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COVID-CAPS

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A Capsule Network-based framework for identification of COVID-19 cases from chest X-ray Images

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# COVID-CAPS
<h4> A Capsule Network-based framework for identification of COVID-19 cases from chest X-ray Images </h4>

Novel Coronavirus disease 2019 pneumonia (COVID-19), with its relatively high intensive care unit (ICU) admission and mortality
rate, is rapidly spreading all over the world. Early diagnosis of this
disease is of paramount importance as it enables physicians to isolate
the patients and prevent the further transitions. The current gold standard
in COVID-19 diagnosis requires specific equipment, is timeconsuming,
and has relatively low sensitivity. Computed tomography
(CT) scans and X-ray images, on the other hand, reveal specific
manifestations associated with this disease. However, the overlap
between different bacterial and viral cases, makes the humancentered
diagnosis difficult and challenging.

The capsule network-based model (COVID-CAPS), proposed in this
study, for diagnosis of COVID-19, is capable of handling small
datasets, which is of significant importance as this disease has been
only recently identified and large datasets are not available.

So far, our results has shown that COVID-CAPS has competitive advantageous over
previous CNN-based models, on a public dataset of chest X-ray images. <br> 
<b>The detailed COVID-CAPS's structure and methodology is explained in detail at</b> <a href="https://doi.org/10.1016/j.patrec.2020.09.010">https://doi.org/10.1016/j.patrec.2020.09.010</a>

<h3>UPDATE 1:</h3> Our team has recently released <b>a large CT scan dataset of COVID-19, Community Acquired Pneumonia, and Normal cases</b> called <a href="https://github.com/ShahinSHH/COVID-CT-MD">COVID-CT-MD</a> containing labels and information applicable in Deep Learning and Medical Image Processing.
You can access this dataset through the <a href="https://figshare.com/s/c20215f3d42c98f09ad0">figshare data repository</a>.
<h3>UPDATE 2:</h3> Two newly proposed models working with COVID-19 CT scans are now available at <a href="https://github.com/ShahinSHH/COVID-FACT">https://github.com/ShahinSHH/COVID-FACT</a> and <a href="https://github.com/ShahinSHH/CT-CAPS">https://github.com/ShahinSHH/CT-CAPS</a>.

<h3>Note : Please don’t use COVID-CAPS as the self-diagnostic model without performing a clinical study.</h3>
  COVID-CAPS is currently a research model aiming to accelerate building a comprehensive and safe diagnostic system to identify COVID-19 cases. This model is not a replacement for clinical diagnostic tests and should not be used as a self-diagnosis tool to look for COVID-19 features without a clinical study at this stage. Our team is working on enhancing the performance and generalizing the model upon receiving more data from medical collaborators and scientific community. You can track new results and versions as they will be updated on this page.<br>

![Roadmap](https://raw.githubusercontent.com/ShahinSHH/COVID-CAPS/master/COVID-CAPS/model.jpg)
## COVID-CAPS Team
* Intelligent Signal and Information Processing (I-SIP) Lab, Concordia University, Montreal, Canada
    * Dr.Arash Mohammdi
    * Dr.Farnoosh Naderkhani
    * Parnian Afshar
    * Shahin Heidarian
* Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada
    * Dr.Konstantinos N. Plataniotis
* Sunnybrook Health Sciences Centre, Department of Medical Imaging, University of Toronto, Canada
    * Dr.Anastasia Oikonomou
## Dataset
We used the same dataset as the one used <a href="https://github.com/lindawangg/COVID-Net">here.</a>
This dataset is generated from the following two publicly available chest
X-ray datasets.
* <a href="https://github.com/ieee8023/covid-chestxray-dataset">covid-chestxray-dataset</a> : A new data collection project to make COVID-19 data publicly available to the scientific community.
* <a href="https://www.kaggle.com/c/rsna-pneumonia-detection-challenge">RSNA Pneumonia Detection Challenge</a> : The dataset used in the Pneumonia Detection Challenge organized by the Radiological Society of North America.

