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https://github.com/lindawangg/covid-net
COVID-Net Open Source Initiative
https://github.com/lindawangg/covid-net
chest-radiography coronavirus coronavirus-dataset coronavirus-detect covid-19 covid-net covidx-dataset sars-cov-2
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COVID-Net Open Source Initiative
- Host: GitHub
- URL: https://github.com/lindawangg/covid-net
- Owner: lindawangg
- License: other
- Created: 2020-03-18T21:31:06.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-02-16T02:35:17.000Z (almost 2 years ago)
- Last Synced: 2024-02-12T23:21:25.278Z (9 months ago)
- Topics: chest-radiography, coronavirus, coronavirus-dataset, coronavirus-detect, covid-19, covid-net, covidx-dataset, sars-cov-2
- Language: Jupyter Notebook
- Homepage:
- Size: 64.9 MB
- Stars: 1,144
- Watchers: 74
- Forks: 480
- Open Issues: 46
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
# COVID-Net Open Source Initiative
**Note: The COVID-Net models provided here are intended to be used as reference models that can be built upon and enhanced as new data becomes available. They are currently at a research stage and not yet intended as production-ready models (not meant for direct clinical diagnosis), and we are working continuously to improve them as new data becomes available. Please do not use COVID-Net for self-diagnosis and seek help from your local health authorities.**
**Recording to webinar on [How we built COVID-Net in 7 days with Gensynth](https://darwinai.news/fny)**
**Update 11/28/2021:** We released a new training dataset with over 30,000 CXR images from a multinational cohort of over 16,400 patients. The dataset contains 16,490 positive COVID-19 images from over 2,800 patients. The COVIDx V9A dataset is for detection of no pneumonia/non-COVID-19 pneumonia/COVID-19 pneumonia, and COVIDx V9B dataset is for COVID-19 positive/negative detection.\
**Update 10/19/2021:** We released a new COVID-Net CXR-3 [model](docs/models.md) for COVID-19 positive/negative detection which was trained and tested on the COVIDx8B dataset leveraging the new MEDUSA (Multi-scale Encoder-Decoder Self-Attention) architecture.\
**Update 04/21/2021:** We released a new COVIDNet CXR-S [model](docs/models.md) and [COVIDxSev](create_COVIDxSev.ipynb) dataset for airspace severity grading in COVID-19 positive patient CXR images. For more information on training, testing and inference please refer to severity [docs](docs/covidnet_severity.md).\
**Update 03/20/2021:** We released a new COVID-Net CXR-2 [model](docs/models.md) for COVID-19 positive/negative detection which was trained on the new COVIDx8B dataset with 16,352 CXR images from a multinational cohort of 15,346 patients from at least 51 countries. The test results are based on the new COVIDx8B test set of 200 COVID-19 positive and 200 negative CXR images.\
**Update 03/19/2021:** We released updated datasets and dataset curation scripts. The COVIDx V8A dataset and create_COVIDx.ipynb are for detection of no pneumonia/non-COVID-19 pneumonia/COVID-19 pneumonia, and COVIDx V8B dataset and create_COVIDx_binary.ipynb are for COVID-19 positive/negative detection. Both datasets contain over 16000 CXR images with over 2300 positive COVID-19 images.\
**Update 01/28/2021:** We released updated datasets and dataset curation scripts. The COVIDx V7A dataset and create_COVIDx.ipynb are for detection of no pneumonia/non-COVID-19 pneumonia/COVID-19 pneumonia, and COVIDx V7B dataset and create_COVIDx_binary.ipynb are for COVID-19 positive/negative detection. Both datasets contain over 15600 CXR images with over 1700 positive COVID-19 images.\
**Update 01/05/2021:** We released a new COVIDx6 dataset for binary classification (COVID-19 positive or COVID-19 negative) with over 14500 CXR images and 617 positive COVID-19 images.\
**Update 11/24/2020:** We released [CancerNet-SCa](https://github.com/jamesrenhoulee/CancerNet-SCa) for skin cancer detection, part of the CancerNet initiatives.\
**Update 11/15/2020:** We released COVIDNet-P [inference](inference_pneumonia.py) and [evaluation](eval_pneumonia.py) scripts for identifying pneumonia in CXR images using the COVIDx5 dataset. For more information please refer to this [doc](docs/covidnet_pneumonia.md).