pt-sk/ml_research_abs huggingface dataset:
Detection of COVID-19 Using Deep Learning Algorithms on Chest Radiographs.
Authors: Wan Hang KeithChiu, VarutVardhanabhuti, DmytroPoplavskiy, Philip Leung HoYu, RichardDu, Alistair Yun HeeYap, SailongZhang, Ambrose Ho-TungFong, Thomas Wing-YanChin, Jonan Chun YinLee, Siu TingLeung, Christine Shing YenLo, Macy Mei-SzeLui, Benjamin Xin HaoFang, Ming-YenNg, Michael DKuo
Journal: Journal of thoracic imaging

To evaluate the performance of a deep learning (DL) algorithm for the detection of COVID-19 on chest radiographs (CXR).
In this retrospective study, a DL model was trained on 112,120 CXR images with 14 labeled classifiers (ChestX-ray14) and fine-tuned using initial CXR on hospital admission of 509 patients, who had undergone COVID-19 reverse transcriptase-polymerase chain reaction (RT-PCR). The test set consisted of a CXR on presentation of 248 individuals suspected of COVID-19 pneumonia between February 16 and March 3, 2020 from 4 centers (72 RT-PCR positives and 176 RT-PCR negatives). The CXR were independently reviewed by 3 radiologists and using the DL algorithm. Diagnostic performance was compared with radiologists' performance and was assessed by area under the receiver operating characteristics (AUC).
The median age of the subjects in the test set was 61 (interquartile range: 39 to 79) years (51% male). The DL algorithm achieved an AUC of 0.81, sensitivity of 0.85, and specificity of 0.72 in detecting COVID-19 using RT-PCR as the reference standard. On subgroup analyses, the model achieved an AUC of 0.79, sensitivity of 0.80, and specificity of 0.74 in detecting COVID-19 in patients presented with fever or respiratory systems and an AUC of 0.87, sensitivity of 0.85, and specificity of 0.81 in distinguishing COVID-19 from other forms of pneumonia. The algorithm significantly outperforms human readers (P<0.001 using DeLong test) with higher sensitivity (P=0.01 using McNemar test).
A DL algorithm (COV19NET) for the detection of COVID-19 on chest radiographs can potentially be an effective tool in triaging patients, particularly in resource-stretched health-care systems.
Advancing COVID-19 differentiation with a robust preprocessing and integration of multi-institutional open-repository computer tomography datasets for deep learning analysis.
Authors: EleftheriosTrivizakis, NikosTsiknakis, Evangelia EVassalou, Georgios ZPapadakis, Demetrios ASpandidos, DimosthenisSarigiannis, AristidisTsatsakis, NikolaosPapanikolaou, Apostolos HKarantanas, KostasMarias
Journal: Experimental and therapeutic medicine

The coronavirus pandemic and its unprecedented consequences globally has spurred the interest of the artificial intelligence research community. A plethora of published studies have investigated the role of imaging such as chest X-rays and computer tomography in coronavirus disease 2019 (COVID-19) automated diagnosis. Οpen repositories of medical imaging data can play a significant role by promoting cooperation among institutes in a world-wide scale. However, they may induce limitations related to variable data quality and intrinsic differences due to the wide variety of scanner vendors and imaging parameters. In this study, a state-of-the-art custom U-Net model is presented with a dice similarity coefficient performance of 99.6% along with a transfer learning VGG-19 based model for COVID-19 versus pneumonia differentiation exhibiting an area under curve of 96.1%. The above was significantly improved over the baseline model trained with no segmentation in selected tomographic slices of the same dataset. The presented study highlights the importance of a robust preprocessing protocol for image analysis within a heterogeneous imaging dataset and assesses the potential diagnostic value of the presented COVID-19 model by comparing its performance to the state of the art.
COVID19XrayNet: A Two-Step Transfer Learning Model for the COVID-19 Detecting Problem Based on a Limited Number of Chest X-Ray Images.
Authors: RuochiZhang, ZhehaoGuo, YueSun, QiLu, ZijianXu, ZhaominYao, MeiyuDuan, ShuaiLiu, YanjiaoRen, LanHuang, FengfengZhou
Journal: Interdisciplinary sciences, computational life sciences