As the main goal of this study is to identify
positive COVID-19 cases, we binarized the labels as either positive
or negative. In other words the three labels of normal, bacterial, and
non-COVID viral together form the negative class.

<h3>Note that the provided dataset has been undergone some updates as of the time we first used the data, so make sure to check the dimension of images and number of different classes in the latest version of the dataset before running the COVID-CAPS model.</h3>

## Pre-Training
Our pre-training dataset consists of 94323 frontal view chest X-ray images for common thorax diseases. This dataset is extracted from the NIH Chest X-ray dataset available online for public access <a href="https://nihcc.app.box.com/v/ChestXray-NIHCC/folder/36938765345">here</a>. Chest X-ray14 dataset originally contains 112120 X-ray images for 14 thorax abnormalities. This dataset also contains normal cases without specific findings in their corresponding images.<br>To reduce the number of categories, we classified these 15 groups into 5 categories based on the underlying relations between the abnormalities in each disease. The first four groups are dedicated to No findings, Tumors, Pleural diseases, and Lung infections categories. The fifth group encompasses other images without specific relations with the first four groups.
We then removed 17797 cases with multiple labels (appeared in more than one category) to reduce the complexity and downscaled all images from (1024,1024) to (224,224).

### Steps to prepare the pre-training dataset
<ol>
  <li>Follow the guideline in the database folder to download and unpack the original dataset.</li>
  <li>Run xray14_preprocess.py<br>
This will create another folder in the current directory named database_preprocessed to store downscaled images all in one place.</li>
  <li>Run xray14_selection.py<br>
It will import preprocessed images generated in the 2nd step as numpy arrays and stack them to form two numpy arrays named X_images and Y_labels. These two numpy arrays will then be used to pretrain our model.<br>
    <b>Note:</b> In some computers, you may face errors regarding memory allocation or limited capacity due to high volume of the data. The simplest solution is to split the process into several steps and save the data in seperate numpy arrays (e.g. each containing 10k images) and then combine them. There are more general ways to address this issue such as customizing a datagenerator, however if your system couldn't run the xray14_selection.py efficiently, the splitting option will be a quick solution.</li>
</ol>

## Requirements
* Tested with tensorflow-gpu 2 and keras-gpu 2.2.4
* Python 3.6
* OpenCV
* Pandas
* Itertools
* Glob
* OS
* Scikit-image
* Scikit-learn
* Matplotlib

## Code
The code for the Capsule Network implementation is adopted from <a href="https://keras.io/examples/cifar10_cnn_capsule/">here.</a>
Codes to prepare the X-ray14 dataset are adopted from <a href="https://github.com/ManuelPalermo/X-Ray-ConvNet">here</a>.
Codes are available as the following list:

* pre-train.py : Codes for pre-training
* binary-after.py : Codes for fine-tuning
* test_binary.py : Test and Evaluation
* weight-improvement-binary-after-44.h5 : COVID-CAPS weights after fine-tuning
* pre-train.h5 : Weights for the pre-trained model
* binary.py : Main code without pre-training
* weights-improvement-binary-86.h5 : Best model's weights without pre-training
* xray14_preprocess.py : Extracting and rescaling the Chest XRay14 dataset
* xray14_selection.py : Converting downscaled Xray14 images into numpy arrays and saving them

## Citation
If you found this code and the related paper useful in your research, please consider citing:

```
@article{Afshar2020,
author = {Afshar, Parnian and Heidarian, Shahin and Naderkhani, Farnoosh and Oikonomou, Anastasia and Plataniotis, Konstantinos N. and Mohammadi, Arash},
doi = {10.1016/j.patrec.2020.09.010},
issn = {01678655},
journal = {Pattern Recognition Letters},
month = {oct},
pages = {638--643},
title = {{COVID-CAPS: A capsule network-based framework for identification of COVID-19 cases from X-ray images}},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0167865520303512},
volume = {138},
year = {2020}
}
```

COVID-CAPS

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