pt-sk/ml_research_abs huggingface dataset:
COVID-19 pneumonia accurately detected on chest radiographs with artificial intelligence.
Authors: FranciscoDorr, HernánChaves, María MercedesSerra, AndrésRamirez, Martín ElíasCosta, JoaquínSeia, ClaudiaCejas, MarceloCastro, EduardoEyheremendy, DiegoFernández Slezak, Mauricio FFarez, NoneNone
Journal: Intelligence-based medicine

To investigate the diagnostic performance of an Artificial Intelligence (AI) system for detection of COVID-19 in chest radiographs (CXR), and compare results to those of physicians working alone, or with AI support.
An AI system was fine-tuned to discriminate confirmed COVID-19 pneumonia, from other viral and bacterial pneumonia and non-pneumonia patients and used to review 302 CXR images from adult patients retrospectively sourced from nine different databases. Fifty-four physicians blind to diagnosis, were invited to interpret images under identical conditions in a test set, and randomly assigned either to receive or not receive support from the AI system. Comparisons were then made between diagnostic performance of physicians working with and without AI support. AI system performance was evaluated using the area under the receiver operating characteristic (AUROC), and sensitivity and specificity of physician performance compared to that of the AI system.
Discrimination by the AI system of COVID-19 pneumonia showed an AUROC curve of 0.96 in the validation and 0.83 in the external test set, respectively. The AI system outperformed physicians in the AUROC overall (70% increase in sensitivity and 1% increase in specificity, p < 0.0001). When working with AI support, physicians increased their diagnostic sensitivity from 47% to 61% (p < 0.001), although specificity decreased from 79% to 75% (p = 0.007).
Our results suggest interpreting chest radiographs (CXR) supported by AI, increases physician diagnostic sensitivity for COVID-19 detection. This approach involving a human-machine partnership may help expedite triaging efforts and improve resource allocation in the current crisis.
Abnormal lung quantification in chest CT images of COVID-19 patients with deep learning and its application to severity prediction.
Authors: FeiShan, YaozongGao, JunWang, WeiyaShi, NannanShi, MiaofeiHan, ZhongXue, DinggangShen, YuxinShi
Journal: Medical physics

Computed tomography (CT) provides rich diagnosis and severity information of COVID-19 in clinical practice. However, there is no computerized tool to automatically delineate COVID-19 infection regions in chest CT scans for quantitative assessment in advanced applications such as severity prediction. The aim of this study was to develop a deep learning (DL)-based method for automatic segmentation and quantification of infection regions as well as the entire lungs from chest CT scans.
The DL-based segmentation method employs the "VB-Net" neural network to segment COVID-19 infection regions in CT scans. The developed DL-based segmentation system is trained by CT scans from 249 COVID-19 patients, and further validated by CT scans from other 300 COVID-19 patients. To accelerate the manual delineation of CT scans for training, a human-involved-model-iterations (HIMI) strategy is also adopted to assist radiologists to refine automatic annotation of each training case. To evaluate the performance of the DL-based segmentation system, three metrics, that is, Dice similarity coefficient, the differences of volume, and percentage of infection (POI), are calculated between automatic and manual segmentations on the validation set. Then, a clinical study on severity prediction is reported based on the quantitative infection assessment.
The proposed DL-based segmentation system yielded Dice similarity coefficients of 91.6% ± 10.0% between automatic and manual segmentations, and a mean POI estimation error of 0.3% for the whole lung on the validation dataset. Moreover, compared with the cases with fully manual delineation that often takes hours, the proposed HIMI training strategy can dramatically reduce the delineation time to 4 min after three iterations of model updating. Besides, the best accuracy of severity prediction was 73.4% ± 1.3% when the mass of infection (MOI) of multiple lung lobes and bronchopulmonary segments were used as features for severity prediction, indicating the potential clinical application of our quantification technique on severity prediction.
A DL-based segmentation system has been developed to automatically segment and quantify infection regions in CT scans of COVID-19 patients. Quantitative evaluation indicated high accuracy in automatic infection delineation and severity prediction.
Rapid COVID-19 diagnosis using ensemble deep transfer learning models from chest radiographic images.
Authors: NehaGianchandani, AayushJaiswal, DilbagSingh, VijayKumar, ManjitKaur
Journal: Journal of ambient intelligence and humanized computing

