pt-sk/ml_research_abs huggingface dataset:
COVID-Net CXR-S: Deep Convolutional Neural Network for Severity Assessment of COVID-19 Cases from Chest X-ray Images.
Authors: HosseinAboutalebi, MayaPavlova, Mohammad JavadShafiee, AliSabri, AmerAlaref, AlexanderWong
Journal: Diagnostics (Basel, Switzerland)

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 patient's 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 SARS-CoV-2 positive and negative patient cases into a custom network architecture for severity assessment. Experimental results using the RSNA RICORD dataset 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.
Objective evaluation of deep uncertainty predictions for COVID-19 detection.
Authors: HamzehAsgharnezhad, AfsharShamsi, RoohallahAlizadehsani, AbbasKhosravi, SaeidNahavandi, Zahra AlizadehSani, DiptiSrinivasan, Sheikh Mohammed SharifulIslam
Journal: Scientific reports

Deep neural networks (DNNs) have been widely applied for detecting COVID-19 in medical images. Existing studies mainly apply transfer learning and other data representation strategies to generate accurate point estimates. The generalization power of these networks is always questionable due to being developed using small datasets and failing to report their predictive confidence. Quantifying uncertainties associated with DNN predictions is a prerequisite for their trusted deployment in medical settings. Here we apply and evaluate three uncertainty quantification techniques for COVID-19 detection using chest X-Ray (CXR) images. The novel concept of uncertainty confusion matrix is proposed and new performance metrics for the objective evaluation of uncertainty estimates are introduced. Through comprehensive experiments, it is shown that networks pertained on CXR images outperform networks pretrained on natural image datasets such as ImageNet. Qualitatively and quantitatively evaluations also reveal that the predictive uncertainty estimates are statistically higher for erroneous predictions than correct predictions. Accordingly, uncertainty quantification methods are capable of flagging risky predictions with high uncertainty estimates. We also observe that ensemble methods more reliably capture uncertainties during the inference. DNN-based solutions for COVID-19 detection have been mainly proposed without any principled mechanism for risk mitigation. Previous studies have mainly focused on on generating single-valued predictions using pretrained DNNs. In this paper, we comprehensively apply and comparatively evaluate three uncertainty quantification techniques for COVID-19 detection using chest X-Ray images. The novel concept of uncertainty confusion matrix is proposed and new performance metrics for the objective evaluation of uncertainty estimates are introduced for the first time. Using these new uncertainty performance metrics, we quantitatively demonstrate when we could trust DNN predictions for COVID-19 detection from chest X-rays. It is important to note the proposed novel uncertainty evaluation metrics are generic and could be applied for evaluation of probabilistic forecasts in all classification problems.
Survey on Diagnosing CORONA VIRUS from Radiography Chest X-ray Images Using Convolutional Neural Networks.
Authors: J TThirukrishna, Sanda Reddy SaiKrishna, PolicherlaShashank, SSrikanth, VRaghu
Journal: Wireless personal communications

Corona Virus continues to harms its effects on the people lives across the globe. The screening of infected persons has to be identified is a vital step because it is a fast and low-cost way. Certain above mentioned things can be recognized by chest X-ray images that plays a significant role and also used for examining in detection of CORONA VIRUS(COVID-19). Here radiological chest X-rays are easily available with low cost only. In this survey paper, Convolutional Neural Network(CNN) based solution that will benefit in detection of the Covid-19 positive patients using radiography chest X-Ray images. To test the efficiency of the solution, using data sets of publicly available X-Ray images of Corona virus positive cases and negative cases. Images of positive Corona Virus patients and pictures of healthy person images are divided into testing images and trainable images. The solution which are providing the good results with classification accuracy within the test set-up. Then GUI based application supports for medical examination areas. This GUI application can be used on any computer and performed by any medical examiner or technician to determine Corona Virus positive patients using radiography X-ray images. The result will be precisely obtaining the Covid-19 Patient analysis through the chest X-ray images and also results may be retrieve within a few seconds.
Segmentation and classification on chest radiography: a systematic survey.
Authors: TarunAgrawal, PrakashChoudhary
Journal: The Visual computer

