pt-sk/ml_research_abs huggingface dataset:
Correlation between lung infection severity and clinical laboratory indicators in patients with COVID-19: a cross-sectional study based on machine learning.
Authors: XingruiWang, QinglinChe, XiaoxiaoJi, XinyiMeng, LangZhang, RongrongJia, HairongLyu, WeixianBai, LingjieTan, YanjunGao
Journal: BMC infectious diseases

Coronavirus disease 2019 (COVID-19) has caused a global pandemic that has raised worldwide concern. This study aims to investigate the correlation between the extent of lung infection and relevant clinical laboratory testing indicators in COVID-19 and to analyse its underlying mechanism.
Chest high-resolution computer tomography (CT) images and laboratory examination data of 31 patients with COVID-19 were extracted, and the lesion areas in CT images were quantitatively segmented and calculated using a deep learning (DL) system. A cross-sectional study method was carried out to explore the differences among the proportions of lung lobe infection and to correlate the percentage of infection (POI) of the whole lung in all patients with clinical laboratory examination values.
No significant difference in the proportion of infection was noted among various lung lobes (P > 0.05). The POI of total lung was negatively correlated with the peripheral blood lymphocyte percentage (L%) (r = - 0.633, P < 0.001) and lymphocyte (LY) count (r = - 0.555, P = 0.001) but positively correlated with the neutrophil percentage (N%) (r = 0.565, P = 0.001). Otherwise, the POI was not significantly correlated with the peripheral blood white blood cell (WBC) count, monocyte percentage (M%) or haemoglobin (HGB) content. In some patients, as the infection progressed, the L% and LY count decreased progressively accompanied by a continuous increase in the N%.
Lung lesions in COVID-19 patients are significantly correlated with the peripheral blood lymphocyte and neutrophil levels, both of which could serve as prognostic indicators that provide warning implications, and contribute to clinical interventions in patients.
Deep Learning-Based Measurement of Total Plaque Area in B-Mode Ultrasound Images.
Authors: RanZhou, FuminGuo, M RezaAzarpazhooh, SaminehHashemi, XinyaoCheng, J DavidSpence, MingyueDing, AaronFenster
Journal: IEEE journal of biomedical and health informatics

Measurement of total-plaque-area (TPA) is important for determining long term risk for stroke and monitoring carotid plaque progression. Since delineation of carotid plaques is required, a deep learning method can provide automatic plaque segmentations and TPA measurements; however, it requires large datasets and manual annotations for training with unknown performance on new datasets. A UNet++ ensemble algorithm was proposed to segment plaques from 2D carotid ultrasound images, trained on three small datasets (n = 33, 33, 34 subjects) and tested on 44 subjects from the SPARC dataset (n = 144, London, Canada). The ensemble was also trained on the entire SPARC dataset and tested with a different dataset (n = 497, Zhongnan Hospital, China). Algorithm and manual segmentations were compared using Dice-similarity-coefficient (DSC), and TPAs were compared using the difference ( ∆TPA), Pearson correlation coefficient (r) and Bland-Altman analyses. Segmentation variability was determined using the intra-class correlation coefficient (ICC) and coefficient-of-variation (CoV). For 44 SPARC subjects, algorithm DSC was 83.3-85.7%, and algorithm TPAs were strongly correlated (r = 0.985-0.988; p < 0.001) with manual results with marginal biases (0.73-6.75) mm
JCS: An Explainable COVID-19 Diagnosis System by Joint Classification and Segmentation.
Authors: Yu-HuanWu, Shang-HuaGao, JieMei, JunXu, Deng-PingFan, Rong-GuoZhang, Ming-MingCheng
Journal: IEEE transactions on image processing : a publication of the IEEE Signal Processing Society