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes novel coronavirus disease (COVID-19) outbreak in more than 200 countries around the world. The early diagnosis of infected patients is needed to discontinue this outbreak. The diagnosis of coronavirus infection from radiography images is the fastest method. In this paper, two different ensemble deep transfer learning models have been designed for COVID-19 diagnosis utilizing the chest X-rays. Both models have utilized pre-trained models for better performance. They are able to differentiate COVID-19, viral pneumonia, and bacterial pneumonia. Both models have been developed to improve the generalization capability of the classifier for binary and multi-class problems. The proposed models have been tested on two well-known datasets. Experimental results reveal that the proposed framework outperforms the existing techniques in terms of sensitivity, specificity, and accuracy.
Automatic detection of COVID-19 from chest radiographs using deep learning.
Authors: M KPandit, S ABanday, RNaaz, M AChishti
Journal: Radiography (London, England : 1995)

The breakdown of a deadly infectious disease caused by a newly discovered coronavirus (named SARS n-CoV2) back in December 2019 has shown no respite to slow or stop in general. This contagious disease has spread across different lengths and breadths of the globe, taking a death toll to nearly 700 k by the start of August 2020. The number is well expected to rise even more significantly. In the absence of a thoroughly tested and approved vaccine, the onus primarily lies on obliging to standard operating procedures and timely detection and isolation of the infected persons. The detection of SARS n-CoV2 has been one of the core concerns during the fight against this pandemic. To keep up with the scale of the outbreak, testing needs to be scaled at par with it. With the conventional PCR testing, most of the countries have struggled to minimize the gap between the scale of outbreak and scale of testing.
One way of expediting the scale of testing is to shift to a rigorous computational model driven by deep neural networks, as proposed here in this paper. The proposed model is a non-contact process of determining whether a subject is infected or not and is achieved by using chest radiographs; one of the most widely used imaging technique for clinical diagnosis due to fast imaging and low cost. The dataset used in this work contains 1428 chest radiographs with confirmed COVID-19 positive, common bacterial pneumonia, and healthy cases (no infection). We explored the pre-trained VGG-16 model for classification tasks in this. Transfer learning with fine-tuning was used in this study to train the network on relatively small chest radiographs effectively.
Initial experiments showed that the model achieved promising results and can be significantly used to expedite COVID-19 detection. The experimentation showed an accuracy of 96% and 92.5% in two and three output class cases, respectively.
We believe that this study could be used as an initial screening, which can help healthcare professionals to treat the COVID patients by timely detecting better and screening the presence of disease.
Its simplicity drives the proposed deep neural network model, the capability to work on small image dataset, the non-contact method with acceptable accuracy is a potential alternative for rapid COVID-19 testing that can be adapted by the medical fraternity considering the criticality of the time along with the magnitudes of the outbreak.
Epicardial adipose tissue is associated with extent of pneumonia and adverse outcomes in patients with COVID-19.
Authors: KajetanGrodecki, AndrewLin, AryabodRazipour, SebastienCadet, Priscilla AMcElhinney, CatoChan, Barry DPressman, PeterJulien, PalMaurovich-Horvat, NicolaGaibazzi, UditThakur, ElisabettaMancini, CeciliaAgalbato, RobertMenè, GianfrancoParati, FrancoCernigliaro, NiteshNerlekar, CamillaTorlasco, GianlucaPontone, Piotr JSlomka, DaminiDey
Journal: Metabolism: clinical and experimental