\
**Update 10/30/2020:** We released a new COVIDx5 dataset with over 14200 CXR images and 617 positive COVID-19 images.\
**Update 09/11/2020:** We released updated COVIDNet-S [models](docs/models.md) for geographic and opacity extent scoring of SARS-CoV-2 lung severity and updated the [inference script](docs/covidnet_severity.md) for an opacity extent scoring ranging from 0-8.\
**Update 07/08/2020:** We released COVIDNet-CT, which was trained and tested on 104,009 CT images from 1,489 patients. For more information, as well as instructions to run and download the models, refer to [this repo](https://github.com/haydengunraj/COVIDNet-CT).\
**Update 06/26/2020:** We released 3 new models, COVIDNet-CXR4-A, COVIDNet-CXR4-B, COVIDNet-CXR4-C, which were trained on the new COVIDx4 dataset with over 14000 CXR images and 473 positive COVID-19 images for training. The test results are based on the same test dataset as COVIDNet-CXR3 models.\
**Update 06/01/2020:** We released an [inference script](docs/covidnet_severity.md) and the [models](docs/models.md) for geographic and opacity extent scoring of SARS-CoV-2 lung severity.\
**Update 05/26/2020:** For a detailed description of the methodology behind COVID-Net based deep neural networks for geographic extent and opacity extent scoring of chest X-rays for SARS-CoV-2 lung disease severity, see the paper [here](https://arxiv.org/abs/2005.12855).\
**Update 05/13/2020:** We released 3 new models, COVIDNet-CXR3-A, COVIDNet-CXR3-B, COVIDNet-CXR3-C, which were trained on a new COVIDx dataset with both PA and AP X-Rays. The results are now based on a test set containing 100 COVID-19 samples.\
**Update 04/16/2020:** If you have questions, please check the new [FAQ](docs/FAQ.md) page first.
COVID-Net CXR-2 for COVID-19 positive/negative detection architecture and example chest radiography images of COVID-19 cases from 2 different patients and their associated critical factors (highlighted in red) as identified by GSInquire.
The COVID-19 pandemic continues to have a devastating effect on the health and well-being of the global population. A critical step in the fight against COVID-19 is effective screening of infected patients, with one of the key screening approaches being radiology examination using chest radiography. It was found in early studies that patients present abnormalities in chest radiography images that are characteristic of those infected with COVID-19. Motivated by this and inspired by the open source efforts of the research community, in this study we introduce COVID-Net, a deep convolutional neural network design tailored for the detection of COVID-19 cases from chest X-ray (CXR) images that is open source and available to the general public. To the best of the authors' knowledge, COVID-Net is one of the first open source network designs for COVID-19 detection from CXR images at the time of initial release. We also introduce COVIDx, an open access benchmark dataset that we generated comprising of 13,975 CXR images across 13,870 patient patient cases, with the largest number of publicly available COVID-19 positive cases to the best of the authors' knowledge. Furthermore, we investigate how COVID-Net makes predictions using an explainability method in an attempt to not only gain deeper insights into critical factors associated with COVID cases, which can aid clinicians in improved screening, but also audit COVID-Net in a responsible and transparent manner to validate that it is making decisions based on relevant information from the CXR images. **By no means a production-ready solution**, the hope is that the open access COVID-Net, along with the description on constructing the open source COVIDx dataset, will be leveraged and build upon by both researchers and citizen data scientists alike to accelerate the development of highly accurate yet practical deep learning solutions for detecting COVID-19 cases and accelerate treatment of those who need it the most.
For a detailed description of the methodology behind COVID-Net and a full description of the COVIDx dataset, please click [here](https://www.nature.com/articles/s41598-020-76550-z).
