pt-sk/ml_research_abs huggingface dataset:
Multi-feature Multi-Scale CNN-Derived COVID-19 Classification from Lung Ultrasound Data.
Authors: HuiChe, JaredRadbel, JagSunderram, John LNosher, Vishal MPatel, IlkerHacihaliloglu
Journal: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

The global pandemic of the novel coronavirus disease 2019 (COVID-19) has put tremendous pressure on the medical system. Imaging plays a complementary role in the management of patients with COVID-19. Computed tomography (CT) and chest X-ray (CXR) are the two dominant screening tools. However, difficulty in eliminating the risk of disease transmission, radiation exposure and not being cost-effective are some of the challenges for CT and CXR imaging. This fact induces the implementation of lung ultrasound (LUS) for evaluating COVID-19 due to its practical advantages of noninvasiveness, repeatability, and sensitive bedside property. In this paper, we utilize a deep learning model to perform the classification of COVID-19 from LUS data, which could produce objective diagnostic information for clinicians. Specifically, all LUS images are processed to obtain their corresponding local phase filtered images and radial symmetry transformed images before fed into the multi-scale residual convolutional neural network (CNN). Secondly, image combination as the input of the network is used to explore rich and reliable features. Feature fusion strategy at different levels is adopted to investigate the relationship between the depth of feature aggregation and the classification accuracy. Our proposed method is evaluated on the point-of-care US (POCUS) dataset together with the Italian COVID-19 Lung US database (ICLUS-DB) and shows promising performance for COVID-19 prediction.
Precision Medicine: Using Artificial Intelligence to Improve Diagnostics and Healthcare.
Authors: RoxanaDaneshjou, Steven EBrenner, Jonathan HChen, Dana CCrawford, Samuel GFinlayson, ŁukaszKidziński, Martha LBulyk
Journal: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

The continued generation of large amounts of data within healthcare-from imaging to electronic medical health records to genomics and multi-omics -necessitates tools and methods to parse and interpret these data to improve healthcare outcomes. Artificial intelligence, and in particular deep learning, has enabled researchers to gain new insights from large scale and multimodal data. At the 2022 Pacific Symposium on Biocomputing (PSB) session entitled "Precision Medicine: Using Artificial Intelligence to Improve Diagnostics and Healthcare", we showcase the latest research, influenced and inspired by the idea of using technology to build a more fair, tailored, and cost-effective healthcare system after the COVID-19 pandemic.
The diagnostic performance of deep-learning-based CT severity score to identify COVID-19 pneumonia.
Authors: Anna SáraKardos, JuditSimon, ChiaraNardocci, István ViktorSzabó, NorbertNagy, Renad HeyamAbdelrahman, EmeseZsarnóczay, BenceFejér, BalázsFutácsi, VeronikaMüller, BélaMerkely, PálMaurovich-Horvat
Journal: The British journal of radiology

To determine the diagnostic accuracy of a deep-learning (DL)-based algorithm using chest computed tomography (CT) scans for the rapid diagnosis of coronavirus disease 2019 (COVID-19), as compared to the reference standard reverse-transcription polymerase chain reaction (RT-PCR) test.
In this retrospective analysis, data of COVID-19 suspected patients who underwent RT-PCR and chest CT examination for the diagnosis of COVID-19 were assessed. By quantifying the affected area of the lung parenchyma, severity score was evaluated for each lobe of the lung with the DL-based algorithm. The diagnosis was based on the total lung severity score ranging from 0 to 25. The data were randomly split into a 40% training set and a 60% test set. Optimal cut-off value was determined using Youden-index method on the training cohort.
A total of 1259 patients were enrolled in this study. The prevalence of RT-PCR positivity in the overall investigated period was 51.5%. As compared to RT-PCR, sensitivity, specificity, positive predictive value, negative predictive value and accuracy on the test cohort were 39.0%, 80.2%, 68.0%, 55.0% and 58.9%, respectively. Regarding the whole data set, when adding those with positive RT-PCR test at any time during hospital stay or "COVID-19 without virus detection", as final diagnosis to the true positive cases, specificity increased from 80.3% to 88.1% and the positive predictive value increased from 68.4% to 81.7%.
DL-based CT severity score was found to have a good specificity and positive predictive value, as compared to RT-PCR. This standardized scoring system can aid rapid diagnosis and clinical decision making.
DL-based CT severity score can detect COVID-19-related lung alterations even at early stages, when RT-PCR is not yet positive.
Role of Artificial Intelligence in COVID-19 Detection.
Authors: AnjanGudigar, URaghavendra, SnehaNayak, Chui PingOoi, Wai YeeChan, Mokshagna RohitGangavarapu, ChinmayDharmik, JyothiSamanth, Nahrizul AdibKadri, KhairunnisaHasikin, Prabal DattaBarua, SubrataChakraborty, Edward JCiaccio, U RajendraAcharya
Journal: Sensors (Basel, Switzerland)