We sought to examine the association of epicardial adipose tissue (EAT) quantified on chest computed tomography (CT) with the extent of pneumonia and adverse outcomes in patients with coronavirus disease 2019 (COVID-19).
We performed a post-hoc analysis of a prospective international registry comprising 109 consecutive patients (age 64 ± 16 years; 62% male) with laboratory-confirmed COVID-19 and noncontrast chest CT imaging. Using semi-automated software, we quantified the burden (%) of lung abnormalities associated with COVID-19 pneumonia. EAT volume (mL) and attenuation (Hounsfield units) were measured using deep learning software. The primary outcome was clinical deterioration (intensive care unit admission, invasive mechanical ventilation, or vasopressor therapy) or in-hospital death.
In multivariable linear regression analysis adjusted for patient comorbidities, the total burden of COVID-19 pneumonia was associated with EAT volume (β = 10.6, p = 0.005) and EAT attenuation (β = 5.2, p = 0.004). EAT volume correlated with serum levels of lactate dehydrogenase (r = 0.361, p = 0.001) and C-reactive protein (r = 0.450, p < 0.001). Clinical deterioration or death occurred in 23 (21.1%) patients at a median of 3 days (IQR 1-13 days) following the chest CT. In multivariable logistic regression analysis, EAT volume (OR 5.1 [95% CI 1.8-14.1] per doubling p = 0.011) and EAT attenuation (OR 3.4 [95% CI 1.5-7.5] per 5 Hounsfield unit increase, p = 0.003) were independent predictors of clinical deterioration or death, as was total pneumonia burden (OR 2.5, 95% CI 1.4-4.6, p = 0.002), chronic lung disease (OR 1.3 [95% CI 1.1-1.7], p = 0.011), and history of heart failure (OR 3.5 [95% 1.1-8.2], p = 0.037).
EAT measures quantified from chest CT are independently associated with extent of pneumonia and adverse outcomes in patients with COVID-19, lending support to their use in clinical risk stratification.
Deep learning applications to combat the dissemination of COVID-19 disease: a review.
Authors: M HAlsharif, Y HAlsharif, KYahya, O AAlomari, M AAlbreem, AJahid
Journal: European review for medical and pharmacological sciences

Recent Coronavirus (COVID-19) is one of the respiratory diseases, and it is known as fast infectious ability. This dissemination can be decelerated by diagnosing and quarantining patients with COVID-19 at early stages, thereby saving numerous lives. Reverse transcription-polymerase chain reaction (RT-PCR) is known as one of the primary diagnostic tools. However, RT-PCR tests are costly and time-consuming; it also requires specific materials, equipment, and instruments. Moreover, most countries are suffering from a lack of testing kits because of limitations on budget and techniques. Thus, this standard method is not suitable to meet the requirements of fast detection and tracking during the COVID-19 pandemic, which motived to employ deep learning (DL)/convolutional neural networks (CNNs) technology with X-ray and CT scans for efficient analysis and diagnostic. This study provides insight about the literature that discussed the deep learning technology and its various techniques that are recently developed to combat the dissemination of COVID-19 disease.
Open resource of clinical data from patients with pneumonia for the prediction of COVID-19 outcomes via deep learning.
Authors: WanshanNing, ShijunLei, JingjingYang, YukunCao, PeiranJiang, QianqianYang, JiaoZhang, XiaobeiWang, FenghuaChen, ZhiGeng, LiangXiong, HongmeiZhou, YapingGuo, YulanZeng, HeshuiShi, LinWang, YuXue, ZhengWang
Journal: Nature biomedical engineering

Data from patients with coronavirus disease 2019 (COVID-19) are essential for guiding clinical decision making, for furthering the understanding of this viral disease, and for diagnostic modelling. Here, we describe an open resource containing data from 1,521 patients with pneumonia (including COVID-19 pneumonia) consisting of chest computed tomography (CT) images, 130 clinical features (from a range of biochemical and cellular analyses of blood and urine samples) and laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clinical status. We show the utility of the database for prediction of COVID-19 morbidity and mortality outcomes using a deep learning algorithm trained with data from 1,170 patients and 19,685 manually labelled CT slices. In an independent validation cohort of 351 patients, the algorithm discriminated between negative, mild and severe cases with areas under the receiver operating characteristic curve of 0.944, 0.860 and 0.884, respectively. The open database may have further uses in the diagnosis and management of patients with COVID-19.
An efficient mixture of deep and machine learning models for COVID-19 diagnosis in chest X-ray images.
Authors: DingdingWang, JiaqingMo, GangZhou, LiangXu, YajunLiu
Journal: PloS one