Recently, the coronavirus disease 2019 (COVID-19) has caused a pandemic disease in over 200 countries, influencing billions of humans. To control the infection, identifying and separating the infected people is the most crucial step. The main diagnostic tool is the Reverse Transcription Polymerase Chain Reaction (RT-PCR) test. Still, the sensitivity of the RT-PCR test is not high enough to effectively prevent the pandemic. The chest CT scan test provides a valuable complementary tool to the RT-PCR test, and it can identify the patients in the early-stage with high sensitivity. However, the chest CT scan test is usually time-consuming, requiring about 21.5 minutes per case. This paper develops a novel Joint Classification and Segmentation (JCS) system to perform real-time and explainable COVID- 19 chest CT diagnosis. To train our JCS system, we construct a large scale COVID- 19 Classification and Segmentation (COVID-CS) dataset, with 144,167 chest CT images of 400 COVID- 19 patients and 350 uninfected cases. 3,855 chest CT images of 200 patients are annotated with fine-grained pixel-level labels of opacifications, which are increased attenuation of the lung parenchyma. We also have annotated lesion counts, opacification areas, and locations and thus benefit various diagnosis aspects. Extensive experiments demonstrate that the proposed JCS diagnosis system is very efficient for COVID-19 classification and segmentation. It obtains an average sensitivity of 95.0% and a specificity of 93.0% on the classification test set, and 78.5% Dice score on the segmentation test set of our COVID-CS dataset. The COVID-CS dataset and code are available at https://github.com/yuhuan-wu/JCS.
A deep learning integrated radiomics model for identification of coronavirus disease 2019 using computed tomography.
Authors: XiaoguoZhang, DaweiWang, JiangShao, SongTian, WeixiongTan, YanMa, QingnanXu, XiaomanMa, DashengLi, JunChai, DingjunWang, WenwenLiu, LingboLin, JiangfenWu, ChenXia, ZhongfaZhang
Journal: Scientific reports

Since its first outbreak, Coronavirus Disease 2019 (COVID-19) has been rapidly spreading worldwide and caused a global pandemic. Rapid and early detection is essential to contain COVID-19. Here, we first developed a deep learning (DL) integrated radiomics model for end-to-end identification of COVID-19 using CT scans and then validated its clinical feasibility. We retrospectively collected CT images of 386 patients (129 with COVID-19 and 257 with other community-acquired pneumonia) from three medical centers to train and externally validate the developed models. A pre-trained DL algorithm was utilized to automatically segment infected lesions (ROIs) on CT images which were used for feature extraction. Five feature selection methods and four machine learning algorithms were utilized to develop radiomics models. Trained with features selected by L1 regularized logistic regression, classifier multi-layer perceptron (MLP) demonstrated the optimal performance with AUC of 0.922 (95% CI 0.856-0.988) and 0.959 (95% CI 0.910-1.000), the same sensitivity of 0.879, and specificity of 0.900 and 0.887 on internal and external testing datasets, which was equivalent to the senior radiologist in a reader study. Additionally, diagnostic time of DL-MLP was more efficient than radiologists (38 s vs 5.15 min). With an adequate performance for identifying COVID-19, DL-MLP may help in screening of suspected cases.
A novel multiple instance learning framework for COVID-19 severity assessment via data augmentation and self-supervised learning.
Authors: ZekunLi, WeiZhao, FengShi, LeiQi, XingzhiXie, YingWei, ZhongxiangDing, YangGao, ShangjieWu, JunLiu, YinghuanShi, DinggangShen
Journal: Medical image analysis

How to fast and accurately assess the severity level of COVID-19 is an essential problem, when millions of people are suffering from the pandemic around the world. Currently, the chest CT is regarded as a popular and informative imaging tool for COVID-19 diagnosis. However, we observe that there are two issues - weak annotation and insufficient data that may obstruct automatic COVID-19 severity assessment with CT images. To address these challenges, we propose a novel three-component method, i.e., 1) a deep multiple instance learning component with instance-level attention to jointly classify the bag and also weigh the instances, 2) a bag-level data augmentation component to generate virtual bags by reorganizing high confidential instances, and 3) a self-supervised pretext component to aid the learning process. We have systematically evaluated our method on the CT images of 229 COVID-19 cases, including 50 severe and 179 non-severe cases. Our method could obtain an average accuracy of 95.8%, with 93.6% sensitivity and 96.4% specificity, which outperformed previous works.
DON: Deep Learning and Optimization-Based Framework for Detection of Novel Coronavirus Disease Using X-ray Images.
Authors: GauravDhiman, VVinoth Kumar, AmandeepKaur, AshutoshSharma
Journal: Interdisciplinary sciences, computational life sciences