The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a major pandemic outbreak recently. Various diagnostic technologies have been under active development. The novel coronavirus disease (COVID-19) may induce pulmonary failures, and chest X-ray imaging becomes one of the major confirmed diagnostic technologies. The very limited number of publicly available samples has rendered the training of the deep neural networks unstable and inaccurate. This study proposed a two-step transfer learning pipeline and a deep residual network framework COVID19XrayNet for the COVID-19 detection problem based on chest X-ray images. COVID19XrayNet firstly tunes the transferred model on a large dataset of chest X-ray images, which is further tuned using a small dataset of annotated chest X-ray images. The final model achieved 0.9108 accuracy. The experimental data also suggested that the model may be improved with more training samples being released. COVID19XrayNet, a two-step transfer learning framework designed for biomedical images.
COVID-CAPS: A capsule network-based framework for identification of COVID-19 cases from X-ray images.
Authors: ParnianAfshar, ShahinHeidarian, FarnooshNaderkhani, AnastasiaOikonomou, Konstantinos NPlataniotis, ArashMohammadi
Journal: Pattern recognition letters

Novel Coronavirus disease (COVID-19) has abruptly and undoubtedly changed the world as we know it at the end of the 2nd decade of the 21st century. COVID-19 is extremely contagious and quickly spreading globally making its early diagnosis of paramount importance. Early diagnosis of COVID-19 enables health care professionals and government authorities to break the chain of transition and flatten the epidemic curve. The common type of COVID-19 diagnosis test, however, requires specific equipment and has relatively low sensitivity. Computed tomography (CT) scans and X-ray images, on the other hand, reveal specific manifestations associated with this disease. Overlap with other lung infections makes human-centered diagnosis of COVID-19 challenging. Consequently, there has been an urgent surge of interest to develop Deep Neural Network (DNN)-based diagnosis solutions, mainly based on Convolutional Neural Networks (CNNs), to facilitate identification of positive COVID-19 cases. CNNs, however, are prone to lose spatial information between image instances and require large datasets. The paper presents an alternative modeling framework based on Capsule Networks, referred to as the COVID-CAPS, being capable of handling small datasets, which is of significant importance due to sudden and rapid emergence of COVID-19. Our results based on a dataset of X-ray images show that COVID-CAPS has advantage over previous CNN-based models. COVID-CAPS achieved an Accuracy of 95.7%, Sensitivity of 90%, Specificity of 95.8%, and Area Under the Curve (AUC) of 0.97, while having far less number of trainable parameters in comparison to its counterparts. To potentially and further improve diagnosis capabilities of the COVID-CAPS, pre-training and transfer learning are utilized based on a new dataset constructed from an external dataset of X-ray images. This is in contrary to existing works on COVID-19 detection where pre-training is performed based on natural images. Pre-training with a dataset of similar nature further improved accuracy to 98.3% and specificity to 98.6%.
COVID-19 image classification using deep features and fractional-order marine predators algorithm.
Authors: Ahmed TSahlol, DaliaYousri, Ahmed AEwees, Mohammed A AAl-Qaness, RobertasDamasevicius, Mohamed AbdElaziz
Journal: Scientific reports

Currently, we witness the severe spread of the pandemic of the new Corona virus, COVID-19, which causes dangerous symptoms to humans and animals, its complications may lead to death. Although convolutional neural networks (CNNs) is considered the current state-of-the-art image classification technique, it needs massive computational cost for deployment and training. In this paper, we propose an improved hybrid classification approach for COVID-19 images by combining the strengths of CNNs (using a powerful architecture called Inception) to extract features and a swarm-based feature selection algorithm (Marine Predators Algorithm) to select the most relevant features. A combination of fractional-order and marine predators algorithm (FO-MPA) is considered an integration among a robust tool in mathematics named fractional-order calculus (FO). The proposed approach was evaluated on two public COVID-19 X-ray datasets which achieves both high performance and reduction of computational complexity. The two datasets consist of X-ray COVID-19 images by international Cardiothoracic radiologist, researchers and others published on Kaggle. The proposed approach selected successfully 130 and 86 out of 51 K features extracted by inception from dataset 1 and dataset 2, while improving classification accuracy at the same time. The results are the best achieved on these datasets when compared to a set of recent feature selection algorithms. By achieving 98.7%, 98.2% and 99.6%, 99% of classification accuracy and F-Score for dataset 1 and dataset 2, respectively, the proposed approach outperforms several CNNs and all recent works on COVID-19 images.
Cascaded deep learning classifiers for computer-aided diagnosis of COVID-19 and pneumonia diseases in X-ray scans.
Authors: Mohamed EsmailKarar, Ezz El-DinHemdan, Marwa AShouman
Journal: Complex & intelligent systems