A newly emerged coronavirus (COVID-19) seriously threatens human life and health worldwide. In coping and fighting against COVID-19, the most critical step is to effectively screen and diagnose infected patients. Among them, chest X-ray imaging technology is a valuable imaging diagnosis method. The use of computer-aided diagnosis to screen X-ray images of COVID-19 cases can provide experts with auxiliary diagnosis suggestions, which can reduce the burden of experts to a certain extent. In this study, we first used conventional transfer learning methods, using five pre-trained deep learning models, which the Xception model showed a relatively ideal effect, and the diagnostic accuracy reached 96.75%. In order to further improve the diagnostic accuracy, we propose an efficient diagnostic method that uses a combination of deep features and machine learning classification. It implements an end-to-end diagnostic model. The proposed method was tested on two datasets and performed exceptionally well on both of them. We first evaluated the model on 1102 chest X-ray images. The experimental results show that the diagnostic accuracy of Xception + SVM is as high as 99.33%. Compared with the baseline Xception model, the diagnostic accuracy is improved by 2.58%. The sensitivity, specificity and AUC of this model reached 99.27%, 99.38% and 99.32%, respectively. To further illustrate the robustness of our method, we also tested our proposed model on another dataset. Finally also achieved good results. Compared with related research, our proposed method has higher classification accuracy and efficient diagnostic performance. Overall, the proposed method substantially advances the current radiology based methodology, it can be very helpful tool for clinical practitioners and radiologists to aid them in diagnosis and follow-up of COVID-19 cases.
AI-assisted CT imaging analysis for COVID-19 screening: Building and deploying a medical AI system.
Authors: BoWang, ShuoJin, QingsenYan, HaiboXu, ChuanLuo, LaiWei, WeiZhao, XuexueHou, WenshuoMa, ZhengqingXu, ZhuozhaoZheng, WenboSun, LanLan, WeiZhang, XiangdongMu, ChenxiShi, ZhongxiaoWang, JihaeLee, ZijianJin, MingguiLin, HongboJin, LiangZhang, JunGuo, BenqiZhao, ZhizhongRen, ShuhaoWang, WeiXu, XinghuanWang, JianmingWang, ZhengYou, JiahongDong
Journal: Applied soft computing

The sudden outbreak of novel coronavirus 2019 (COVID-19) increased the diagnostic burden of radiologists. In the time of an epidemic crisis, we hope artificial intelligence (AI) to reduce physician workload in regions with the outbreak, and improve the diagnosis accuracy for physicians before they could acquire enough experience with the new disease. In this paper, we present our experience in building and deploying an AI system that automatically analyzes CT images and provides the probability of infection to rapidly detect COVID-19 pneumonia. The proposed system which consists of classification and segmentation will save about 30%-40% of the detection time for physicians and promote the performance of COVID-19 detection. Specifically, working in an interdisciplinary team of over 30 people with medical and/or AI background, geographically distributed in Beijing and Wuhan, we are able to overcome a series of challenges (
The ensemble deep learning model for novel COVID-19 on CT images.
Authors: TaoZhou, HuilingLu, ZaoliYang, ShiQiu, BingqiangHuo, YaliDong
Journal: Applied soft computing

