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Register a new userDPN-SENet:A self-attention mechanism neural network for detection and diagnosis of COVID-19 from chest x-ray images
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Background and Objective: The new type of coronavirus is also called COVID-19. It began to spread at the end of 2019 and has now spread across the world. Until October 2020, It has infected around 37 million people and claimed about 1 million lives. We propose a deep learning model that can help radiologists and clinicians use chest X-rays to diagnose COVID-19 cases and show the diagnostic features of pneumonia. Methods: The approach in this study is: 1) we propose a data enhancement method to increase the diversity of the data set, thereby improving the generalization performance of the model. 2) Our deep convolution neural network model DPN-SE adds a self-attention mechanism to the DPN network. The addition of a self-attention mechanism has greatly improved the performance of the network. 3) Use the Lime interpretable library to mark the feature regions on the X-ray medical image that helps doctors more quickly diagnose COVID-19 in people. Results: Under the same network model, the data with and without data enhancement is put into the model for training respectively. At last, comparing two experimental results: among the 10 network models with different structures, 7 network models have improved their effects after using data enhancement, with an average improvement of 1% in recognition accuracy. We propose that the accuracy and recall rates of the DPN-SE network are 93% and 98% of cases (COVID vs. pneumonia bacteria vs. viral pneumonia vs. normal). Compared with the original DPN, the respective accuracy is improved by 2%. Conclusion: The data augmentation method we used has achieved effective results on a small amount of data set, showing that a reasonable data augmentation method can improve the recognition accuracy without changing the sample size and model structure. Overall, the proposed method and model can effectively become a very useful tool for clinical radiologists.
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With a Coronavirus disease (COVID-19) case count exceeding 10 million worldwide, there is an increased need for a diagnostic capability. The main variables in increasing diagnostic capability are reduced cost, turnaround or diagnosis time, and upfront equipment cost and accessibility. Two candidates for machine learning COVID-19 diagnosis are Computed Tomography (CT) scans and plain chest X-rays. While CT scans score higher in sensitivity, they have a higher cost, maintenance requirement, and turnaround time as compared to plain chest X-rays. The use of portable chest X-radiograph (CXR) is recommended by the American College of Radiology (ACR) since using CT places a massive burden on radiology services. Therefore, X-ray imagery paired with machine learning techniques is proposed a first-line triage tool for COVID-19 diagnostics. In this paper we propose a computer-aided diagnosis (CAD) to accurately classify chest X-ray scans of COVID-19 and normal subjects by fine-tuning several neural networks (ResNet18, ResNet50, DenseNet201) pre-trained on the ImageNet dataset. These neural networks are fused in a parallel architecture and the voting criteria are applied in the final classification decision between the candidate object classes where the output of each neural network is representing a single vote. Several experiments are conducted on the weakly labeled COVID-19-CT-CXR dataset consisting of 263 COVID-19 CXR images extracted from PubMed Central Open Access subsets combined with 25 normal classification CXR images. These experiments show an optimistic result and a capability of the proposed model to outperforming many state-of-the-art algorithms on several measures. Using k-fold cross-validation and a bagging classifier ensemble, we achieve an accuracy of 99.7% and a sensitivity of 100%.
Coronavirus disease 2019 (COVID-19) has emerged the need for computer-aided diagnosis with automatic, accurate, and fast algorithms. Recent studies have applied Machine Learning algorithms for COVID-19 diagnosis over chest X-ray (CXR) images. However, the data scarcity in these studies prevents a reliable evaluation with the potential of overfitting and limits the performance of deep networks. Moreover, these networks can discriminate COVID-19 pneumonia usually from healthy subjects only or occasionally, from limited pneumonia types. Thus, there is a need for a robust and accurate COVID-19 detector evaluated over a large CXR dataset. To address this need, in this study, we propose a reliable COVID-19 detection network: ReCovNet, which can discriminate COVID-19 pneumonia from 14 different thoracic diseases and healthy subjects. To accomplish this, we have compiled the largest COVID-19 CXR dataset: QaTa-COV19 with 124,616 images including 4603 COVID-19 samples. The proposed ReCovNet achieved a detection performance with 98.57% sensitivity and 99.77% specificity.