The global pandemic of coronavirus disease (COVID-19) has caused millions of deaths and affected the livelihood of many more people. Early and rapid detection of COVID-19 is a challenging task for the medical community, but it is also crucial in stopping the spread of the SARS-CoV-2 virus. Prior substantiation of artificial intelligence (AI) in various fields of science has encouraged researchers to further address this problem. Various medical imaging modalities including X-ray, computed tomography (CT) and ultrasound (US) using AI techniques have greatly helped to curb the COVID-19 outbreak by assisting with early diagnosis. We carried out a systematic review on state-of-the-art AI techniques applied with X-ray, CT, and US images to detect COVID-19. In this paper, we discuss approaches used by various authors and the significance of these research efforts, the potential challenges, and future trends related to the implementation of an AI system for disease detection during the COVID-19 pandemic.
MHA-CoroCapsule: Multi-Head Attention Routing-Based Capsule Network for COVID-19 Chest X-Ray Image Classification.
Authors: FudongLi, XingyuLu, JianjunYuan
Journal: IEEE transactions on medical imaging

The outbreak of COVID-19 threatens the lives and property safety of countless people and brings a tremendous pressure to health care systems worldwide. The principal challenge in the fight against this disease is the lack of efficient detection methods. AI-assisted diagnosis based on deep learning can detect COVID-19 cases for chest X-ray images automatically, and also improve the accuracy and efficiency of doctors' diagnosis. However, large scale annotation of chest X-ray images is difficult because of limited resources and heavy burden on the medical system. To meet the challenge, we propose a capsule network model with multi-head attention routing algorithm, called MHA-CoroCapsule, to provide fast and accurate diagnostics for COVID-19 diseases from chest X-ray images. The MHA-CoroCapsule consists of convolutional layers, two capsule layers, and a non-iterative, parameterized multi-head attention routing algorithm is used to quantify the relationship between the two capsule layers. The experiments are performed on a combined dataset constituted by two publicly available datasets including normal, non-COVID pneumonia and COVID-19 images. The model achieves the accuracy of 97.28%, recall of 97.36%, and precision of 97.38% even with a limited number of samples. The experimental results demonstrate that, contrary to the transfer learning and deep feature extraction approaches, the proposed MHA-CoroCapsule has an encouraging performance with fewer trainable parameters and does not require pretraining and plenty of training samples.
Application of CycleGAN and transfer learning techniques for automated detection of COVID-19 using X-ray images.
Authors: GhazalBargshady, XujuanZhou, Prabal DattaBarua, RajGururajan, YuefengLi, U RajendraAcharya
Journal: Pattern recognition letters

Coronavirus (which is also known as COVID-19) is severely impacting the wellness and lives of many across the globe. There are several methods currently to detect and monitor the progress of the disease such as radiological image from patients' chests, measuring the symptoms and applying polymerase chain reaction (RT-PCR) test. X-ray imaging is one of the popular techniques used to visualise the impact of the virus on the lungs. Although manual detection of this disease using radiology images is more popular, it can be time-consuming, and is prone to human errors. Hence, automated detection of lung pathologies due to COVID-19 utilising deep learning (Bowles et al.) techniques can assist with yielding accurate results for huge databases. Large volumes of data are needed to achieve generalizable DL models; however, there are very few public databases available for detecting COVID-19 disease pathologies automatically. Standard data augmentation method can be used to enhance the models' generalizability. In this research, the Extensive COVID-19 X-ray and CT Chest Images Dataset has been used and generative adversarial network (GAN) coupled with trained, semi-supervised CycleGAN (SSA- CycleGAN) has been applied to augment the training dataset. Then a newly designed and finetuned Inception V3 transfer learning model has been developed to train the algorithm for detecting COVID-19 pandemic. The obtained results from the proposed Inception-CycleGAN model indicated Accuracy = 94.2%, Area under Curve = 92.2%, Mean Squared Error = 0.27, Mean Absolute Error = 0.16. The developed Inception-CycleGAN framework is ready to be tested with further COVID-19 X-Ray images of the chest.
Detection of COVID-19 With CT Images Using Hybrid Complex Shearlet Scattering Networks.
Authors: QingyunRen, BingyinZhou, LiangTian, WeiGuo
Journal: IEEE journal of biomedical and health informatics