In the hospital, a limited number of COVID-19 test kits are available due to the spike in cases every day. For this reason, a rapid alternative diagnostic option should be introduced as an automated detection method to prevent COVID-19 spreading among individuals. This article proposes multi-objective optimization and a deep-learning methodology for the detection of infected coronavirus patients with X-rays. J48 decision tree method classifies the deep characteristics of affected X-ray corona images to detect the contaminated patients effectively. Eleven different convolutional neuronal network-based (CNN) models were developed in this study to detect infected patients with coronavirus pneumonia using X-ray images (AlexNet, VGG16, VGG19, GoogleNet, ResNet18, ResNet500, ResNet101, InceptionV3, InceptionResNetV2, DenseNet201 and XceptionNet). In addition, the parameters of the CNN profound learning model are described using an emperor penguin optimizer with several objectives (MOEPO). A broad review reveals that the proposed model can categorise the X-ray images at the correct rates of precision, accuracy, recall, specificity and F1-score. Extensive test results show that the proposed model outperforms competitive models with well-known efficiency metrics. The proposed model is, therefore, useful for the real-time classification of X-ray chest images of COVID-19 disease.
Current limitations to identify COVID-19 using artificial intelligence with chest X-ray imaging.
Authors: José DanielLópez-Cabrera, RubénOrozco-Morales, Jorge ArmandoPortal-Diaz, OrlandoLovelle-Enríquez, MarlénPérez-Díaz
Journal: Health and technology

The scientific community has joined forces to mitigate the scope of the current COVID-19 pandemic. The early identification of the disease, as well as the evaluation of its evolution is a primary task for the timely application of medical protocols. The use of medical images of the chest provides valuable information to specialists. Specifically, chest X-ray images have been the focus of many investigations that apply artificial intelligence techniques for the automatic classification of this disease. The results achieved to date on the subject are promising. However, some results of these investigations contain errors that must be corrected to obtain appropriate models for clinical use. This research discusses some of the problems found in the current scientific literature on the application of artificial intelligence techniques in the automatic classification of COVID-19. It is evident that in most of the reviewed works an incorrect evaluation protocol is applied, which leads to overestimating the results.
Transfer learning for establishment of recognition of COVID-19 on CT imaging using small-sized training datasets.
Authors: ChunLi, YunyunYang, HuiLiang, BoyingWu
Journal: Knowledge-based systems

The coronavirus disease, called COVID-19, which is spreading fast worldwide since the end of 2019, and has become a global challenging pandemic. Until 27th May 2020, it caused more than 5.6 million individuals infected throughout the world and resulted in greater than 348,145 deaths. CT images-based classification technique has been tried to use the identification of COVID-19 with CT imaging by hospitals, which aims to minimize the possibility of virus transmission and alleviate the burden of clinicians and radiologists. Early diagnosis of COVID-19, which not only prevents the disease from spreading further but allows more reasonable allocation of limited medical resources. Therefore, CT images play an essential role in identifying cases of COVID-19 that are in great need of intensive clinical care. Unfortunately, the current public health emergency, which has caused great difficulties in collecting a large set of precise data for training neural networks. To tackle this challenge, our first thought is transfer learning, which is a technique that aims to transfer the knowledge from one or more source tasks to a target task when the latter has fewer training data. Since the training data is relatively limited, so a transfer learning-based DensNet-121 approach for the identification of COVID-19 is established. The proposed method is inspired by the precious work of predecessors such as CheXNet for identifying common Pneumonia, which was trained using the large Chest X-ray14 dataset, and the dataset contains 112,120 frontal chest X-rays of 14 different chest diseases (including Pneumonia) that are individually labeled and achieved good performance. Therefore, CheXNet as the pre-trained network was used for the target task (COVID-19 classification) by fine-tuning the network weights on the small-sized dataset in the target task. Finally, we evaluated our proposed method on the COVID-19-CT dataset. Experimentally, our method achieves state-of-the-art performance for the accuracy (ACC) and F1-score. The quantitative indicators show that the proposed method only uses a GPU can reach the best performance, up to 0.87 and 0.86, respectively, compared with some widely used and recent deep learning methods, which are helpful for COVID-19 diagnosis and patient triage. The codes used in this manuscript are publicly available on GitHub at (https://github.com/lichun0503/CT-Classification).
An Uncertainty-Aware Transfer Learning-Based Framework for COVID-19 Diagnosis.
Authors: AfsharShamsi, HamzehAsgharnezhad, Shirin ShamsiJokandan, AbbasKhosravi, Parham MKebria, DariusNahavandi, SaeidNahavandi, DiptiSrinivasan
Journal: IEEE transactions on neural networks and learning systems