Computer-aided diagnosis has become a necessity for accurate and immediate coronavirus disease 2019 (COVID-19) detection to aid treatment and prevent the spread of the virus. Numerous studies have proposed to use Deep Learning techniques for COVID-19 diagnosis. However, they have used very limited chest X-ray (CXR) image repositories for evaluation with a small number, a few hundreds, of COVID-19 samples. Moreover, these methods can neither localize nor grade the severity of COVID-19 infection. For this purpose, recent studies proposed to explore the activation maps of deep networks. However, they remain inaccurate for localizing the actual infestation making them unreliable for clinical use. This study proposes a novel method for the joint localization, severity grading, and detection of COVID-19 from CXR images by generating the so-called infection maps. To accomplish this, we have compiled the largest dataset with 119,316 CXR images including 2951 COVID-19 samples, where the annotation of the ground-truth segmentation masks is performed on CXRs by a novel collaborative human-machine approach. Furthermore, we publicly release the first CXR dataset with the ground-truth segmentation masks of the COVID-19 infected regions. A detailed set of experiments show that state-of-the-art segmentation networks can learn to localize COVID-19 infection with an F1-score of 83.20%, which is significantly superior to the activation maps created by the previous methods. Finally, the proposed approach achieved a COVID-19 detection performance with 94.96% sensitivity and 99.88% specificity.
The world is still struggling in controlling and containing the spread of the COVID-19 pandemic caused by the SARS-CoV-2 virus. The medical conditions associated with SARS-CoV-2 infections have resulted in a surge in the number of patients at clinics and hospitals, leading to a significantly increased strain on healthcare resources. As such, an important part of managing and handling patients with SARS-CoV-2 infections within the clinical workflow is severity assessment, which is often conducted with the use of chest x-ray (CXR) images. In this work, we introduce COVID-Net CXR-S, a convolutional neural network for predicting the airspace severity of a SARS-CoV-2 positive patient based on a CXR image of the patients chest. More specifically, we leveraged transfer learning to transfer representational knowledge gained from over 16,000 CXR images from a multinational cohort of over 15,000 patient cases into a custom network architecture for severity assessment. Experimental results with a multi-national patient cohort curated by the Radiological Society of North America (RSNA) RICORD initiative showed that the proposed COVID-Net CXR-S has potential to be a powerful tool for computer-aided severity assessment of CXR images of COVID-19 positive patients. Furthermore, radiologist validation on select cases by two board-certified radiologists with over 10 and 19 years of experience, respectively, showed consistency between radiologist interpretation and critical factors leveraged by COVID-Net CXR-S for severity assessment. While not a production-ready solution, the ultimate goal for the open source release of COVID-Net CXR-S is to act as a catalyst for clinical scientists, machine learning researchers, as well as citizen scientists to develop innovative new clinical decision support solutions for helping clinicians around the world manage the continuing pandemic.
The infection of respiratory coronavirus disease 2019 (COVID-19) starts with the upper respiratory tract and as the virus grows, the infection can progress to lungs and develop pneumonia. The conventional way of COVID-19 diagnosis is reverse transcription polymerase chain reaction (RT-PCR), which is less sensitive during early stages; especially if the patient is asymptomatic, which may further cause more severe pneumonia. In this context, several deep learning models have been proposed to identify pulmonary infections using publicly available chest X-ray (CXR) image datasets for early diagnosis, better treatment and quick cure. In these datasets, presence of less number of COVID-19 positive samples compared to other classes (normal, pneumonia and Tuberculosis) raises the challenge for unbiased learning of deep learning models. All deep learning models opted class balancing techniques to solve this issue; which however should be avoided in any medical diagnosis process. Moreover, the deep learning models are also data hungry and need massive computation resources. Therefore for quicker diagnosis, this research proposes a novel pinball loss function based one-class support vector machine (PB-OCSVM), that can work in presence of limited COVID-19 positive CXR samples with objectives to maximize the learning efficiency and to minimize the false predictions. The performance of the proposed model is compared with conventional OCSVM and existing deep learning models, and the experimental results prove that the proposed model outperformed over state-of-the-art methods. To validate the robustness of the proposed model, experiments are also performed with noisy CXR images and UCI benchmark datasets.
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