With the ongoing worldwide coronavirus disease 2019 (COVID-19) pandemic, it is desirable to develop effective algorithms to automatically detect COVID-19 with chest computed tomography (CT) images. Recently, a considerable number of methods based on deep learning have indeed been proposed. However, training an accurate deep learning model requires a large-scale chest CT dataset, which is hard to collect due to the high contagiousness of COVID-19. To achieve improved detection performance, this paper proposes a hybrid framework that fuses the complex shearlet scattering transform (CSST) and a suitable convolutional neural network into a single model. The introduced CSST cascades complex shearlet transforms with modulus nonlinearities and low-pass filter convolutions to compute a sparse and locally invariant image representation. The features computed from the input chest CT images are discriminative for COVID-19 detection. Furthermore, a wide residual network with a redesigned residual block (WR2N) is developed to learn more granular multiscale representations by applying it to scattering features. The combination of model-based CSST and data-driven WR2N leads to a more convenient neural network for image representation, where the idea is to learn only the image parts that the CSST cannot handle instead of all parts. Experiments on two public datasets demonstrate the superiority of our method. We can obtain more accurate results than several state-of-the-art COVID-19 classification methods in terms of measures such as accuracy, the F1-score, and the area under the receiver operating characteristic curve.
Validation of expert system enhanced deep learning algorithm for automated screening for COVID-Pneumonia on chest X-rays.
Authors: Prashant SadashivGidde, Shyam SunderPrasad, Ajay PratapSingh, NitinBhatheja, SatyarthaPrakash, PrateekSingh, AakashSaboo, RohitTakhar, SalilGupta, SumeetSaurav, RaghunandananM V, AmritpalSingh, VirenSardana, HarshMahajan, ArjunKalyanpur, Atanendu ShekharMandal, VidurMahajan, AnuragAgrawal, AnjaliAgrawal, Vasantha KumarVenugopal, SanjaySingh, DebasisDash
Journal: Scientific reports

SARS-CoV2 pandemic exposed the limitations of artificial intelligence based medical imaging systems. Earlier in the pandemic, the absence of sufficient training data prevented effective deep learning (DL) solutions for the diagnosis of COVID-19 based on X-Ray data. Here, addressing the lacunae in existing literature and algorithms with the paucity of initial training data; we describe CovBaseAI, an explainable tool using an ensemble of three DL models and an expert decision system (EDS) for COVID-Pneumonia diagnosis, trained entirely on pre-COVID-19 datasets. The performance and explainability of CovBaseAI was primarily validated on two independent datasets. Firstly, 1401 randomly selected CxR from an Indian quarantine center to assess effectiveness in excluding radiological COVID-Pneumonia requiring higher care. Second, curated dataset; 434 RT-PCR positive cases and 471 non-COVID/Normal historical scans, to assess performance in advanced medical settings. CovBaseAI had an accuracy of 87% with a negative predictive value of 98% in the quarantine-center data. However, sensitivity was 0.66-0.90 taking RT-PCR/radiologist opinion as ground truth. This work provides new insights on the usage of EDS with DL methods and the ability of algorithms to confidently predict COVID-Pneumonia while reinforcing the established learning; that benchmarking based on RT-PCR may not serve as reliable ground truth in radiological diagnosis. Such tools can pave the path for multi-modal high throughput detection of COVID-Pneumonia in screening and referral.
Trends in the application of deep learning networks in medical image analysis: Evolution between 2012 and 2020.
Authors: LuWang, HairuiWang, YingnaHuang, BaihuiYan, ZhihuiChang, ZhaoyuLiu, MingfangZhao, LeiCui, JiangdianSong, FanLi
Journal: European journal of radiology

