Dataset Information

Deep Ensemble Model for Classification of Novel Coronavirus in Chest X-Ray Images.

ABSTRACT: The novel coronavirus, SARS-CoV-2, can be deadly to people, causing COVID-19. The ease of its propagation, coupled with its high capacity for illness and death in infected individuals, makes it a hazard to the community. Chest X-rays are one of the most common but most difficult to interpret radiographic examination for early diagnosis of coronavirus-related infections. They carry a considerable amount of anatomical and physiological information, but it is sometimes difficult even for the expert radiologist to derive the related information they contain. Automatic classification using deep learning models can help in better assessing these infections swiftly. Deep CNN models, namely, MobileNet, ResNet50, and InceptionV3, were applied with different variations, including training the model from the start, fine-tuning along with adjusting learned weights of all layers, and fine-tuning with learned weights along with augmentation. Fine-tuning with augmentation produced the best results in pretrained models. Out of these, two best-performing models (MobileNet and InceptionV3) selected for ensemble learning produced accuracy and FScore of 95.18% and 90.34%, and 95.75% and 91.47%, respectively. The proposed hybrid ensemble model generated with the merger of these deep models produced a classification accuracy and FScore of 96.49% and 92.97%. For test dataset, which was separately kept, the model generated accuracy and FScore of 94.19% and 88.64%. Automatic classification using deep ensemble learning can help radiologists in the correct identification of coronavirus-related infections in chest X-rays. Consequently, this swift and computer-aided diagnosis can help in saving precious human lives and minimizing the social and economic impact on society.

SUBMITTER: Ahmad F

PROVIDER: S-EPMC7805527 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Deep Ensemble Model for Classification of Novel Coronavirus in Chest X-Ray Images.

Ahmad Fareed F Farooq Amjad A Ghani Muhammad Usman MU

Computational intelligence and neuroscience 20210105

The novel coronavirus, SARS-CoV-2, can be deadly to people, causing COVID-19. The ease of its propagation, coupled with its high capacity for illness and death in infected individuals, makes it a hazard to the community. Chest X-rays are one of the most common but most difficult to interpret radiographic examination for early diagnosis of coronavirus-related infections. They carry a considerable amount of anatomical and physiological information, but it is sometimes difficult even for the expert ...[more]

PMID: 33488691

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Project description:Novel Coronavirus is deadly for humans and animals. The ease of its dispersion, coupled with its tremendous capability for ailment and death in infected people, makes it a risk to society. The chest X-ray is conventional but hard to interpret radiographic test for initial diagnosis of coronavirus from other related infections. It bears a considerable amount of information on physiological and anatomical features. To extract relevant information from it can occasionally become challenging even for a professional radiologist. In this regard, deep-learning models can help in swift, accurate and reliable outcomes. Existing datasets are small and suffer from the balance issue. In this paper, we prepare a relatively larger and well-balanced dataset as compared to the available datasets. Furthermore, we analyze deep learning models, namely, AlexNet, SqueezeNet, DenseNet201, MobileNetV2 and InceptionV3 with numerous variations such as training the models from scratch, fine-tuning without pre-trained weights, fine-tuning along with updating pre-trained weights of all layers, and fine-tuning with pre-trained weights along with applying augmentation. Our results show that fine-tuning with augmentation generates best results in pre-trained models. Finally, we have made architectural adjustments in MobileNetV2 and InceptionV3 models to learn more intricate features, which are then merged in our proposed ensemble model. The performance of our model is statistically analyzed against other models using four different performance metrics with paired two-sided t-test on 5 different splits of training and test sets of our dataset. We find that it is statistically better than its competing methods for the four metrics. Thus, the computer-aided classification based on the proposed model can assist radiologists in identifying coronavirus from other related infections in chest X-rays with higher accuracy. This can help in a reliable and speedy diagnosis, thereby saving valuable lives and mitigating the adverse impact on the socioeconomics of our community.

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.

