Dataset Information

A deep-learning pipeline for the diagnosis and discrimination of viral, non-viral and COVID-19 pneumonia from chest X-ray images.

ABSTRACT: Common lung diseases are first diagnosed using chest X-rays. Here, we show that a fully automated deep-learning pipeline for the standardization of chest X-ray images, for the visualization of lesions and for disease diagnosis can identify viral pneumonia caused by coronavirus disease 2019 (COVID-19) and assess its severity, and can also discriminate between viral pneumonia caused by COVID-19 and other types of pneumonia. The deep-learning system was developed using a heterogeneous multicentre dataset of 145,202 images, and tested retrospectively and prospectively with thousands of additional images across four patient cohorts and multiple countries. The system generalized across settings, discriminating between viral pneumonia, other types of pneumonia and the absence of disease with areas under the receiver operating characteristic curve (AUCs) of 0.94-0.98; between severe and non-severe COVID-19 with an AUC of 0.87; and between COVID-19 pneumonia and other viral or non-viral pneumonia with AUCs of 0.87-0.97. In an independent set of 440 chest X-rays, the system performed comparably to senior radiologists and improved the performance of junior radiologists. Automated deep-learning systems for the assessment of pneumonia could facilitate early intervention and provide support for clinical decision-making.

SUBMITTER: Wang G

PROVIDER: S-EPMC7611049 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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A deep-learning pipeline for the diagnosis and discrimination of viral, non-viral and COVID-19 pneumonia from chest X-ray images.

Wang Guangyu G Liu Xiaohong X Shen Jun J Wang Chengdi C Li Zhihuan Z Ye Linsen L Wu Xingwang X Chen Ting T Wang Kai K Zhang Xuan X Zhou Zhongguo Z Yang Jian J Sang Ye Y Deng Ruiyun R Liang Wenhua W Yu Tao T Gao Ming M Wang Jin J Yang Zehong Z Cai Huimin H Lu Guangming G Zhang Lingyan L Yang Lei L Xu Wenqin W Wang Winston W Olvera Andrea A Ziyar Ian I Zhang Charlotte C Li Oulan O Liao Weihua W Liu Jun J Chen Wen W Chen Wei W Shi Jichan J Zheng Lianghong L Zhang Longjiang L Yan Zhihan Z Zou Xiaoguang X Lin Guiping G Cao Guiqun G Lau Laurance L LL Mo Long L Liang Yong Y Roberts Michael M Sala Evis E Schönlieb Carola-Bibiane CB Fok Manson M Lau Johnson Yiu-Nam JY Xu Tao T He Jianxing J Zhang Kang K Li Weimin W Lin Tianxin T

Nature biomedical engineering 20210415 6

Common lung diseases are first diagnosed using chest X-rays. Here, we show that a fully automated deep-learning pipeline for the standardization of chest X-ray images, for the visualization of lesions and for disease diagnosis can identify viral pneumonia caused by coronavirus disease 2019 (COVID-19) and assess its severity, and can also discriminate between viral pneumonia caused by COVID-19 and other types of pneumonia. The deep-learning system was developed using a heterogeneous multicentre d ...[more]

PMID: 33859385

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Project description:Background and Aims Chest X-ray (CXR) is indispensable to the assessment of severity, diagnosis, and management of pneumonia. Deep learning is an artificial intelligence (AI) technology that has been applied to the interpretation of medical images. This study investigated the feasibility of classifying fatal pneumonia based on CXR images using deep learning models on publicly available platforms. Methods CXR images of patients with pneumonia at diagnosis were labeled as fatal or nonfatal based on medical records. We applied CXR images from 1031 patients with nonfatal pneumonia and 243 patients with fatal pneumonia for training and self-evaluation of the deep learning models. All labeled CXR images were randomly allocated to the training, validation, and test datasets of deep learning models. Data augmentation techniques were not used in this study. We created two deep learning models using two publicly available platforms. Results The first model showed an area under the precision-recall curve of 0.929 with a sensitivity of 50.0% and a specificity of 92.4% for classifying fatal pneumonia. We evaluated the performance of our deep learning models using sensitivity, specificity, PPV, negative predictive value (NPV), accuracy, and F1 score. Using the external validation test dataset of 100 CXR images, the sensitivity, specificity, accuracy, and F1 score were 68.0%, 86.0%, 77.0%, and 74.7%, respectively. In the original dataset, the performance of the second model showed a sensitivity, specificity, and accuracy of 39.6%, 92.8%, and 82.7%, respectively, while external validation showed values of 38.0%, 92.0%, and 65.0%, respectively. The F1 score was 52.1%. These results were comparable to those obtained by respiratory physicians and residents. Conclusions The deep learning models yielded good accuracy in classifying fatal pneumonia. By further improving the performance, AI could assist physicians in the severity assessment of patients with pneumonia.