For a detailed description of the methodology behind COVIDNet CXR-S severity assessment, please click [here](https://www.mdpi.com/2075-4418/12/1/25). \
For more information on COVIDNet-S deep neural networks for geographic extent and opacity extent scoring of chest X-rays for SARS-CoV-2 lung disease severity, please click [here](https://arxiv.org/abs/2005.12855).
For a detailed description of the methodology behind COVIDNet-CT and the associated dataset of 104,009 CT images from 1,489 patients, please click [here](https://github.com/haydengunraj/COVIDNet-CT).
Currently, the COVID-Net team is working on **COVID-RiskNet**, a deep neural network tailored for COVID-19 risk stratification. Currently this is available as a work-in-progress via included `train_risknet.py` script, help to contribute data and we can improve this tool.
If you would like to **contribute COVID-19 x-ray images**, please submit to https://figure1.typeform.com/to/lLrHwv. Lets all work together to stop the spread of COVID-19!
If you are a researcher or healthcare worker and you would like access to the **GSInquire tool to use to interpret COVID-Net results** on your data or existing data, please reach out to [email protected] or [email protected]
Our desire is to encourage broad adoption and contribution to this project. Accordingly this project has been licensed under the GNU Affero General Public License 3.0. Please see [license file](LICENSE.md) for terms. If you would like to discuss alternative licensing models, please reach out to us at [email protected] and [email protected] or [email protected]
If there are any technical questions after the README, FAQ, and past/current issues have been read, please post an issue or contact:
* [email protected]
* [email protected]
* [email protected]
* [email protected]
* [email protected]
If you find our work useful, can cite our paper using:
```
@Article{Wang2020,
author={Wang, Linda and Lin, Zhong Qiu and Wong, Alexander},
title={COVID-Net: a tailored deep convolutional neural network design for detection of COVID-19 cases from chest X-ray images},
journal={Scientific Reports},
year={2020},
month={Nov},
day={11},
volume={10},
number={1},
pages={19549},
issn={2045-2322},
doi={10.1038/s41598-020-76550-z},
url={https://doi.org/10.1038/s41598-020-76550-z}
}
```
## Quick Links
1. COVIDNet-CXR models (COVID-19 detection using chest x-rays): https://github.com/lindawangg/COVID-Net/blob/master/docs/models.md
2. COVIDNet-CT models (COVID-19 detection using chest CT scans): https://github.com/haydengunraj/COVIDNet-CT/blob/master/docs/models.md
3. COVIDNet-CXR-S models (COVID-19 airspace severity grading using chest x-rays): https://github.com/lindawangg/COVID-Net/blob/master/docs/models.md
4. COVIDNet-S models (COVID-19 lung severity assessment using chest x-rays): https://github.com/lindawangg/COVID-Net/blob/master/docs/models.md
5. COVIDx-CXR dataset: https://github.com/lindawangg/COVID-Net/blob/master/docs/COVIDx.md
6. COVIDx-CT dataset: https://github.com/haydengunraj/COVIDNet-CT/blob/master/docs/dataset.md
7. COVIDx-S dataset: https://github.com/lindawangg/COVID-Net/tree/master/annotations
8. COVIDNet-P inference for pneumonia: https://github.com/lindawangg/COVID-Net/blob/master/docs/covidnet_pneumonia.md
9. CancerNet-SCa models for skin cancer detection: https://github.com/jamesrenhoulee/CancerNet-SCa/blob/main/docs/models.md