Project description:Recently, the infectious disease COVID-19 remains to have a catastrophic effect on the lives of human beings all over the world. To combat this deadliest disease, it is essential to screen the affected people quickly and least inexpensively. Radiological examination is considered the most feasible step toward attaining this objective; however, chest X-ray (CXR) and computed tomography (CT) are the most easily accessible and inexpensive options. This paper proposes a novel ensemble deep learning-based solution to predict the COVID-19-positive patients using CXR and CT images. The main aim of the proposed model is to provide an effective COVID-19 prediction model with a robust diagnosis and increase the prediction performance. Initially, pre-processing, like image resizing and noise removal, is employed using image scaling and median filtering techniques to enhance the input data for further processing. Various data augmentation styles, such as flipping and rotation, are applied to capable the model to learn the variations during training and attain better results on a small dataset. Finally, a new ensemble deep honey architecture (EDHA) model is introduced to effectively classify the COVID-19-positive and -negative cases. EDHA combines three pre-trained architectures like ShuffleNet, SqueezeNet, and DenseNet-201, to detect the class value. Moreover, a new optimization algorithm, the honey badger algorithm (HBA), is adapted in EDHA to determine the best values for the hyper-parameters of the proposed model. The proposed EDHA is implemented in the Python platform and evaluates the performance in terms of accuracy, sensitivity, specificity, precision, f1-score, AUC, and MCC. The proposed model has utilized the publicly available CXR and CT datasets to test the solution's efficiency. As a result, the simulated outcomes showed that the proposed EDHA had achieved better performance than the existing techniques in terms of Accuracy, Sensitivity, Specificity, Precision, F1-Score, MCC, AUC, and Computation time are 99.1%, 99%, 98.6%, 99.6%, 98.9%, 99.2%, 0.98, and 820 s using the CXR dataset.

Project description:COVID-19 (SARS-CoV-2), which causes acute respiratory syndrome, is a contagious and deadly disease that has devastating effects on society and human life. COVID-19 can cause serious complications, especially in patients with pre-existing chronic health problems such as diabetes, hypertension, lung cancer, weakened immune systems, and the elderly. The most critical step in the fight against COVID-19 is the rapid diagnosis of infected patients. Computed Tomography (CT), chest X-ray (CXR), and RT-PCR diagnostic kits are frequently used to diagnose the disease. However, due to difficulties such as the inadequacy of RT-PCR test kits and false negative (FN) results in the early stages of the disease, the time-consuming examination of medical images obtained from CT and CXR imaging techniques by specialists/doctors, and the increasing workload on specialists, it is challenging to detect COVID-19. Therefore, researchers have suggested searching for new methods in COVID- 19 detection. In analysis studies with CT and CXR radiography images, it was determined that COVID-19-infected patients experienced abnormalities related to COVID-19. The anomalies observed here are the primary motivation for artificial intelligence researchers to develop COVID-19 detection applications with deep convolutional neural networks. Here, convolutional neural network-based deep learning algorithms from artificial intelligence technologies with high discrimination capabilities can be considered as an alternative approach in the disease detection process. This study proposes a deep convolutional neural network, COVID-DSNet, to diagnose typical pneumonia (bacterial, viral) and COVID-19 diseases from CT, CXR, hybrid CT + CXR images. In the multi-classification study with the CT dataset, 97.60 % accuracy and 97.60 % sensitivity values were obtained from the COVID-DSNet model, and 100 %, 96.30 %, and 96.58 % sensitivity values were obtained in the detection of typical, common pneumonia and COVID-19, respectively. The proposed model is an economical, practical deep learning network that data scientists can benefit from and develop. Although it is not a definitive solution in disease diagnosis, it may help experts as it produces successful results in detecting pneumonia and COVID-19. Graphical abstract Unlabelled Image

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.

Dataset Information

Deep Ensemble Model for Classification of Novel Coronavirus in Chest X-Ray Images.

Publications

Deep Ensemble Model for Classification of Novel Coronavirus in Chest X-Ray Images.

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