Chest radiography (X-ray) is the most common diagnostic method for pulmonary disorders. A trained radiologist is required for interpreting the radiographs. But sometimes, even experienced radiologists can misinterpret the findings. This leads to the need for computer-aided detection diagnosis. For decades, researchers were automatically detecting pulmonary disorders using the traditional computer vision (CV) methods. Now the availability of large annotated datasets and computing hardware has made it possible for deep learning to dominate the area. It is now the modus operandi for feature extraction, segmentation, detection, and classification tasks in medical imaging analysis. This paper focuses on the research conducted using chest X-rays for the lung segmentation and detection/classification of pulmonary disorders on publicly available datasets. The studies performed using the Generative Adversarial Network (GAN) models for segmentation and classification on chest X-rays are also included in this study. GAN has gained the interest of the CV community as it can help with medical data scarcity. In this study, we have also included the research conducted before the popularity of deep learning models to have a clear picture of the field. Many surveys have been published, but none of them is dedicated to chest X-rays. This study will help the readers to know about the existing techniques, approaches, and their significance.
Detecting Racial/Ethnic Health Disparities Using Deep Learning From Frontal Chest Radiography.
Authors: AyisPyrros, Jorge MarioRodríguez-Fernández, Stephen MBorstelmann, Judy WawiraGichoya, Jeanne MHorowitz, BrianFornelli, NasirSiddiqui, YuryVelichko, OluwasanmiKoyejo Sanmi, WilliamGalanter
Journal: Journal of the American College of Radiology : JACR

The aim of this study was to assess racial/ethnic and socioeconomic disparities in the difference between atherosclerotic vascular disease prevalence measured by a multitask convolutional neural network (CNN) deep learning model using frontal chest radiographs (CXRs) and the prevalence reflected by administrative hierarchical condition category codes in two cohorts of patients with coronavirus disease 2019 (COVID-19).
A CNN model, previously published, was trained to predict atherosclerotic disease from ambulatory frontal CXRs. The model was then validated on two cohorts of patients with COVID-19: 814 ambulatory patients from a suburban location (presenting from March 14, 2020, to October 24, 2020, the internal ambulatory cohort) and 485 hospitalized patients from an inner-city location (hospitalized from March 14, 2020, to August 12, 2020, the external hospitalized cohort). The CNN model predictions were validated against electronic health record administrative codes in both cohorts and assessed using the area under the receiver operating characteristic curve (AUC). The CXRs from the ambulatory cohort were also reviewed by two board-certified radiologists and compared with the CNN-predicted values for the same cohort to produce a receiver operating characteristic curve and the AUC. The atherosclerosis diagnosis discrepancy, Δ
The CNN prediction for vascular disease from frontal CXRs in the ambulatory cohort had an AUC of 0.85 (95% confidence interval, 0.82-0.89) and in the hospitalized cohort had an AUC of 0.69 (95% confidence interval, 0.64-0.75) against the electronic health record data. In the ambulatory cohort, the consensus radiologists' reading had an AUC of 0.89 (95% confidence interval, 0.86-0.92) relative to the CNN. Multivariate linear regression of Δ
A CNN model was predictive of aortic atherosclerosis in two cohorts (one ambulatory and one hospitalized) with COVID-19. The discrepancy between the CNN model and the administrative code, Δ
Bayesian-based optimized deep learning model to detect COVID-19 patients using chest X-ray image data.
Authors: MohamedLoey, ShakerEl-Sappagh, SeyedaliMirjalili
Journal: Computers in biology and medicine

