pt-sk/ml_research_abs huggingface dataset:
COVID-19 disease identification network based on weakly supervised feature selection.
Authors: JingyaoLiu, QingheFeng, YuMiao, WeiHe, WeiliShi, ZhengangJiang
Journal: Mathematical biosciences and engineering : MBE

The coronavirus disease 2019 (COVID-19) outbreak has resulted in countless infections and deaths worldwide, posing increasing challenges for the health care system. The use of artificial intelligence to assist in diagnosis not only had a high accuracy rate but also saved time and effort in the sudden outbreak phase with the lack of doctors and medical equipment. This study aimed to propose a weakly supervised COVID-19 classification network (W-COVNet). This network was divided into three main modules: weakly supervised feature selection module (W-FS), deep learning bilinear feature fusion module (DBFF) and Grad-CAM++ based network visualization module (Grad-Ⅴ). The first module, W-FS, mainly removed redundant background features from computed tomography (CT) images, performed feature selection and retained core feature regions. The second module, DBFF, mainly used two symmetric networks to extract different features and thus obtain rich complementary features. The third module, Grad-Ⅴ, allowed the visualization of lesions in unlabeled images. A fivefold cross-validation experiment showed an average classification accuracy of 85.3%, and a comparison with seven advanced classification models showed that our proposed network had a better performance.
An efficient, lightweight MobileNetV2-based fine-tuned model for COVID-19 detection using chest X-ray images.
Authors: ShubashiniVelu
Journal: Mathematical biosciences and engineering : MBE

In recent years, deep learning's identification of cancer, lung disease and heart disease, among others, has contributed to its rising popularity. Deep learning has also contributed to the examination of COVID-19, which is a subject that is currently the focus of considerable scientific debate. COVID-19 detection based on chest X-ray (CXR) images primarily depends on convolutional neural network transfer learning techniques. Moreover, the majority of these methods are evaluated by using CXR data from a single source, which makes them prohibitively expensive. On a variety of datasets, current methods for COVID-19 detection may not perform as well. Moreover, most current approaches focus on COVID-19 detection. This study introduces a rapid and lightweight MobileNetV2-based model for accurate recognition of COVID-19 based on CXR images; this is done by using machine vision algorithms that focused largely on robust and potent feature-learning capabilities. The proposed model is assessed by using a dataset obtained from various sources. In addition to COVID-19, the dataset includes bacterial and viral pneumonia. This model is capable of identifying COVID-19, as well as other lung disorders, including bacterial and viral pneumonia, among others. Experiments with each model were thoroughly analyzed. According to the findings of this investigation, MobileNetv2, with its 92% and 93% training validity and 88% precision, was the most applicable and reliable model for this diagnosis. As a result, one may infer that this study has practical value in terms of giving a reliable reference to the radiologist and theoretical significance in terms of establishing strategies for developing robust features with great presentation ability.
Data augmentation based semi-supervised method to improve COVID-19 CT classification.
Authors: XiangtaoChen, YutingBai, PengWang, JiaweiLuo
Journal: Mathematical biosciences and engineering : MBE

The Coronavirus (COVID-19) outbreak of December 2019 has become a serious threat to people around the world, creating a health crisis that infected millions of lives, as well as destroying the global economy. Early detection and diagnosis are essential to prevent further transmission. The detection of COVID-19 computed tomography images is one of the important approaches to rapid diagnosis. Many different branches of deep learning methods have played an important role in this area, including transfer learning, contrastive learning, ensemble strategy, etc. However, these works require a large number of samples of expensive manual labels, so in order to save costs, scholars adopted semi-supervised learning that applies only a few labels to classify COVID-19 CT images. Nevertheless, the existing semi-supervised methods focus primarily on class imbalance and pseudo-label filtering rather than on pseudo-label generation. Accordingly, in this paper, we organized a semi-supervised classification framework based on data augmentation to classify the CT images of COVID-19. We revised the classic teacher-student framework and introduced the popular data augmentation method Mixup, which widened the distribution of high confidence to improve the accuracy of selected pseudo-labels and ultimately obtain a model with better performance. For the COVID-CT dataset, our method makes precision, F1 score, accuracy and specificity 21.04%, 12.95%, 17.13% and 38.29% higher than average values for other methods respectively, For the SARS-COV-2 dataset, these increases were 8.40%, 7.59%, 9.35% and 12.80% respectively. For the Harvard Dataverse dataset, growth was 17.64%, 18.89%, 19.81% and 20.20% respectively. The codes are available at https://github.com/YutingBai99/COVID-19-SSL.
A deep learning-based application for COVID-19 diagnosis on CT: The Imaging COVID-19 AI initiative.
Authors: LaurensTopff, JoséSánchez-García, RafaelLópez-González, Ana JiménezPastor, Jacob JVisser, MerelHuisman, JulienGuiot, Regina G HBeets-Tan, AngelAlberich-Bayarri, AlmudenaFuster-Matanzo, Erik RRanschaert, NoneNone
Journal: PloS one