Training, inference, and evaluation scripts for COVIDNet-CXR, COVIDNet-CT, COVIDNet-S, and CancerNet-SCa models are available at the respective repos
## Core COVID-Net Team
* DarwinAI Corp., Canada and Vision and Image Processing Research Group, University of Waterloo, Canada
* Linda Wang
* Alexander Wong
* Zhong Qiu Lin
* Paul McInnis
* Audrey Chung
* Melissa Rinch
* Maya Pavlova
* Naomi Terhljan
* Siddharth Surana
* Andy Zhao
* Hayden Gunraj, COVIDNet for CT: https://github.com/haydengunraj/COVIDNet-CT
* Jeffer Peng, COVIDNet UI: https://github.com/darwinai/covidnet_ui
* Vision and Image Processing Research Group, University of Waterloo, Canada
* James Lee
* Hossein Aboutalebi
* Alex MacLean
* Saad Abbasi
* Ashkan Ebadi and Pengcheng Xi (National Research Council Canada)
* Kim-Ann Git (Selayang Hospital)
* Abdul Al-Haimi, COVID-19 ShuffleNet Chest X-Ray Model: https://github.com/aalhaimi/covid-net-cxr-shuffle
## Table of Contents
1. [Requirements](#requirements) to install on your system
2. How to [generate COVIDx dataset](docs/COVIDx.md)
3. Steps for [training, evaluation and inference](docs/train_eval_inference.md) of COVIDNet
4. Steps for [inference](docs/covidnet_severity.md) of COVIDNet lung severity scoring
5. [Results](#results)
6. [Links to pretrained models](docs/models.md)
## Requirements
The main requirements are listed below:
* Tested with Tensorflow 1.13 and 1.15
* OpenCV 4.2.0
* Python 3.6
* Numpy
* Scikit-Learn
* Matplotlib
Additional requirements to generate dataset:
* PyDicom
* Pandas
* Jupyter
## Results
These are the final results for the COVIDNet models.
### COVIDNet-CXR-3 on COVIDx8B (200 COVID-19 test)
Sensitivity (%)
Negative
Positive
99.0
97.5
Positive Predictive Value (%)
Negative
Positive
97.5
99.0
### COVIDNet-CXR-2 on COVIDx8B (200 COVID-19 test)
Sensitivity (%)
Negative
Positive
97.0
95.5
Positive Predictive Value (%)
Negative
Positive
95.6
97.0
### COVIDNet-CXR4-A on COVIDx4 (100 COVID-19 test)
Sensitivity (%)
Normal
Pneumonia
COVID-19
94.0
94.0
95.0
Positive Predictive Value (%)
Normal
Pneumonia
COVID-19
91.3
93.1
99.0
### COVIDNet-CXR4-B on COVIDx4 (100 COVID-19 test)
Sensitivity (%)
Normal
Pneumonia
COVID-19
96.0
92.0
93.0
Positive Predictive Value (%)
Normal
Pneumonia
COVID-19
88.9
93.9
98.9
### COVIDNet-CXR4-C on COVIDx4 (100 COVID-19 test)
Sensitivity (%)
Normal
Pneumonia
COVID-19
95.0
89.0
96.0
Positive Predictive Value (%)
Normal
Pneumonia
COVID-19
90.5
93.7
96.0
### COVIDNet-CXR3-A on COVIDx3 (100 COVID-19 test)
Sensitivity (%)
Normal
Pneumonia
COVID-19
93.0
93.0
94.0
Positive Predictive Value (%)
Normal
Pneumonia
COVID-19
92.1
90.3
97.9
### COVIDNet-CXR3-B on COVIDx3 (100 COVID-19 test)
Sensitivity (%)
Normal
Pneumonia
COVID-19
95.0
94.0
91.0
Positive Predictive Value (%)
Normal
Pneumonia
COVID-19
90.5
91.3
98.9
### COVIDNet-CXR3-C on COVIDx3 (100 COVID-19 test)
Sensitivity (%)
Normal
Pneumonia
COVID-19
92.0
90.0
95.0
Positive Predictive Value (%)
Normal
Pneumonia
COVID-19
90.2
91.8
95.0
### COVIDNet-CXR Small on COVIDx2 (31 COVID-19 test)
Sensitivity (%)
Normal
Pneumonia
COVID-19
97.0
90.0
87.1
Positive Predictive Value (%)
Normal
Pneumonia
COVID-19
89.8
94.7
96.4
### COVIDNet-CXR Large on COVIDx2 (31 COVID-19 test)
Sensitivity (%)
Normal
Pneumonia
COVID-19
99.0
89.0
96.8
Positive Predictive Value (%)
Normal
Pneumonia
COVID-19
91.7
98.9
90.9