Coronavirus Disease 2019 (COVID-19) is extremely infectious and rapidly spreading around the globe. As a result, rapid and precise identification of COVID-19 patients is critical. Deep Learning has shown promising performance in a variety of domains and emerged as a key technology in Artificial Intelligence. Recent advances in visual recognition are based on image classification and artefacts detection within these images. The purpose of this study is to classify chest X-ray images of COVID-19 artefacts in changed real-world situations. A novel Bayesian optimization-based convolutional neural network (CNN) model is proposed for the recognition of chest X-ray images. The proposed model has two main components. The first one utilizes CNN to extract and learn deep features. The second component is a Bayesian-based optimizer that is used to tune the CNN hyperparameters according to an objective function. The used large-scale and balanced dataset comprises 10,848 images (i.e., 3616 COVID-19, 3616 normal cases, and 3616 Pneumonia). In the first ablation investigation, we compared Bayesian optimization to three distinct ablation scenarios. We used convergence charts and accuracy to compare the three scenarios. We noticed that the Bayesian search-derived optimal architecture achieved 96% accuracy. To assist qualitative researchers, address their research questions in a methodologically sound manner, a comparison of research method and theme analysis methods was provided. The suggested model is shown to be more trustworthy and accurate in real world.
COVID-19 disease diagnosis from paper-based ECG trace image data using a novel convolutional neural network model.
Authors: EmrahIrmak
Journal: Physical and engineering sciences in medicine

Clinical reports show that COVID-19 disease has impacts on the cardiovascular system in addition to the respiratory system. Available COVID-19 diagnostic methods have been shown to have limitations. In addition to current diagnostic methods such as low-sensitivity standard RT-PCR tests and expensive medical imaging devices, the development of alternative methods for the diagnosis of COVID-19 disease would be beneficial for control of the COVID-19 pandemic. Further, it is important to quickly and accurately detect abnormalities caused by COVID-19 on the cardiovascular system via ECG. In this study, the diagnosis of COVID-19 disease is proposed using a novel deep Convolutional Neural Network model by using only ECG trace images created from ECG signals of COVID-19 infected patients based on the abnormalities caused by the COVID-19 virus on the cardiovascular system. An overall classification accuracy of 98.57%, 93.20%, 96.74% and AUC value of 0.9966, 0.9771, 0.9905 is achieved for COVID-19 vs. Normal, COVID-19 vs. Abnormal Heartbeats, COVID-19 vs. Myocardial Infarction binary classification tasks, respectively. In addition, an overall classification accuracy of 86.55% and 83.05% is achieved for COVID-19 vs. Abnormal Heartbeats vs. Myocardial Infarction and Normal vs. COVID-19 vs. Abnormal Heartbeats vs. Myocardial Infarction multi-classification tasks. This study is believed to have great potential to speed up the diagnosis and treatment of COVID-19 patients, saving clinicians time and facilitating the control of the pandemic.
Inverted bell-curve-based ensemble of deep learning models for detection of COVID-19 from chest X-rays.
Authors: AshisPaul, ArpanBasu, MuftiMahmud, M ShamimKaiser, RamSarkar
Journal: Neural computing & applications

Novel Coronavirus 2019 disease or COVID-19 is a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The use of chest X-rays (CXRs) has become an important practice to assist in the diagnosis of COVID-19 as they can be used to detect the abnormalities developed in the infected patients' lungs. With the fast spread of the disease, many researchers across the world are striving to use several deep learning-based systems to identify the COVID-19 from such CXR images. To this end, we propose an inverted bell-curve-based ensemble of deep learning models for the detection of COVID-19 from CXR images. We first use a selection of models pretrained on ImageNet dataset and use the concept of transfer learning to retrain them with CXR datasets. Then the trained models are combined with the proposed inverted bell curve weighted ensemble method, where the output of each classifier is assigned a weight, and the final prediction is done by performing a weighted average of those outputs. We evaluate the proposed method on two publicly available datasets: the COVID-19 Radiography Database and the IEEE COVID Chest X-ray Dataset. The accuracy, F1 score and the AUC ROC achieved by the proposed method are 99.66%, 99.75% and 99.99%, respectively, in the first dataset, and, 99.84%, 99.81% and 99.99%, respectively, in the other dataset. Experimental results ensure that the use of transfer learning-based models and their combination using the proposed ensemble method result in improved predictions of COVID-19 in CXRs.
Classifier Fusion for Detection of COVID-19 from CT Scans.
Authors: TaranjitKaur, Tapan KumarGandhi
Journal: Circuits, systems, and signal processing