Computer-aided diagnosis (CAD) systems are considered a powerful tool for physicians to support identification of the novel Coronavirus Disease 2019 (COVID-19) using medical imaging modalities. Therefore, this article proposes a new framework of cascaded deep learning classifiers to enhance the performance of these CAD systems for highly suspected COVID-19 and pneumonia diseases in X-ray images. Our proposed deep learning framework constitutes two major advancements as follows. First, complicated multi-label classification of X-ray images have been simplified using a series of binary classifiers for each tested case of the health status. That mimics the clinical situation to diagnose potential diseases for a patient. Second, the cascaded architecture of COVID-19 and pneumonia classifiers is flexible to use different fine-tuned deep learning models simultaneously, achieving the best performance of confirming infected cases. This study includes eleven pre-trained convolutional neural network models, such as Visual Geometry Group Network (VGG) and Residual Neural Network (ResNet). They have been successfully tested and evaluated on public X-ray image dataset for normal and three diseased cases. The results of proposed cascaded classifiers showed that VGG16, ResNet50V2, and Dense Neural Network (DenseNet169) models achieved the best detection accuracy of COVID-19, viral (Non-COVID-19) pneumonia, and bacterial pneumonia images, respectively. Furthermore, the performance of our cascaded deep learning classifiers is superior to other multi-label classification methods of COVID-19 and pneumonia diseases in previous studies. Therefore, the proposed deep learning framework presents a good option to be applied in the clinical routine to assist the diagnostic procedures of COVID-19 infection.
COVID-19 detection in CT images with deep learning: A voting-based scheme and cross-datasets analysis.
Authors: PedroSilva, EduardoLuz, GuilhermeSilva, GladstonMoreira, RodrigoSilva, DiegoLucio, DavidMenotti
Journal: Informatics in medicine unlocked

Early detection and diagnosis are critical factors to control the COVID-19 spreading. A number of deep learning-based methodologies have been recently proposed for COVID-19 screening in CT scans as a tool to automate and help with the diagnosis. These approaches, however, suffer from at least one of the following problems: (i) they treat each CT scan slice independently and (ii) the methods are trained and tested with sets of images from the same dataset. Treating the slices independently means that the same patient may appear in the training and test sets at the same time which may produce misleading results. It also raises the question of whether the scans from the same patient should be evaluated as a group or not. Moreover, using a single dataset raises concerns about the generalization of the methods. Different datasets tend to present images of varying quality which may come from different types of CT machines reflecting the conditions of the countries and cities from where they come from. In order to address these two problems, in this work, we propose an Efficient Deep Learning Technique for the screening of COVID-19 with a voting-based approach. In this approach, the images from a given patient are classified as group in a voting system. The approach is tested in the two biggest datasets of COVID-19 CT analysis with a patient-based split. A cross dataset study is also presented to assess the robustness of the models in a more realistic scenario in which data comes from different distributions. The cross-dataset analysis has shown that the generalization power of deep learning models is far from acceptable for the task since accuracy drops from 87.68% to 56.16% on the best evaluation scenario. These results highlighted that the methods that aim at COVID-19 detection in CT-images have to improve significantly to be considered as a clinical option and larger and more diverse datasets are needed to evaluate the methods in a realistic scenario.
Detection of COVID-19 from Chest X-Ray Images Using Convolutional Neural Networks.
Authors: BoranSekeroglu, IlkerOzsahin
Journal: SLAS technology