The rapid detection of the novel coronavirus disease, COVID-19, has a positive effect on preventing propagation and enhancing therapeutic outcomes. This article focuses on the rapid detection of COVID-19. We propose an ensemble deep learning model for novel COVID-19 detection from CT images. 2933 lung CT images from COVID-19 patients were obtained from previous publications, authoritative media reports, and public databases. The images were preprocessed to obtain 2500 high-quality images. 2500 CT images of lung tumor and 2500 from normal lung were obtained from a hospital. Transfer learning was used to initialize model parameters and pretrain three deep convolutional neural network models: AlexNet, GoogleNet, and ResNet. These models were used for feature extraction on all images. Softmax was used as the classification algorithm of the fully connected layer. The ensemble classifier EDL-COVID was obtained via relative majority voting. Finally, the ensemble classifier was compared with three component classifiers to evaluate accuracy, sensitivity, specificity, F value, and Matthews correlation coefficient. The results showed that the overall classification performance of the ensemble model was better than that of the component classifier. The evaluation indexes were also higher. This algorithm can better meet the rapid detection requirements of the novel coronavirus disease COVID-19.
Automated detection of COVID-19 using ensemble of transfer learning with deep convolutional neural network based on CT scans.
Authors: ParisaGifani, AhmadShalbaf, MajidVafaeezadeh
Journal: International journal of computer assisted radiology and surgery

COVID-19 has infected millions of people worldwide. One of the most important hurdles in controlling the spread of this disease is the inefficiency and lack of medical tests. Computed tomography (CT) scans are promising in providing accurate and fast detection of COVID-19. However, determining COVID-19 requires highly trained radiologists and suffers from inter-observer variability. To remedy these limitations, this paper introduces an automatic methodology based on an ensemble of deep transfer learning for the detection of COVID-19.
A total of 15 pre-trained convolutional neural networks (CNNs) architectures: EfficientNets(B0-B5), NasNetLarge, NasNetMobile, InceptionV3, ResNet-50, SeResnet 50, Xception, DenseNet121, ResNext50 and Inception_resnet_v2 are used and then fine-tuned on the target task. After that, we built an ensemble method based on majority voting of the best combination of deep transfer learning outputs to further improve the recognition performance. We have used a publicly available dataset of CT scans, which consists of 349 CT scans labeled as being positive for COVID-19 and 397 negative COVID-19 CT scans that are normal or contain other types of lung diseases.
The experimental results indicate that the majority voting of 5 deep transfer learning architecture with EfficientNetB0, EfficientNetB3, EfficientNetB5, Inception_resnet_v2, and Xception has the higher results than the individual transfer learning structure and among the other models based on precision (0.857), recall (0.854) and accuracy (0.85) metrics in diagnosing COVID-19 from CT scans.
Our study based on an ensemble deep transfer learning system with different pre-trained CNNs architectures can work well on a publicly available dataset of CT images for the diagnosis of COVID-19 based on CT scans.
Deep learning analysis provides accurate COVID-19 diagnosis on chest computed tomography.
Authors: DJavor, HKaplan, AKaplan, S BPuchner, CKrestan, PBaltzer
Journal: European journal of radiology

Computed Tomography is an essential diagnostic tool in the management of COVID-19. Considering the large amount of examinations in high case-load scenarios, an automated tool could facilitate and save critical time in the diagnosis and risk stratification of the disease.
A novel deep learning derived machine learning (ML) classifier was developed using a simplified programming approach and an open source dataset consisting of 6868 chest CT images from 418 patients which was split into training and validation subsets. The diagnostic performance was then evaluated and compared to experienced radiologists on an independent testing dataset. Diagnostic performance metrics were calculated using Receiver Operating Characteristics (ROC) analysis. Operating points with high positive (>10) and low negative (<0.01) likelihood ratios to stratify the risk of COVID-19 being present were identified and validated.
The model achieved an overall accuracy of 0.956 (AUC) on an independent testing dataset of 90 patients. Both rule-in and rule out thresholds were identified and tested. At the rule-in operating point, sensitivity and specificity were 84.4 % and 93.3 % and did not differ from both radiologists (p > 0.05). At the rule-out threshold, sensitivity (100 %) and specificity (60 %) differed significantly from the radiologists (p < 0.05). Likelihood ratios and a Fagan nomogram provide prevalence independent test performance estimates.
Accurate diagnosis of COVID-19 using a basic deep learning approach is feasible using open-source CT image data. In addition, the machine learning classifier provided validated rule-in and rule-out criteria could be used to stratify the risk of COVID-19 being present.