Recently, artificial intelligence (AI)-based applications for chest imaging have emerged as potential tools to assist clinicians in the diagnosis and management of patients with coronavirus disease 2019 (COVID-19).
To develop a deep learning-based clinical decision support system for automatic diagnosis of COVID-19 on chest CT scans. Secondarily, to develop a complementary segmentation tool to assess the extent of lung involvement and measure disease severity.
The Imaging COVID-19 AI initiative was formed to conduct a retrospective multicentre cohort study including 20 institutions from seven different European countries. Patients with suspected or known COVID-19 who underwent a chest CT were included. The dataset was split on the institution-level to allow external evaluation. Data annotation was performed by 34 radiologists/radiology residents and included quality control measures. A multi-class classification model was created using a custom 3D convolutional neural network. For the segmentation task, a UNET-like architecture with a backbone Residual Network (ResNet-34) was selected.
A total of 2,802 CT scans were included (2,667 unique patients, mean [standard deviation] age = 64.6 [16.2] years, male/female ratio 1.3:1). The distribution of classes (COVID-19/Other type of pulmonary infection/No imaging signs of infection) was 1,490 (53.2%), 402 (14.3%), and 910 (32.5%), respectively. On the external test dataset, the diagnostic multiclassification model yielded high micro-average and macro-average AUC values (0.93 and 0.91, respectively). The model provided the likelihood of COVID-19 vs other cases with a sensitivity of 87% and a specificity of 94%. The segmentation performance was moderate with Dice similarity coefficient (DSC) of 0.59. An imaging analysis pipeline was developed that returned a quantitative report to the user.
We developed a deep learning-based clinical decision support system that could become an efficient concurrent reading tool to assist clinicians, utilising a newly created European dataset including more than 2,800 CT scans.
Contemporary Concise Review 2022: Interstitial lung disease.
Authors: David J FSmith, R GisliJenkins
Journal: Respirology (Carlton, Vic.)

Novel genetic associations for idiopathic pulmonary fibrosis (IPF) risk have been identified. Common genetic variants associated with IPF are also associated with chronic hypersensitivity pneumonitis. The characterization of underlying mechanisms, such as pathways involved in myofibroblast differentiation, may reveal targets for future treatments. Newly identified circulating biomarkers are associated with disease progression and mortality. Deep learning and machine learning may increase accuracy in the interpretation of CT scans. Novel treatments have shown benefit in phase 2 clinical trials. Hospitalization with COVID-19 is associated with residual lung abnormalities in a substantial number of patients. Inequalities exist in delivering and accessing interstitial lung disease specialist care.
Progressive attention integration-based multi-scale efficient network for medical imaging analysis with application to COVID-19 diagnosis.
Authors: TingyiXie, ZidongWang, HanLi, PeishuWu, HuixiangHuang, HongyiZhang, Fuad EAlsaadi, NianyinZeng
Journal: Computers in biology and medicine