The detection of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), which is responsible for coronavirus disease 2019 (COVID-19), using chest X-ray images has life-saving importance for both patients and doctors. In addition, in countries that are unable to purchase laboratory kits for testing, this becomes even more vital. In this study, we aimed to present the use of deep learning for the high-accuracy detection of COVID-19 using chest X-ray images. Publicly available X-ray images (1583 healthy, 4292 pneumonia, and 225 confirmed COVID-19) were used in the experiments, which involved the training of deep learning and machine learning classifiers. Thirty-eight experiments were performed using convolutional neural networks, 10 experiments were performed using five machine learning models, and 14 experiments were performed using the state-of-the-art pre-trained networks for transfer learning. Images and statistical data were considered separately in the experiments to evaluate the performances of models, and eightfold cross-validation was used. A mean sensitivity of 93.84%, mean specificity of 99.18%, mean accuracy of 98.50%, and mean receiver operating characteristics-area under the curve scores of 96.51% are achieved. A convolutional neural network without pre-processing and with minimized layers is capable of detecting COVID-19 in a limited number of, and in imbalanced, chest X-ray images.
Initial chest radiographs and artificial intelligence (AI) predict clinical outcomes in COVID-19 patients: analysis of 697 Italian patients.
Authors: JunaidMushtaq, RenatoPennella, SalvatoreLavalle, AnnaColarieti, StephanieSteidler, Carlo M AMartinenghi, DiegoPalumbo, AntonioEsposito, PatriziaRovere-Querini, MorenoTresoldi, GiovanniLandoni, FabioCiceri, AlbertoZangrillo, FrancescoDe Cobelli
Journal: European radiology

To evaluate whether the initial chest X-ray (CXR) severity assessed by an AI system may have prognostic utility in patients with COVID-19.
This retrospective single-center study included adult patients presenting to the emergency department (ED) between February 25 and April 9, 2020, with SARS-CoV-2 infection confirmed on real-time reverse transcriptase polymerase chain reaction (RT-PCR). Initial CXRs obtained on ED presentation were evaluated by a deep learning artificial intelligence (AI) system and compared with the Radiographic Assessment of Lung Edema (RALE) score, calculated by two experienced radiologists. Death and critical COVID-19 (admission to intensive care unit (ICU) or deaths occurring before ICU admission) were identified as clinical outcomes. Independent predictors of adverse outcomes were evaluated by multivariate analyses.
Six hundred ninety-seven 697 patients were included in the study: 465 males (66.7%), median age of 62 years (IQR 52-75). Multivariate analyses adjusting for demographics and comorbidities showed that an AI system-based score ≥ 30 on the initial CXR was an independent predictor both for mortality (HR 2.60 (95% CI 1.69 - 3.99; p < 0.001)) and critical COVID-19 (HR 3.40 (95% CI 2.35-4.94; p < 0.001)). Other independent predictors were RALE score, older age, male sex, coronary artery disease, COPD, and neurodegenerative disease.
AI- and radiologist-assessed disease severity scores on CXRs obtained on ED presentation were independent and comparable predictors of adverse outcomes in patients with COVID-19.
ClinicalTrials.gov NCT04318366 ( https://clinicaltrials.gov/ct2/show/NCT04318366 ).
• AI system-based score ≥ 30 and a RALE score ≥ 12 at CXRs performed at ED presentation are independent and comparable predictors of death and/or ICU admission in COVID-19 patients. • Other independent predictors are older age, male sex, coronary artery disease, COPD, and neurodegenerative disease. • The comparable performance of the AI system in relation to a radiologist-assessed score in predicting adverse outcomes may represent a game-changer in resource-constrained settings.
Development of a volumetric pancreas segmentation CT dataset for AI applications through trained technologists: a study during the COVID 19 containment phase.
Authors: GarimaSuman, AnanyaPanda, PanagiotisKorfiatis, Marie EEdwards, SushilGarg, Daniel JBlezek, Suresh TChari, Ajit HGoenka
Journal: Abdominal radiology (New York)

