pt-sk/ml_research_abs huggingface dataset:
Dual attention multiple instance learning with unsupervised complementary loss for COVID-19 screening.
Authors: PhilipChikontwe, MiguelLuna, MyeongkyunKang, Kyung SooHong, June HongAhn, Sang HyunPark
Journal: Medical image analysis

Chest computed tomography (CT) based analysis and diagnosis of the Coronavirus Disease 2019 (COVID-19) plays a key role in combating the outbreak of the pandemic that has rapidly spread worldwide. To date, the disease has infected more than 18 million people with over 690k deaths reported. Reverse transcription polymerase chain reaction (RT-PCR) is the current gold standard for clinical diagnosis but may produce false positives; thus, chest CT based diagnosis is considered more viable. However, accurate screening is challenging due to the difficulty in annotation of infected areas, curation of large datasets, and the slight discrepancies between COVID-19 and other viral pneumonia. In this study, we propose an attention-based end-to-end weakly supervised framework for the rapid diagnosis of COVID-19 and bacterial pneumonia based on multiple instance learning (MIL). We further incorporate unsupervised contrastive learning for improved accuracy with attention applied both in spatial and latent contexts, herein we propose Dual Attention Contrastive based MIL (DA-CMIL). DA-CMIL takes as input several patient CT slices (considered as bag of instances) and outputs a single label. Attention based pooling is applied to implicitly select key slices in the latent space, whereas spatial attention learns slice spatial context for interpretable diagnosis. A contrastive loss is applied at the instance level to encode similarity of features from the same patient against representative pooled patient features. Empirical results show that our algorithm achieves an overall accuracy of 98.6% and an AUC of 98.4%. Moreover, ablation studies show the benefit of contrastive learning with MIL.
Deep Learning on Chest X-ray Images to Detect and Evaluate Pneumonia Cases at the Era of COVID-19.
Authors: KarimHammoudi, HalimBenhabiles, MahmoudMelkemi, FadiDornaika, IgnacioArganda-Carreras, DominiqueCollard, ArnaudScherpereel
Journal: Journal of medical systems

Coronavirus disease 2019 (COVID-19) is an infectious disease with first symptoms similar to the flu. COVID-19 appeared first in China and very quickly spreads to the rest of the world, causing then the 2019-20 coronavirus pandemic. In many cases, this disease causes pneumonia. Since pulmonary infections can be observed through radiography images, this paper investigates deep learning methods for automatically analyzing query chest X-ray images with the hope to bring precision tools to health professionals towards screening the COVID-19 and diagnosing confirmed patients. In this context, training datasets, deep learning architectures and analysis strategies have been experimented from publicly open sets of chest X-ray images. Tailored deep learning models are proposed to detect pneumonia infection cases, notably viral cases. It is assumed that viral pneumonia cases detected during an epidemic COVID-19 context have a high probability to presume COVID-19 infections. Moreover, easy-to-apply health indicators are proposed for estimating infection status and predicting patient status from the detected pneumonia cases. Experimental results show possibilities of training deep learning models over publicly open sets of chest X-ray images towards screening viral pneumonia. Chest X-ray test images of COVID-19 infected patients are successfully diagnosed through detection models retained for their performances. The efficiency of proposed health indicators is highlighted through simulated scenarios of patients presenting infections and health problems by combining real and synthetic health data.
COVID-19 pneumonia on chest X-rays: Performance of a deep learning-based computer-aided detection system.
Authors: Eui JinHwang, Ki BeomKim, Jin YoungKim, Jae-KwangLim, Ju GangNam, HyewonChoi, HyungjinKim, Soon HoYoon, Jin MoGoo, Chang MinPark
Journal: PloS one