In this paper, a novel deep learning-based medical imaging analysis framework is developed, which aims to deal with the insufficient feature learning caused by the imperfect property of imaging data. Named as multi-scale efficient network (MEN), the proposed method integrates different attention mechanisms to realize sufficient extraction of both detailed features and semantic information in a progressive learning manner. In particular, a fused-attention block is designed to extract fine-grained details from the input, where the squeeze-excitation (SE) attention mechanism is applied to make the model focus on potential lesion areas. A multi-scale low information loss (MSLIL)-attention block is proposed to compensate for potential global information loss and enhance the semantic correlations among features, where the efficient channel attention (ECA) mechanism is adopted. The proposed MEN is comprehensively evaluated on two COVID-19 diagnostic tasks, and the results show that as compared with some other advanced deep learning models, the proposed method is competitive in accurate COVID-19 recognition, which yields the best accuracy of 98.68% and 98.85%, respectively, and exhibits satisfactory generalization ability as well.
A novel CT image de-noising and fusion based deep learning network to screen for disease (COVID-19).
Authors: Sajid UllahKhan, ImdadUllah, NajeebUllah, SajidShah, Mohammed ElAffendi, BumshikLee
Journal: Scientific reports

A COVID-19, caused by SARS-CoV-2, has been declared a global pandemic by WHO. It first appeared in China at the end of 2019 and quickly spread throughout the world. During the third layer, it became more critical. COVID-19 spread is extremely difficult to control, and a huge number of suspected cases must be screened for a cure as soon as possible. COVID-19 laboratory testing takes time and can result in significant false negatives. To combat COVID-19, reliable, accurate and fast methods are urgently needed. The commonly used Reverse Transcription Polymerase Chain Reaction has a low sensitivity of approximately 60% to 70%, and sometimes even produces negative results. Computer Tomography (CT) has been observed to be a subtle approach to detecting COVID-19, and it may be the best screening method. The scanned image's quality, which is impacted by motion-induced Poisson or Impulse noise, is vital. In order to improve the quality of the acquired image for post segmentation, a novel Impulse and Poisson noise reduction method employing boundary division max/min intensities elimination along with an adaptive window size mechanism is proposed. In the second phase, a number of CNN techniques are explored for detecting COVID-19 from CT images and an Assessment Fusion Based model is proposed to predict the result. The AFM combines the results for cutting-edge CNN architectures and generates a final prediction based on choices. The empirical results demonstrate that our proposed method performs extensively and is extremely useful in actual diagnostic situations.
Quo vadis Radiomics? Bibliometric analysis of 10-year Radiomics journey.
Authors: StefaniaVolpe, FedericoMastroleo, MarcoKrengli, Barbara AlicjaJereczek-Fossa
Journal: European radiology

Radiomics is the high-throughput extraction of mineable and-possibly-reproducible quantitative imaging features from medical imaging. The aim of this work is to perform an unbiased bibliometric analysis on Radiomics 10 years after the first work became available, to highlight its status, pitfalls, and growing interest.
Scopus database was used to investigate all the available English manuscripts about Radiomics. R Bibliometrix package was used for data analysis: a cumulative analysis of document categories, authors affiliations, country scientific collaborations, institution collaboration networks, keyword analysis, comprehensive of co-occurrence network, thematic map analysis, and 2021 sub-analysis of trend topics was performed.
A total of 5623 articles and 16,833 authors from 908 different sources have been identified. The first available document was published in March 2012, while the most recent included was released on the 31st of December 2021. China and USA were the most productive countries. Co-occurrence network analysis identified five words clusters based on top 50 authors' keywords: Radiomics, computed tomography, radiogenomics, deep learning, tomography. Trend topics analysis for 2021 showed an increased interest in artificial intelligence (n = 286), nomogram (n = 166), hepatocellular carcinoma (n = 125), COVID-19 (n = 63), and X-ray computed (n = 60).
Our work demonstrates the importance of bibliometrics in aggregating information that otherwise would not be available in a granular analysis, detecting unknown patterns in Radiomics publications, while highlighting potential developments to ensure knowledge dissemination in the field and its future real-life applications in the clinical practice.
This work aims to shed light on the state of the art in radiomics, which offers numerous tangible and intangible benefits, and to encourage its integration in the contemporary clinical practice for more precise imaging analysis.
• ML-based bibliometric analysis is fundamental to detect unknown pattern of data in Radiomics publications. • A raising interest in the field, the most relevant collaborations, keywords co-occurrence network, and trending topics have been investigated. • Some pitfalls still exist, including the scarce standardization and the relative lack of homogeneity across studies.
Analysis of Covid-19 CT chest image classification using Dl4jMlp classifier and Multilayer Perceptron in WEKA Environment.
Authors: NoneSreejith S, NoneJ Ajayan, NoneN V Uma Reddy, BabuDevasenapati S, ShashankRebelli
Journal: Current medical imaging