To evaluate the performance of trained technologists vis-à-vis radiologists for volumetric pancreas segmentation and to assess the impact of supplementary training on their performance.
In this IRB-approved study, 22 technologists were trained in pancreas segmentation on portal venous phase CT through radiologist-led interactive videoconferencing sessions based on an image-rich curriculum. Technologists segmented pancreas in 188 CTs using freehand tools on custom image-viewing software. Subsequent supplementary training included multimedia videos focused on common errors, which were followed by second batch of 159 segmentations. Two radiologists reviewed all cases and corrected inaccurate segmentations. Technologists' segmentations were compared against radiologists' segmentations using Dice-Sorenson coefficient (DSC), Jaccard coefficient (JC), and Bland-Altman analysis.
Corrections were made in 71 (38%) cases from first batch [26 (37%) oversegmentations and 45 (63%) undersegmentations] and in 77 (48%) cases from second batch [12 (16%) oversegmentations and 65 (84%) undersegmentations]. DSC, JC, false positive (FP), and false negative (FN) [mean (SD)] in first versus second batches were 0.63 (0.15) versus 0.63 (0.16), 0.48 (0.15) versus 0.48 (0.15), 0.29 (0.21) versus 0.21 (0.10), and 0.36 (0.20) versus 0.43 (0.19), respectively. Differences were not significant (p > 0.05). However, range of mean pancreatic volume difference reduced in the second batch [- 2.74 cc (min - 92.96 cc, max 87.47 cc) versus - 23.57 cc (min - 77.32, max 30.19)].
Trained technologists could perform volumetric pancreas segmentation with reasonable accuracy despite its complexity. Supplementary training further reduced range of volume difference in segmentations. Investment into training technologists could augment and accelerate development of body imaging datasets for AI applications.
Development and clinical implementation of tailored image analysis tools for COVID-19 in the midst of the pandemic: The synergetic effect of an open, clinically embedded software development platform and machine learning.
Authors: ConstantinAnastasopoulos, ThomasWeikert, ShanYang, AhmedAbdulkadir, LenaSchmülling, ClaudiaBühler, FabianoPaciolla, RaphaelSexauer, JoshyCyriac, IvanNesic, RaphaelTwerenbold, JensBremerich, BramStieltjes, Alexander WSauter, GregorSommer
Journal: European journal of radiology

During the emerging COVID-19 pandemic, radiology departments faced a substantial increase in chest CT admissions coupled with the novel demand for quantification of pulmonary opacities. This article describes how our clinic implemented an automated software solution for this purpose into an established software platform in 10 days. The underlying hypothesis was that modern academic centers in radiology are capable of developing and implementing such tools by their own efforts and fast enough to meet the rapidly increasing clinical needs in the wake of a pandemic.
Deep convolutional neural network algorithms for lung segmentation and opacity quantification on chest CTs were trained using semi-automatically and manually created ground-truth (N
The final algorithm was available at day 10 and achieved human-like performance (Dice coefficient = 0.97). For opacity quantification, a slight underestimation was seen both for the in-house (1.8 %) and for the external algorithm (0.9 %). In contrast to the external reference, the underestimation for the in-house algorithm showed no dependency on total opacity load, making it more suitable for follow-up.
The combination of machine learning and a clinically embedded software development platform enabled time-efficient development, instant deployment, and rapid adoption in clinical routine. The algorithm for fully automated lung segmentation and opacity quantification that we developed in the midst of the COVID-19 pandemic was ready for clinical use within just 10 days and achieved human-level performance even in complex cases.
A deep learning approach to detect Covid-19 coronavirus with X-Ray images.
Authors: GovardhanJain, DeeptiMittal, DakshThakur, Madhup KMittal
Journal: Biocybernetics and biomedical engineering

Rapid and accurate detection of COVID-19 coronavirus is necessity of time to prevent and control of this pandemic by timely quarantine and medical treatment in absence of any vaccine. Daily increase in cases of COVID-19 patients worldwide and limited number of available detection kits pose difficulty in identifying the presence of disease. Therefore, at this point of time, necessity arises to look for other alternatives. Among already existing, widely available and low-cost resources, X-ray is frequently used imaging modality and on the other hand, deep learning techniques have achieved state-of-the-art performances in computer-aided medical diagnosis. Therefore, an alternative diagnostic tool to detect COVID-19 cases utilizing available resources and advanced deep learning techniques is proposed in this work. The proposed method is implemented in four phases, viz., data augmentation, preprocessing, stage-I and stage-II deep network model designing. This study is performed with online available resources of 1215 images and further strengthen by utilizing data augmentation techniques to provide better generalization of the model and to prevent the model overfitting by increasing the overall length of dataset to 1832 images. Deep network implementation in two stages is designed to differentiate COVID-19 induced pneumonia from healthy cases, bacterial and other virus induced pneumonia on X-ray images of chest. Comprehensive evaluations have been performed to demonstrate the effectiveness of the proposed method with both (i) training-validation-testing and (ii) 5-fold cross validation procedures. High classification accuracy as 97.77%, recall as 97.14% and precision as 97.14% in case of COVID-19 detection shows the efficacy of proposed method in present need of time. Further, the deep network architecture showing averaged accuracy/sensitivity/specificity/precision/F1-score of 98.93/98.93/98.66/96.39/98.15 with 5-fold cross validation makes a promising outcome in COVID-19 detection using X-ray images.