Chest X-rays (CXRs) can help triage for Coronavirus disease (COVID-19) patients in resource-constrained environments, and a computer-aided detection system (CAD) that can identify pneumonia on CXR may help the triage of patients in those environment where expert radiologists are not available. However, the performance of existing CAD for identifying COVID-19 and associated pneumonia on CXRs has been scarcely investigated. In this study, CXRs of patients with and without COVID-19 confirmed by reverse transcriptase polymerase chain reaction (RT-PCR) were retrospectively collected from four and one institution, respectively, and a commercialized, regulatory-approved CAD that can identify various abnormalities including pneumonia was used to analyze each CXR. Performance of the CAD was evaluated using area under the receiver operating characteristic curves (AUCs), with reference standards of the RT-PCR results and the presence of findings of pneumonia on chest CTs obtained within 24 hours from the CXR. For comparison, 5 thoracic radiologists and 5 non-radiologist physicians independently interpreted the CXRs. Afterward, they re-interpreted the CXRs with corresponding CAD results. The performance of CAD (AUCs, 0.714 and 0.790 against RT-PCR and chest CT, respectively hereinafter) were similar with those of thoracic radiologists (AUCs, 0.701 and 0.784), and higher than those of non-radiologist physicians (AUCs, 0.584 and 0.650). Non-radiologist physicians showed significantly improved performance when assisted with the CAD (AUCs, 0.584 to 0.664 and 0.650 to 0.738). In addition, inter-reader agreement among physicians was also improved in the CAD-assisted interpretation (Fleiss' kappa coefficient, 0.209 to 0.322). In conclusion, radiologist-level performance of the CAD in identifying COVID-19 and associated pneumonia on CXR and enhanced performance of non-radiologist physicians with the CAD assistance suggest that the CAD can support physicians in interpreting CXRs and helping image-based triage of COVID-19 patients in resource-constrained environment.
Learning from imbalanced COVID-19 chest X-ray (CXR) medical imaging data.
Authors: Jonathan HChan, ChenqiLi
Journal: Methods (San Diego, Calif.)

The trendy task of digital medical image analysis has been continually evolving. It has been an area of prominent and growing importance from both research and deployment perspectives. Nonetheless, it is necessary to realize that the use of algorithms, methodology, as well as the source of medical image data, must be strictly scrutinized. As the COVID-19 pandemic has been gripping much of the world recently, there has been much efforts gone into developing affordable testing for the masses, and it has been shown that the established and widely available chest X-rays (CXR) images may be used as a screening criteria for assistive diagnosis purpose. Thanks to the dedicated work by various individuals and organizations, publicly available CXR of COVID-19 subjects are available for analytic usage. We have also provided a publicly available CXR dataset on the Kaggle platform. As a case study, this paper presents a systematic approach to learn from a typically imbalanced set of CXR images, which consists of a limited number of publicly available COVID-19 images. Our results show that we are able to outperform the top finishers in a related Kaggle multi-class CXR challenge. The proposed methodology should be able to help guide medical personnel in obtaining a robust diagnosis model to discern COVID-19 from other conditions confidently.
DUDA-Net: a double U-shaped dilated attention network for automatic infection area segmentation in COVID-19 lung CT images.
Authors: FengXie, ZhengHuang, ZhengjinShi, TianyuWang, GuoliSong, BolunWang, ZihongLiu
Journal: International journal of computer assisted radiology and surgery

The global health crisis caused by coronavirus disease 2019 (COVID-19) is a common threat facing all humankind. In the process of diagnosing COVID-19 and treating patients, automatic COVID-19 lesion segmentation from computed tomography images helps doctors and patients intuitively understand lung infection. To effectively quantify lung infections, a convolutional neural network for automatic lung infection segmentation based on deep learning is proposed.
This new type of COVID-19 lesion segmentation network is based on a U-Net backbone. First, a coarse segmentation network is constructed to extract the lung areas. Second, in the encoding and decoding process of the fine segmentation network, a new soft attention mechanism, namely the dilated convolutional attention (DCA) mechanism, is introduced to enable the network to focus on better quantitative information to strengthen the network's segmentation ability in the subtle areas of the lesions.
The experimental results show that the average Dice similarity coefficient (DSC), sensitivity (SEN), specificity (SPE) and area under the curve of DUDA-Net are 87.06%, 90.85%, 99.59% and 0.965, respectively. In addition, the introduction of a cascade U-shaped network scheme and DCA mechanism can improve the DSC by 24.46% and 14.33%, respectively.
The proposed DUDA-Net approach can automatically segment COVID-19 lesions with excellent performance, which indicates that the proposed method is of great clinical significance. In addition, the introduction of a coarse segmentation network and DCA mechanism can improve the COVID-19 segmentation performance.
Covid-19 Imaging Tools: How Big Data is Big?
Authors: K CSantosh, SourodipGhosh
Journal: Journal of medical systems