To evaluate the general rules and future trajectories of deep learning (DL) networks in medical image analysis through bibliometric and hot spot analysis of original articles published between 2012 and 2020.
Original articles related to DL and medical imaging were retrieved from the PubMed database. For the analysis, data regarding radiological subspecialties; imaging techniques; DL networks; sample size; study purposes, setting, origins and design; statistical analysis; funding sources; authors; and first authors' affiliation was manually extracted from each article. The Bibliographic Item Co-Occurrence Matrix Builder and VOSviewer were used to identify the research topics of the included articles and illustrate the future trajectories of studies.
The study included 2685 original articles. The number of publications on DL and medical imaging has increased substantially since 2017, accounting for 97.2% of all included articles. We evaluated the rules of the application of 47 DL networks to eight radiological tasks on 11 human organ sites. Neuroradiology, thorax, and abdomen were frequent research subjects, while thyroid was under-represented. Segmentation and classification tasks were the primary purposes. U-Net, ResNet, and VGG were the most frequently used Convolutional neural network-derived networks. GAN-derived networks were widely developed and applied in 2020, and transfer learning was highlighted in the COVID-19 studies. Brain, prostate, and diabetic retinopathy-related studies were mature research topics in the field. Breast- and lung-related studies were in a stage of rapid development.
This study evaluates the general rules and future trajectories of DL network application in medical image analyses and provides guidance for future studies.
Computer-aided COVID-19 diagnosis and a comparison of deep learners using augmented CXRs.
Authors: AsmaNaseer, MariaTamoor, ArifahAzhar
Journal: Journal of X-ray science and technology

Coronavirus Disease 2019 (COVID-19) is contagious, producing respiratory tract infection, caused by a newly discovered coronavirus. Its death toll is too high, and early diagnosis is the main problem nowadays. Infected people show a variety of symptoms such as fatigue, fever, tastelessness, dry cough, etc. Some other symptoms may also be manifested by radiographic visual identification. Therefore, Chest X-Rays (CXR) play a key role in the diagnosis of COVID-19.
In this study, we use Chest X-Rays images to develop a computer-aided diagnosis (CAD) of the disease. These images are used to train two deep networks, the Convolution Neural Network (CNN), and the Long Short-Term Memory Network (LSTM) which is an artificial Recurrent Neural Network (RNN). The proposed study involves three phases. First, the CNN model is trained on raw CXR images. Next, it is trained on pre-processed CXR images and finally enhanced CXR images are used for deep network CNN training. Geometric transformations, color transformations, image enhancement, and noise injection techniques are used for augmentation. From augmentation, we get 3,220 augmented CXRs as training datasets. In the final phase, CNN is used to extract the features of CXR imagery that are fed to the LSTM model. The performance of the four trained models is evaluated by the evaluation techniques of different models, including accuracy, specificity, sensitivity, false-positive rate, and receiver operating characteristic (ROC) curve.
We compare our results with other benchmark CNN models. Our proposed CNN-LSTM model gives superior accuracy (99.02%) than the other state-of-the-art models. Our method to get improved input, helped the CNN model to produce a very high true positive rate (TPR 1) and no false-negative result whereas false negative was a major problem while using Raw CXR images.
We conclude after performing different experiments that some image pre-processing and augmentation, remarkably improves the results of CNN-based models. It will help a better early detection of the disease that will eventually reduce the mortality rate of COVID.
Data augmentation using Generative Adversarial Networks (GANs) for GAN-based detection of Pneumonia and COVID-19 in chest X-ray images.
Authors: SamanMotamed, PatrikRogalla, FarzadKhalvati
Journal: Informatics in medicine unlocked