Project description:The COVID-19 pandemic is causing a major outbreak in more than 150 countries around the world, having a severe impact on the health and life of many people globally. One of the crucial step in fighting COVID-19 is the ability to detect the infected patients early enough, and put them under special care. Detecting this disease from radiography and radiology images is perhaps one of the fastest ways to diagnose the patients. Some of the early studies showed specific abnormalities in the chest radiograms of patients infected with COVID-19. Inspired by earlier works, we study the application of deep learning models to detect COVID-19 patients from their chest radiography images. We first prepare a dataset of 5000 Chest X-rays from the publicly available datasets. Images exhibiting COVID-19 disease presence were identified by board-certified radiologist. Transfer learning on a subset of 2000 radiograms was used to train four popular convolutional neural networks, including ResNet18, ResNet50, SqueezeNet, and DenseNet-121, to identify COVID-19 disease in the analyzed chest X-ray images. We evaluated these models on the remaining 3000 images, and most of these networks achieved a sensitivity rate of 98% ( ± 3%), while having a specificity rate of around 90%. Besides sensitivity and specificity rates, we also present the receiver operating characteristic (ROC) curve, precision-recall curve, average prediction, and confusion matrix of each model. We also used a technique to generate heatmaps of lung regions potentially infected by COVID-19 and show that the generated heatmaps contain most of the infected areas annotated by our board certified radiologist. While the achieved performance is very encouraging, further analysis is required on a larger set of COVID-19 images, to have a more reliable estimation of accuracy rates. The dataset, model implementations (in PyTorch), and evaluations, are all made publicly available for research community at https://github.com/shervinmin/DeepCovid.git.

Project description:BackgroundNowadays doctors and radiologists are overwhelmed with a huge amount of work. This led to the effort to design different Computer-Aided Diagnosis systems (CAD system), with the aim of accomplishing a faster and more accurate diagnosis. The current development of deep learning is a big opportunity for the development of new CADs. In this paper, we propose a novel architecture for a convolutional neural network (CNN) ensemble for classifying chest X-ray (CRX) images into four classes: viral Pneumonia, Tuberculosis, COVID-19, and Healthy. Although Computed tomography (CT) is the best way to detect and diagnoses pulmonary issues, CT is more expensive than CRX. Furthermore, CRX is commonly the first step in the diagnosis, so it's very important to be accurate in the early stages of diagnosis and treatment.ResultsWe applied the transfer learning technique and data augmentation to all CNNs for obtaining better performance. We have designed and evaluated two different CNN-ensembles: Stacking and Voting. This system is ready to be applied in a CAD system to automated diagnosis such a second or previous opinion before the doctors or radiology's. Our results show a great improvement, 99% accuracy of the Stacking Ensemble and 98% of accuracy for the the Voting Ensemble.ConclusionsTo minimize missclassifications, we included six different base CNN models in our architecture (VGG16, VGG19, InceptionV3, ResNet101V2, DenseNet121 and CheXnet) and it could be extended to any number as well as we expect extend the number of diseases to detected. The proposed method has been validated using a large dataset created by mixing several public datasets with different image sizes and quality. As we demonstrate in the evaluation carried out, we reach better results and generalization compared with previous works. In addition, we make a first approach to explainable deep learning with the objective of providing professionals more information that may be valuable when evaluating CRXs.

Dataset Information

A deep-learning pipeline for the diagnosis and discrimination of viral, non-viral and COVID-19 pneumonia from chest X-ray images.

Publications

A deep-learning pipeline for the diagnosis and discrimination of viral, non-viral and COVID-19 pneumonia from chest X-ray images.

Similar Datasets

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