The early and reliable detection of COVID-19 infected patients is essential to prevent and limit its outbreak. The PCR tests for COVID-19 detection are not available in many countries, and also, there are genuine concerns about their reliability and performance. Motivated by these shortcomings, this article proposes a deep uncertainty-aware transfer learning framework for COVID-19 detection using medical images. Four popular convolutional neural networks (CNNs), including VGG16, ResNet50, DenseNet121, and InceptionResNetV2, are first applied to extract deep features from chest X-ray and computed tomography (CT) images. Extracted features are then processed by different machine learning and statistical modeling techniques to identify COVID-19 cases. We also calculate and report the epistemic uncertainty of classification results to identify regions where the trained models are not confident about their decisions (out of distribution problem). Comprehensive simulation results for X-ray and CT image data sets indicate that linear support vector machine and neural network models achieve the best results as measured by accuracy, sensitivity, specificity, and area under the receiver operating characteristic (ROC) curve (AUC). Also, it is found that predictive uncertainty estimates are much higher for CT images compared to X-ray images.
Artificial intelligence and cardiac surgery during COVID-19 era.
Authors: Raveena KKhalsa, ArwaKhashkhusha, SaraZaidi, AmerHarky, MohamadBashir
Journal: Journal of cardiac surgery

The coronavirus disease 2019 (COVID-19) pandemic has increased the burden on hospital staff world-wide. Through the redistribution of scarce resources to these high-priority cases, the cardiac sector has fallen behind. In efforts to reduce transmission, reduction in direct patient-physician contact has led to a backlog of cardiac cases. However, this accumulation of postponed or cancelled nonurgent cardiac care seems to be resolvable with the assistance of technology. From telemedicine to artificial intelligence (AI), technology has transformed healthcare systems nationwide. Telemedicine enables patient monitoring from a distance, while AI unveils a whole new realm of possibilities in clinical practice, examples include: traditional systems replacement with more efficient and accurate processing machines; automation of clerical process; and triage assistance through risk predictions. These possibilities are driven by deep and machine learning. The two subsets of AI are explored and limitations regarding "big data" are discussed. The aims of this review are to explore AI: the advancements in methodology; current integration in cardiac surgery or other clinical scenarios; and potential future roles, which are innately nearing as the COVID-19 era urges alternative approaches for care.
Classification of COVID-19 by Compressed Chest CT Image through Deep Learning on a Large Patients Cohort.
Authors: ZiweiZhu, ZhangXingming, GuihuaTao, TingtingDan, JiaoLi, XijieChen, YangLi, ZhichaoZhou, XiangZhang, JinzhaoZhou, DongpeiChen, HanchunWen, HongminCai
Journal: Interdisciplinary sciences, computational life sciences