The coronavirus disease (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus. COVID-19 is found to be the most infectious disease in last few decades. This disease has infected millions of people worldwide. The inadequate availability and the limited sensitivity of the testing kits have motivated the clinicians and the scientist to use Computer Tomography (CT) scans to screen COVID-19. Recent advances in technology and the availability of deep learning approaches have proved to be very promising in detecting COVID-19 with increased accuracy. However, deep learning approaches require a huge labeled training dataset, and the current availability of benchmark COVID-19 data is still small. For the limited training data scenario, the CNN usually overfits after several iterations. Hence, in this work, we have investigated different pre-trained network architectures with transfer learning for COVID-19 detection that can work even on a small medical imaging dataset. Various variants of the pre-trained ResNet model, namely ResNet18, ResNet50, and ResNet101, are investigated in the current paper for the detection of COVID-19. The experimental results reveal that transfer learned ResNet50 model outperformed other models by achieving a recall of 98.80% and an F1-score of 98.41%. To further improvise the results, the activations from different layers of best performing model are also explored for the detection using the support vector machine, logistic regression and K-nearest neighbor classifiers. Moreover, a classifier fusion strategy is also proposed that fuses the predictions from the different classifiers via majority voting. Experimental results reveal that via using learned image features and classification fusion strategy, the recall, and F1-score have improvised to 99.20% and 99.40%.
BEMD-3DCNN-based method for COVID-19 detection.
Authors: AliRiahi, OmarElharrouss, SomayaAl-Maadeed
Journal: Computers in biology and medicine

The coronavirus outbreak continues to spread around the world and no one knows when it will stop. Therefore, from the first day of the identification of the virus in Wuhan, China, scientists have launched numerous research projects to understand the nature of the virus, how to detect it, and search for the most effective medicine to help and protect patients. Importantly, a rapid diagnostic and detection system is a priority and should be developed to stop COVID-19 from spreading. Medical imaging techniques have been used for this purpose. Current research is focused on exploiting different backbones like VGG, ResNet, DenseNet, or combining them to detect COVID-19. By using these backbones many aspects cannot be analyzed like the spatial and contextual information in the images, although this information can be useful for more robust detection performance. In this paper, we used 3D representation of the data as input for the proposed 3DCNN-based deep learning model. The process includes using the Bi-dimensional Empirical Mode Decomposition (BEMD) technique to decompose the original image into IMFs, and then building a video of these IMF images. The formed video is used as input for the 3DCNN model to classify and detect the COVID-19 virus. The 3DCNN model consists of a 3D VGG-16 backbone followed by a Context-aware attention (CAA) module, and then fully connected layers for classification. Each CAA module takes the feature maps of different blocks of the backbone, which allows learning from different feature maps. In our experiments, we used 6484 X-ray images, of which 1802 were COVID-19 positive cases, 1910 normal cases, and 2772 pneumonia cases. The experiment results showed that our proposed technique achieved the desired results on the selected dataset. Additionally, the use of the 3DCNN model with contextual information processing exploited CAA networks to achieve better performance.
Artificial intelligence for stepwise diagnosis and monitoring of COVID-19.
Authors: HengruiLiang, YuchenGuo, XiangruChen, Keng-LeongAng, YuweiHe, NaJiang, QiangDu, QingsiZeng, LigongLu, ZebinGao, LinduoLi, QuanzhengLi, FangxingNie, GuiguangDing, GaoHuang, AilanChen, YiminLi, WeijieGuan, LingSang, YuandaXu, HuaiChen, ZishengChen, ShiyueLi, NuofuZhang, YingChen, DanxiaHuang, RunLi, JianfuLi, BoCheng, YiZhao, CaichenLi, ShanXiong, RunchenWang, JunLiu, WeiWang, JunHuang, FeiCui, TaoXu, Fleming Y MLure, MeixiaoZhan, YuanyiHuang, QiangYang, QionghaiDai, WenhuaLiang, JianxingHe, NanshanZhong
Journal: European radiology