In recent years, various deep learning algorithms have exhibited remarkable performance in various data-rich applications, like health care, medical imaging, as well as in computer vision. Covid-19, which is a rapidly spreading virus, has affected people of all ages both socially and economically. Early detection of this virus is therefore important in order to prevent its further spread.
Covid-19 crisis has also galvanized researchers to adopt various machine learning as well as deep learning techniques in order to combat the pandemic. Lung images can be used in the diagnosis of Covid-19.
In this paper, we have analysed the Covid-19 chest CT image classification efficiency using multilayer perceptron with different imaging filters, like edge histogram filter, colour histogram equalization filter, color-layout filter, and Garbo filter in the WEKA environment.
The performance of CT image classification has also been compared comprehensively with the deep learning classifier Dl4jMlp. It was observed that the multilayer perceptron with edge histogram filter outperformed other classifiers compared in this paper with 89.6% of correctly classified instances.
CCS-GAN: COVID-19 CT Scan Generation and Classification with Very Few Positive Training Images.
Authors: SumeetMenon, JayalakshmiMangalagiri, JoshGalita, MichaelMorris, BabakSaboury, YaacovYesha, YelenaYesha, PhuongNguyen, AryyaGangopadhyay, DavidChapman
Journal: Journal of digital imaging

We present a novel algorithm that is able to generate deep synthetic COVID-19 pneumonia CT scan slices using a very small sample of positive training images in tandem with a larger number of normal images. This generative algorithm produces images of sufficient accuracy to enable a DNN classifier to achieve high classification accuracy using as few as 10 positive training slices (from 10 positive cases), which to the best of our knowledge is one order of magnitude fewer than the next closest published work at the time of writing. Deep learning with extremely small positive training volumes is a very difficult problem and has been an important topic during the COVID-19 pandemic, because for quite some time it was difficult to obtain large volumes of COVID-19-positive images for training. Algorithms that can learn to screen for diseases using few examples are an important area of research. Furthermore, algorithms to produce deep synthetic images with smaller data volumes have the added benefit of reducing the barriers of data sharing between healthcare institutions. We present the cycle-consistent segmentation-generative adversarial network (CCS-GAN). CCS-GAN combines style transfer with pulmonary segmentation and relevant transfer learning from negative images in order to create a larger volume of synthetic positive images for the purposes of improving diagnostic classification performance. The performance of a VGG-19 classifier plus CCS-GAN was trained using a small sample of positive image slices ranging from at most 50 down to as few as 10 COVID-19-positive CT scan images. CCS-GAN achieves high accuracy with few positive images and thereby greatly reduces the barrier of acquiring large training volumes in order to train a diagnostic classifier for COVID-19.
A lightweight CORONA-NET for COVID-19 detection in X-ray images.
Authors: Muhammad UsmanHadi, RizwanQureshi, AyeshaAhmed, NadeemIftikhar
Journal: Expert systems with applications