In this paper, considering year 2020 and Covid-19, we analyze medical imaging tools and their performance scores in accordance with the dataset size and their complexity. For this, we mainly consider AI-driven tools that employ two different types of image data, namely chest Computed Tomography (CT) and X-ray. We elaborate on their strengths and weaknesses by taking the following important factors into account: i) dataset size; ii) model fitting criteria (over-fitting and under-fitting); iii) transfer learning in the deep learning era; and iv) data augmentation. Medical imaging tools do not explicitly analyze model fitting. Also, using transfer learning, with fewer data, one could possibly build Covid-19 deep learning model but they are limited to education and training. We observe that, in both image modalities, neither the dataset size nor does data augmentation work well for Covid-19 screening purposes because a large dataset does not guarantee all possible Covid-19 manifestations and data augmentation does not create new Covid-19 cases.
Proof of concept for real-time detection of SARS CoV-2 infection with an electronic nose.
Authors: KobiSnitz, MichalAndelman-Gur, LironPinchover, ReutWeissgross, AharonWeissbrod, EvaMishor, RoniZoller, VeraLinetsky, AbebeMedhanie, SagitShushan, EliJaffe, NoamSobel
Journal: PloS one

Rapid diagnosis is key to curtailing the Covid-19 pandemic. One path to such rapid diagnosis may rely on identifying volatile organic compounds (VOCs) emitted by the infected body, or in other words, identifying the smell of the infection. Consistent with this rationale, dogs can use their nose to identify Covid-19 patients. Given the scale of the pandemic, however, animal deployment is a challenging solution. In contrast, electronic noses (eNoses) are machines aimed at mimicking animal olfaction, and these can be deployed at scale. To test the hypothesis that SARS CoV-2 infection is associated with a body-odor detectable by an eNose, we placed a generic eNose in-line at a drive-through testing station. We applied a deep learning classifier to the eNose measurements, and achieved real-time detection of SARS CoV-2 infection at a level significantly better than chance, for both symptomatic and non-symptomatic participants. This proof of concept with a generic eNose implies that an optimized eNose may allow effective real-time diagnosis, which would provide for extensive relief in the Covid-19 pandemic.
COV-SNET: A deep learning model for X-ray-based COVID-19 classification.
Authors: RobertHertel, RachidBenlamri
Journal: Informatics in medicine unlocked

The AI research community has recently been intensely focused on diagnosing COVID-19 by applying deep learning technology to the X-ray scans taken of COVID-19 patients. Differentiating COVID-19 from other pneumonia-inducing illnesses is a highly challenging task as it shares many of the same imaging characteristics as other pulmonary diseases. This is especially true given the small number of COVID-19 X-rays that are publicly available. Deep learning experts commonly use transfer learning to offset the small number of images typically available in medical imaging tasks. Our COV-SNET model is a deep neural network that was pretrained on over one hundred thousand X-ray images. In this paper, we designed two COV-SNET models with the purpose of diagnosing COVID-19. The experimental results demonstrate the robustness of our deep learning models, ultimately achieving sensitivities of 95% for our three-class and two-class models. We also discuss the strengths and weaknesses of such an approach, focusing mainly on the limitations of public X-ray datasets on current COVID-19 deep learning models. Finally, we conclude with possible future directions for this research.
Early prediction of severity in coronavirus disease (COVID-19) using quantitative CT imaging.
Authors: KunweiLi, XueguoLiu, RowenaYip, David FYankelevitz, Claudia IHenschke, YayuanGeng, YijieFang, WenjuanLi, CunxuePan, XiaojunChen, PeixinQin, YinghuaZhong, KunfengLiu, ShaolinLi
Journal: Clinical imaging

