID-Net CT Classification
This is the PyTorch implemention of our paper Contrastive Cross-site Learning with Redesigned Net for COVID-19 CT Classification by Zhao Wang, Quande Liu, Qi Dou
Abatract
This paper proposes a novel joint learning framework to perform accurate COVID-19 identification by effectively learning with heterogeneous datasets with distribution descrepancy. We build a powerful backbone by redesigning the recently proposed COVID-Net in aspects of network architecture and learning strategy to improve the prediction accuracy and learning efficiency. On top of it, we further explicitly tackle the cross-site domain shift by conducting separate feature normalization in latent space. Moreover, we propose a con-trastive training objective to enhance the domain invariance of semantic embeddings for boosting the classification performance on each dataset. We develop and evaluate our method with two public large-scale COVID-19 diagnosis datasets from real CT images. Extensive experiments show that our approach consistently improves the performances on both datasets, as well as outperforms existing state-of-the-art multi-site learning methods.
Usage
Setup
We suggest using Anaconda to setup environment on Linux, if you have installed anaconda, you can skip this step.
wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-x86_64.sh && zsh Anaconda3-2020.11-Linux-x86_64.sh
Then, we can install packages using provided environment.yaml
.
git clone https://github.com/med-air/Contrastive-COVIDNet
cd Contrastive-COVIDNet
conda env create -f environment.yaml
conda activate pytorch0.4.1
Dataset
We employ two publicly available COVID-19 CT datasets:
Download our pre-processed datasets from Google Drive and put into data/
directory.
Pretrained Model
You can directly download our pretrained model from Google Drive and put into saved/
directory for testing.
Training
cd code
python main.py --bna True --bnd True --cosine True --cont True
Test
cd code
python test.py
Citation
If you find this code and dataset useful, please cite in your research papers.
@article{wangcontrastive,
author={Wang, Zhao and Liu, Quande and Dou, Qi},
title={Contrastive Cross-site Learning with Redesigned Net for COVID-19 CT Classification},
journal={IEEE Journal of Biomedical and Health Informatics},
DOI={10.1109/jbhi.2020.3023246},
year={2020},
volume={24},
number={10},
pages={2806-2813}
}
Questions
For further questions, pls feel free to contact Zhao Wang
References
[1] E. Soares, P. Angelov, S. Biaso, M. Higa Froes, and D. Kanda Abe, “Sars-cov-2 ct-scan dataset: A large dataset of real patients ct scans for sars-cov-2 identification,” medRxiv, 2020.
[2] J. Zhao, X. He, X. Yang, Y. Zhang, S. Zhang, and P. Xie, “Covid-ct-dataset: A ct scan dataset about covid-19,” 2020.
[3] A. Paszke, S. Gross, F. Massa, A. Lerer, J. Bradbury, G. Chanan, T. Killeen, Z. Lin, N. Gimelshein, L. Antiga et al., “Pytorch: An imperative style, high-performance deep learning library,” in Advances in neural information processing systems, 2019, pp. 8026–8037.