Since December 2019, COVID-19 has posed the most serious threat to living beings. With the advancement of vaccination programs around the globe, the need to quickly diagnose COVID-19 in general with little logistics is fore important. As a consequence, the fastest diagnostic option to stop COVID-19 from spreading, especially among senior patients, should be the development of an automated detection system. This study aims to provide a lightweight deep learning method that incorporates a convolutional neural network (CNN), discrete wavelet transform (DWT), and a long short-term memory (LSTM), called CORONA-NET for diagnosing COVID-19 from chest X-ray images. In this system, deep feature extraction is performed by CNN, the feature vector is reduced yet strengthened by DWT, and the extracted feature is detected by LSTM for prediction. The dataset included 3000 X-rays, 1000 of which were COVID-19 obtained locally. Within minutes of the test, the proposed test platform's prototype can accurately detect COVID-19 patients. The proposed method achieves state-of-the-art performance in comparison with the existing deep learning methods. We hope that the suggested method will hasten clinical diagnosis and may be used for patients in remote areas where clinical labs are not easily accessible due to a lack of resources, location, or other factors.
A multicenter evaluation of a deep learning software (LungQuant) for lung parenchyma characterization in COVID-19 pneumonia.
Authors: CamillaScapicchio, AndreaChincarini, ElenaBallante, LucaBerta, EleonoraBicci, ChandraBortolotto, FrancescaBrero, Raffaella FiammaCabini, GiuseppeCristofalo, Salvatore ClaudioFanni, Maria EvelinaFantacci, SilviaFigini, MassimoGalia, PietroGemma, EmanueleGrassedonio, AlessandroLascialfari, CristinaLenardi, AliceLionetti, FrancescaLizzi, MaurizioMarrale, MassimoMidiri, CosimoNardi, PiernicolaOliva, NoemiPerillo, IanPostuma, LorenzoPreda, VieriRastrelli, FrancescoRizzetto, NicolaSpina, CinziaTalamonti, AlbertoTorresin, AngeloVanzulli, FedericaVolpi, EmanueleNeri, AlessandraRetico
Journal: European radiology experimental

The role of computed tomography (CT) in the diagnosis and characterization of coronavirus disease 2019 (COVID-19) pneumonia has been widely recognized. We evaluated the performance of a software for quantitative analysis of chest CT, the LungQuant system, by comparing its results with independent visual evaluations by a group of 14 clinical experts. The aim of this work is to evaluate the ability of the automated tool to extract quantitative information from lung CT, relevant for the design of a diagnosis support model.
LungQuant segments both the lungs and lesions associated with COVID-19 pneumonia (ground-glass opacities and consolidations) and computes derived quantities corresponding to qualitative characteristics used to clinically assess COVID-19 lesions. The comparison was carried out on 120 publicly available CT scans of patients affected by COVID-19 pneumonia. Scans were scored for four qualitative metrics: percentage of lung involvement, type of lesion, and two disease distribution scores. We evaluated the agreement between the LungQuant output and the visual assessments through receiver operating characteristics area under the curve (AUC) analysis and by fitting a nonlinear regression model.
Despite the rather large heterogeneity in the qualitative labels assigned by the clinical experts for each metric, we found good agreement on the metrics compared to the LungQuant output. The AUC values obtained for the four qualitative metrics were 0.98, 0.85, 0.90, and 0.81.
Visual clinical evaluation could be complemented and supported by computer-aided quantification, whose values match the average evaluation of several independent clinical experts.
We conducted a multicenter evaluation of the deep learning-based LungQuant automated software. We translated qualitative assessments into quantifiable metrics to characterize coronavirus disease 2019 (COVID-19) pneumonia lesions. Comparing the software output to the clinical evaluations, results were satisfactory despite heterogeneity of the clinical evaluations. An automatic quantification tool may contribute to improve the clinical workflow of COVID-19 pneumonia.
Interpretable CNN-Multilevel Attention Transformer for Rapid Recognition of Pneumonia from Chest X-Ray Images.
Authors: ShengchaoChen, SufenRen, GuanjunWang, MengxingHuang, ChenyangXue
Journal: IEEE journal of biomedical and health informatics

Chest imaging plays an essential role in diagnosing and predicting patients with COVID-19 with evidence of worsening respiratory status. Many deep learning-based approaches for pneumonia recognition have been developed to enable computer-aided diagnosis. However, the long training and inference time makes them inflexible, and the lack of interpretability reduces their credibility in clinical medical practice. This paper aims to develop a pneumonia recognition framework with interpretability, which can understand the complex relationship between lung features and related diseases in chest X-ray (CXR) images to provide high-speed analytics support for medical practice. To reduce the computational complexity to accelerate the recognition process, a novel multi-level self-attention mechanism within Transformer has been proposed to accelerate convergence and emphasize the task-related feature regions. Moreover, a practical CXR image data augmentation has been adopted to address the scarcity of medical image data problems to boost the model's performance. The effectiveness of the proposed method has been demonstrated on the classic COVID-19 recognition task using the widespread pneumonia CXR image dataset. In addition, abundant ablation experiments validate the effectiveness and necessity of all of the components of the proposed method.