To evaluate whether the extent of COVID-19 pneumonia on CT scans using quantitative CT imaging obtained early in the illness can predict its future severity.
We conducted a retrospective single-center study on confirmed COVID-19 patients between January 18, 2020 and March 5, 2020. A quantitative AI algorithm was used to evaluate each patient's CT scan to determine the proportion of the lungs with pneumonia (VR) and the rate of change (RAR) in VR from scan to scan. Patients were classified as being in the severe or non-severe group based on their final symptoms. Penalized B-splines regression modeling was used to examine the relationship between mean VR and days from onset of symptoms in the two groups, with 95% and 99% confidence intervals.
Median VR max was 18.6% (IQR 9.1-32.7%) in 21 patients in the severe group, significantly higher (P < 0.0001) than in the 53 patients in non-severe group (1.8% (IQR 0.4-5.7%)). RAR was increasing with a median RAR of 2.1% (IQR 0.4-5.5%) in severe and 0.4% (IQR 0.1-0.9%) in non-severe group, which was significantly different (P < 0.0001). Penalized B-spline analyses showed positive relationships between VR and days from onset of symptom. The 95% confidence limits of the predicted means for the two groups diverged 5 days after the onset of initial symptoms with a threshold of 11.9%.
Five days after the initial onset of symptoms, CT could predict the patients who later developed severe symptoms with 95% confidence.
Radiologists versus Deep Convolutional Neural Networks: A Comparative Study for Diagnosing COVID-19.
Authors: AbdulkaderHelwan, Mohammad Khaleel SallamMa'aitah, HaniHamdan, Dilber UzunOzsahin, OzumTuncyurek
Journal: Computational and mathematical methods in medicine

The reverse transcriptase polymerase chain reaction (RT-PCR) is still the routinely used test for the diagnosis of SARS-CoV-2 (COVID-19). However, according to several reports, RT-PCR showed a low sensitivity and multiple tests may be required to rule out false negative results. Recently, chest computed tomography (CT) has been an efficient tool to diagnose COVID-19 as it is directly affecting the lungs. In this paper, we investigate the application of pre-trained models in diagnosing patients who are positive for COVID-19 and differentiating it from normal patients, who tested negative for coronavirus. The study aims to compare the generalization capabilities of deep learning models with two thoracic radiologists in diagnosing COVID-19 chest CT images. A dataset of 3000 images was obtained from the Near East Hospital, Cyprus, and used to train and to test the three employed pre-trained models. In a test set of 250 images used to evaluate the deep neural networks and the radiologists, it was found that deep networks (ResNet-18, ResNet-50, and DenseNet-201) can outperform the radiologists in terms of higher accuracy (97.8%), sensitivity (98.1%), specificity (97.3%), precision (98.4%), and F1-score (198.25%), in classifying COVID-19 images.
Checklist for responsible deep learning modeling of medical images based on COVID-19 detection studies.
Authors: WeronikaHryniewska, PrzemysławBombiński, PatrykSzatkowski, PaulinaTomaszewska, ArturPrzelaskowski, PrzemysławBiecek
Journal: Pattern recognition

The sudden outbreak and uncontrolled spread of COVID-19 disease is one of the most important global problems today. In a short period of time, it has led to the development of many deep neural network models for COVID-19 detection with modules for explainability. In this work, we carry out a systematic analysis of various aspects of proposed models. Our analysis revealed numerous mistakes made at different stages of data acquisition, model development, and explanation construction. In this work, we overview the approaches proposed in the surveyed Machine Learning articles and indicate typical errors emerging from the lack of deep understanding of the radiography domain. We present the perspective of both: experts in the field - radiologists and deep learning engineers dealing with model explanations. The final result is a proposed checklist with the minimum conditions to be met by a reliable COVID-19 diagnostic model.
COVID-19 classification of X-ray images using deep neural networks.
Authors: DaphnaKeidar, DanielYaron, ElishaGoldstein, YairShachar, AyeletBlass, LeonidCharbinsky, IsraelAharony, LizaLifshitz, DimitriLumelsky, ZivNeeman, MattiMizrachi, MajdHajouj, NethanelEizenbach, EyalSela, Chedva SWeiss, PhilipLevin, OferBenjaminov, Gil NBachar, ShlomitTamir, YaelRapson, DrorSuhami, EliAtar, Amiel ADror, Naama RBogot, AhuvaGrubstein, NogahShabshin, Yishai MElyada, Yonina CEldar
Journal: European radiology