Successful training of convolutional neural networks (CNNs) requires a substantial amount of data. With small datasets, networks generalize poorly. Data Augmentation techniques improve the generalizability of neural networks by using existing training data more effectively. Standard data augmentation methods, however, produce limited plausible alternative data. Generative Adversarial Networks (GANs) have been utilized to generate new data and improve the performance of CNNs. Nevertheless, data augmentation techniques for training GANs are underexplored compared to CNNs. In this work, we propose a new GAN architecture for augmentation of chest X-rays for semi-supervised detection of pneumonia and COVID-19 using generative models. We show that the proposed GAN can be used to effectively augment data and improve classification accuracy of disease in chest X-rays for pneumonia and COVID-19. We compare our augmentation GAN model with Deep Convolutional GAN and traditional augmentation methods (rotate, zoom, etc.) on two different X-ray datasets and show our GAN-based augmentation method surpasses other augmentation methods for training a GAN in detecting anomalies in X-ray images.
Medical image processing and COVID-19: A literature review and bibliometric analysis.
Authors: Rabab AliAbumalloh, MehrbakhshNilashi, MuhammedYousoof Ismail, AshwaqAlhargan, AbdullahAlghamdi, Ahmed OmarAlzahrani, LinahSaraireh, ReemOsman, ShahlaAsadi
Journal: Journal of infection and public health

COVID-19 crisis has placed medical systems over the world under unprecedented and growing pressure. Medical imaging processing can help in the diagnosis, treatment, and early detection of diseases. It has been considered as one of the modern technologies applied to fight against the COVID-19 crisis. Although several artificial intelligence, machine learning, and deep learning techniques have been deployed in medical image processing in the context of COVID-19 disease, there is a lack of research considering systematic literature review and categorization of published studies in this field. A systematic review locates, assesses, and interprets research outcomes to address a predetermined research goal to present evidence-based practical and theoretical insights. The main goal of this study is to present a literature review of the deployed methods of medical image processing in the context of the COVID-19 crisis. With this in mind, the studies available in reliable databases were retrieved, studied, evaluated, and synthesized. Based on the in-depth review of literature, this study structured a conceptual map that outlined three multi-layered folds: data gathering and description, main steps of image processing, and evaluation metrics. The main research themes were elaborated in each fold, allowing the authors to recommend upcoming research paths for scholars. The outcomes of this review highlighted that several methods have been adopted to classify the images related to the diagnosis and detection of COVID-19. The adopted methods have presented promising outcomes in terms of accuracy, cost, and detection speed.
COVID-19 Detection Using Deep Learning Algorithm on Chest X-ray Images.
Authors: ShamimaAkter, F M Javed MehediShamrat, SovonChakraborty, AsifKarim, SamiAzam
Journal: Biology

COVID-19, regarded as the deadliest virus of the 21st century, has claimed the lives of millions of people around the globe in less than two years. Since the virus initially affects the lungs of patients, X-ray imaging of the chest is helpful for effective diagnosis. Any method for automatic, reliable, and accurate screening of COVID-19 infection would be beneficial for rapid detection and reducing medical or healthcare professional exposure to the virus. In the past, Convolutional Neural Networks (CNNs) proved to be quite successful in the classification of medical images. In this study, an automatic deep learning classification method for detecting COVID-19 from chest X-ray images is suggested using a CNN. A dataset consisting of 3616 COVID-19 chest X-ray images and 10,192 healthy chest X-ray images was used. The original data were then augmented to increase the data sample to 26,000 COVID-19 and 26,000 healthy X-ray images. The dataset was enhanced using histogram equalization, spectrum, grays, cyan and normalized with NCLAHE before being applied to CNN models. Initially using the dataset, the symptoms of COVID-19 were detected by employing eleven existing CNN models; VGG16, VGG19, MobileNetV2, InceptionV3, NFNet, ResNet50, ResNet101, DenseNet, EfficientNetB7, AlexNet, and GoogLeNet. From the models, MobileNetV2 was selected for further modification to obtain a higher accuracy of COVID-19 detection. Performance evaluation of the models was demonstrated using a confusion matrix. It was observed that the modified MobileNetV2 model proposed in the study gave the highest accuracy of 98% in classifying COVID-19 and healthy chest X-rays among all the implemented CNN models. The second-best performance was achieved from the pre-trained MobileNetV2 with an accuracy of 97%, followed by VGG19 and ResNet101 with 95% accuracy for both the models. The study compares the compilation time of the models. The proposed model required the least compilation time with 2 h, 50 min and 21 s. Finally, the Wilcoxon signed-rank test was performed to test the statistical significance. The results suggest that the proposed method can efficiently identify the symptoms of infection from chest X-ray images better than existing methods.