Corona Virus Disease (COVID-19) has spread globally quickly, and has resulted in a large number of causalities and medical resources insufficiency in many countries. Reverse-transcriptase polymerase chain reaction (RT-PCR) testing is adopted as biopsy tool for confirmation of virus infection. However, its accuracy is as low as 60-70%, which is inefficient to uncover the infected. In comparison, the chest CT has been considered as the prior choice in diagnosis and monitoring progress of COVID-19 infection. Although the COVID-19 diagnostic systems based on artificial intelligence have been developed for assisting doctors in diagnosis, the small sample size and the excessive time consumption limit their applications. To this end, this paper proposed a diagnosis prototype system for COVID-19 infection testing. The proposed deep learning model is trained and is tested on 2267 CT sequences from 1357 patients clinically confirmed with COVID-19 and 1235 CT sequences from non-infected people. The main highlights of the prototype system are: (1) no data augmentation is needed to accurately discriminate the COVID-19 from normal controls with the specificity of 0.92 and sensitivity of 0.93; (2) the raw DICOM image is not necessary in testing. Highly compressed image like Jpeg can be used to allow a quick diagnosis; and (3) it discriminates the virus infection within 6 seconds and thus allows an online test with light cost. We also applied our model on 48 asymptomatic patients diagnosed with COVID-19. We found that: (1) the positive rate of RT-PCR assay is 63.5% (687/1082). (2) 45.8% (22/48) of the RT-PCR assay is negative for asymptomatic patients, yet the accuracy of CT scans is 95.8%. The online detection system is available: http://212.64.70.65/covid .
Deep Learning Algorithm Trained with COVID-19 Pneumonia Also Identifies Immune Checkpoint Inhibitor Therapy-Related Pneumonitis.
Authors: Carlo AugustoMallio, AndreaNapolitano, GennaroCastiello, Francesco MariaGiordano, PasqualeD'Alessio, MarioIozzino, YipengSun, SilviaAngeletti, MarcoRussano, DanieleSantini, GiuseppeTonini, Bruno BeomonteZobel, BrunoVincenzi, Carlo CosimoQuattrocchi
Journal: Cancers

Coronavirus disease 2019 (COVID-19) pneumonia and immune checkpoint inhibitor (ICI) therapy-related pneumonitis share common features. The aim of this study was to determine on chest computed tomography (CT) images whether a deep convolutional neural network algorithm is able to solve the challenge of differential diagnosis between COVID-19 pneumonia and ICI therapy-related pneumonitis.
We enrolled three groups: a pneumonia-free group (
The algorithm showed low specificity in distinguishing COVID-19 from ICI therapy-related pneumonitis (sensitivity 97.1%, specificity 14.3%, area under the curve (AUC) = 0.62). ICI therapy-related pneumonitis was identified by the AI when compared to pneumonia-free controls (sensitivity = 85.7%, specificity 100%, AUC = 0.97).
The deep learning algorithm is not able to distinguish between COVID-19 pneumonia and ICI therapy-related pneumonitis. Awareness must be increased among clinicians about imaging similarities between COVID-19 and ICI therapy-related pneumonitis. ICI therapy-related pneumonitis can be applied as a challenge population for cross-validation to test the robustness of AI models used to analyze interstitial pneumonias of variable etiology.
Multiscale Attention Guided Network for COVID-19 Diagnosis Using Chest X-Ray Images.
Authors: JingxiongLi, YaqiWang, ShuaiWang, JunWang, JunLiu, QunJin, LinglingSun
Journal: IEEE journal of biomedical and health informatics

Coronavirus disease 2019 (COVID-19) is one of the most destructive pandemic after millennium, forcing the world to tackle a health crisis. Automated lung infections classification using chest X-ray (CXR) images could strengthen diagnostic capability when handling COVID-19. However, classifying COVID-19 from pneumonia cases using CXR image is a difficult task because of shared spatial characteristics, high feature variation and contrast diversity between cases. Moreover, massive data collection is impractical for a newly emerged disease, which limited the performance of data thirsty deep learning models. To address these challenges, Multiscale Attention Guided deep network with Soft Distance regularization (MAG-SD) is proposed to automatically classify COVID-19 from pneumonia CXR images. In MAG-SD, MA-Net is used to produce prediction vector and attention from multiscale feature maps. To improve the robustness of trained model and relieve the shortage of training data, attention guided augmentations along with a soft distance regularization are posed, which aims at generating meaningful augmentations and reduce noise. Our multiscale attention model achieves better classification performance on our pneumonia CXR image dataset. Plentiful experiments are proposed for MAG-SD which demonstrates its unique advantage in pneumonia classification over cutting-edge models. The code is available at https://github.com/JasonLeeGHub/MAG-SD.