In the midst of the coronavirus disease 2019 (COVID-19) outbreak, chest X-ray (CXR) imaging is playing an important role in diagnosis and monitoring of patients with COVID-19. We propose a deep learning model for detection of COVID-19 from CXRs, as well as a tool for retrieving similar patients according to the model's results on their CXRs. For training and evaluating our model, we collected CXRs from inpatients hospitalized in four different hospitals.
In this retrospective study, 1384 frontal CXRs, of COVID-19 confirmed patients imaged between March and August 2020, and 1024 matching CXRs of non-COVID patients imaged before the pandemic, were collected and used to build a deep learning classifier for detecting patients positive for COVID-19. The classifier consists of an ensemble of pre-trained deep neural networks (DNNS), specifically, ReNet34, ReNet50¸ ReNet152, and vgg16, and is enhanced by data augmentation and lung segmentation. We further implemented a nearest-neighbors algorithm that uses DNN-based image embeddings to retrieve the images most similar to a given image.
Our model achieved accuracy of 90.3%, (95% CI: 86.3-93.7%) specificity of 90% (95% CI: 84.3-94%), and sensitivity of 90.5% (95% CI: 85-94%) on a test dataset comprising 15% (350/2326) of the original images. The AUC of the ROC curve is 0.96 (95% CI: 0.93-0.97).
We provide deep learning models, trained and evaluated on CXRs that can assist medical efforts and reduce medical staff workload in handling COVID-19.
• A machine learning model was able to detect chest X-ray (CXR) images of patients tested positive for COVID-19 with accuracy and detection rate above 90%. • A tool was created for finding existing CXR images with imaging characteristics most similar to a given CXR, according to the model's image embeddings.
Deep learning for predicting COVID-19 malignant progression.
Authors: CongFang, SongBai, QianlanChen, YuZhou, LimingXia, LixinQin, ShiGong, XudongXie, ChunhuaZhou, DandanTu, ChangzhengZhang, XiaowuLiu, WeiweiChen, XiangBai, Philip H STorr
Journal: Medical image analysis

As COVID-19 is highly infectious, many patients can simultaneously flood into hospitals for diagnosis and treatment, which has greatly challenged public medical systems. Treatment priority is often determined by the symptom severity based on first assessment. However, clinical observation suggests that some patients with mild symptoms may quickly deteriorate. Hence, it is crucial to identify patient early deterioration to optimize treatment strategy. To this end, we develop an early-warning system with deep learning techniques to predict COVID-19 malignant progression. Our method leverages CT scans and the clinical data of outpatients and achieves an AUC of 0.920 in the single-center study. We also propose a domain adaptation approach to improve the generalization of our model and achieve an average AUC of 0.874 in the multicenter study. Moreover, our model automatically identifies crucial indicators that contribute to the malignant progression, including Troponin, Brain natriuretic peptide, White cell count, Aspartate aminotransferase, Creatinine, and Hypersensitive C-reactive protein.
Toward understanding COVID-19 pneumonia: a deep-learning-based approach for severity analysis and monitoring the disease.
Authors: MohammadrezaZandehshahvar, Marlyvan Assen, HosseinMaleki, YasharKiarashi, Carlo NDe Cecco, AliAdibi
Journal: Scientific reports

We report a new approach using artificial intelligence (AI) to study and classify the severity of COVID-19 using 1208 chest X-rays (CXRs) of 396 COVID-19 patients obtained through the course of the disease at Emory Healthcare affiliated hospitals (Atlanta, GA, USA). Using a two-stage transfer learning technique to train a convolutional neural network (CNN), we show that the algorithm is able to classify four classes of disease severity (normal, mild, moderate, and severe) with the average Area Under the Curve (AUC) of 0.93. In addition, we show that the outputs of different layers of the CNN under dominant filters provide valuable insight about the subtle patterns in the CXRs, which can improve the accuracy in the reading of CXRs by a radiologist. Finally, we show that our approach can be used for studying the disease progression in a single patient and its influencing factors. The results suggest that our technique can form the foundation of a more concrete clinical model to predict the evolution of COVID-19 severity and the efficacy of different treatments for each patient through using CXRs and clinical data in the early stages of the disease. This use of AI to assess the severity and possibly predicting the future stages of the disease early on, will be essential in dealing with the upcoming waves of COVID-19 and optimizing resource allocation and treatment.