Main challenges for COVID-19 include the lack of a rapid diagnostic test, a suitable tool to monitor and predict a patient's clinical course and an efficient way for data sharing among multicenters. We thus developed a novel artificial intelligence system based on deep learning (DL) and federated learning (FL) for the diagnosis, monitoring, and prediction of a patient's clinical course.
CT imaging derived from 6 different multicenter cohorts were used for stepwise diagnostic algorithm to diagnose COVID-19, with or without clinical data. Patients with more than 3 consecutive CT images were trained for the monitoring algorithm. FL has been applied for decentralized refinement of independently built DL models.
A total of 1,552,988 CT slices from 4804 patients were used. The model can diagnose COVID-19 based on CT alone with the AUC being 0.98 (95% CI 0.97-0.99), and outperforms the radiologist's assessment. We have also successfully tested the incorporation of the DL diagnostic model with the FL framework. Its auto-segmentation analyses co-related well with those by radiologists and achieved a high Dice's coefficient of 0.77. It can produce a predictive curve of a patient's clinical course if serial CT assessments are available.
The system has high consistency in diagnosing COVID-19 based on CT, with or without clinical data. Alternatively, it can be implemented on a FL platform, which would potentially encourage the data sharing in the future. It also can produce an objective predictive curve of a patient's clinical course for visualization.
• CoviDet could diagnose COVID-19 based on chest CT with high consistency; this outperformed the radiologist's assessment. Its auto-segmentation analyses co-related well with those by radiologists and could potentially monitor and predict a patient's clinical course if serial CT assessments are available. It can be integrated into the federated learning framework. • CoviDet can be used as an adjunct to aid clinicians with the CT diagnosis of COVID-19 and can potentially be used for disease monitoring; federated learning can potentially open opportunities for global collaboration.
Fully automatic pipeline of convolutional neural networks and capsule networks to distinguish COVID-19 from community-acquired pneumonia via CT images.
Authors: QianqianQi, ShouliangQi, YananWu, ChenLi, BinTian, ShuyueXia, JigangRen, LimingYang, HanlinWang, HuiYu
Journal: Computers in biology and medicine

Chest computed tomography (CT) is crucial in the diagnosis of coronavirus disease 2019 (COVID-19). However, the persistent pandemic and similar CT manifestations between COVID-19 and community-acquired pneumonia (CAP) raise methodological requirements.
A fully automatic pipeline of deep learning is proposed for distinguishing COVID-19 from CAP using CT images. Inspired by the diagnostic process of radiologists, the pipeline comprises four connected modules for lung segmentation, selection of slices with lesions, slice-level prediction, and patient-level prediction. The roles of the first and second modules and the effectiveness of the capsule network for slice-level prediction were investigated. A dataset of 326 CT scans was collected to train and test the pipeline. Another public dataset of 110 patients was used to evaluate the generalization capability.
LinkNet exhibited the largest intersection over union (0.967) and Dice coefficient (0.983) for lung segmentation. For the selection of slices with lesions, the capsule network with the ResNet50 block achieved an accuracy of 92.5% and an area under the curve (AUC) of 0.933. The capsule network using the DenseNet121 block demonstrated better performance for slice-level prediction, with an accuracy of 97.1% and AUC of 0.992. For both datasets, the prediction accuracy of our pipeline was 100% at the patient level.
The proposed fully automatic deep learning pipeline of deep learning can distinguish COVID-19 from CAP via CT images rapidly and accurately, thereby accelerating diagnosis and augmenting the performance of radiologists. This pipeline is convenient for use by radiologists and provides explainable predictions.