pt-sk/ml_research_abs huggingface dataset:
A Deep Learning Model for Diagnosing COVID-19 and Pneumonia through X-ray.
Authors: XiangbinLiu, WenqianWu, JerryChun-Wei Lin, ShuaiLiu
Journal: Current medical imaging

The new global pandemic caused by the 2019 novel coronavirus (COVID-19), novel coronavirus pneumonia, has spread rapidly around the world, causing enormous damage to daily life, public health security, and the global economy. Early detection and treatment of COVID-19 infected patients are critical to prevent the further spread of the epidemic. However, existing detection methods are unable to rapidly detect COVID-19 patients, so infected individuals are not detected in a timely manner, which complicates the prevention and control of COVID-19 to some extent. Therefore, it is crucial to develop a rapid and practical COVID-19 detection method. In this work, we explored the application of deep learning in COVID-19 detection to develop a rapid COVID-19 detection method.
Existing studies have shown that novel coronavirus pneumonia has significant radiographic performance. In this study, we analyze and select the features of chest radiographs. We propose a chest X-Ray (CXR) classification method based on the selected features and investigate the application of transfer learning in detecting pneumonia and COVID-19. Furthermore, we combine the proposed CXR classification method based on selected features with transfer learning and ensemble learning and propose an ensemble deep learning model based on transfer learning called COVID-ensemble to diagnose pneumonia and COVID-19 using chest x-ray images. The model aims to provide an accurate diagnosis for binary classification (no finding/pneumonia) and multivariate classification (COVID-19/No findings/ Pneumonia).
Our proposed CXR classification method based on selection features can significantly improve the CXR classification accuracy of the CNN model. Using this method, DarkNet19 improved its binary and triple classification accuracies by 3.5% and 5.78%, respectively. In addition, the COVIDensemble achieved 91.5% accuracy in the binary classification task and 91.11% in the multi-category classification task. The experimental results demonstrate that the COVID-ensemble can quickly and accurately detect COVID-19 and pneumonia automatically through X-ray images and that the performance of this model is superior to that of several existing methods.
Our proposed COVID-ensemble can not only overcome the limitations of the conventional COVID-19 detection method RT-PCR and provide convenient and fast COVID-19 detection but also automatically detect pneumonia, thereby reducing the pressure on the medical staff. Using deep learning models to automatically diagnose COVID-19 and pneumonia from X-ray images can serve as a fast and efficient screening method for COVID-19 and pneumonia.
The Pitfalls of Using Open Data to Develop Deep Learning Solutions for COVID-19 Detection in Chest X-Rays.
Authors: RachaelHarkness, GeoffHall, Alejandro FFrangi, NishantRavikumar, KieranZucker
Journal: Studies in health technology and informatics

Since the emergence of COVID-19, deep learning models have been developed to identify COVID-19 from chest X-rays. With little to no direct access to hospital data, the AI community relies heavily on public data comprising numerous data sources. Model performance results have been exceptional when training and testing on open-source data, surpassing the reported capabilities of AI in pneumonia-detection prior to the COVID-19 outbreak. In this study impactful models are trained on a widely used open-source data and tested on an external test set and a hospital dataset, for the task of classifying chest X-rays into one of three classes: COVID-19, non-COVID pneumonia and no-pneumonia. Classification performance of the models investigated is evaluated through ROC curves, confusion matrices and standard classification metrics. Explainability modules are implemented to explore the image features most important to classification. Data analysis and model evalutions show that the popular open-source dataset COVIDx is not representative of the real clinical problem and that results from testing on this are inflated. Dependence on open-source data can leave models vulnerable to bias and confounding variables, requiring careful analysis to develop clinically useful/viable AI tools for COVID-19 detection in chest X-rays.
Evaluation of the models generated from clinical features and deep learning-based segmentations: Can thoracic CT on admission help us to predict hospitalized COVID-19 patients who will require intensive care?
Authors: MutluGülbay, AliyeBaştuğ, ErdemÖzkan, Büşra YüceÖztürk, Bökebatur Ahmet RaşitMendi, HürremBodur
Journal: BMC medical imaging

The aim of the study was to predict the probability of intensive care unit (ICU) care for inpatient COVID-19 cases using clinical and artificial intelligence segmentation-based volumetric and CT-radiomics parameters on admission.
Twenty-eight clinical/laboratory features, 21 volumetric parameters, and 74 radiomics parameters obtained by deep learning (DL)-based segmentations from CT examinations of 191 severe COVID-19 inpatients admitted between March 2020 and March 2021 were collected. Patients were divided into Group 1 (117 patients discharged from the inpatient service) and Group 2 (74 patients transferred to the ICU), and the differences between the groups were evaluated with the T-test and Mann-Whitney test. The sensitivities and specificities of significantly different parameters were evaluated by ROC analysis. Subsequently, 152 (79.5%) patients were assigned to the training/cross-validation set, and 39 (20.5%) patients were assigned to the test set. Clinical, radiological, and combined logit-fit models were generated by using the Bayesian information criterion from the training set and optimized via tenfold cross-validation. To simultaneously use all of the clinical, volumetric, and radiomics parameters, a random forest model was produced, and this model was trained by using a balanced training set created by adding synthetic data to the existing training/cross-validation set. The results of the models in predicting ICU patients were evaluated with the test set.
No parameter individually created a reliable classifier. When the test set was evaluated with the final models, the AUC values were 0.736, 0.708, and 0.794, the specificity values were 79.17%, 79.17%, and 87.50%, the sensitivity values were 66.67%, 60%, and 73.33%, and the F1 values were 0.67, 0.62, and 0.76 for the clinical, radiological, and combined logit-fit models, respectively. The random forest model that was trained with the balanced training/cross-validation set was the most successful model, achieving an AUC of 0.837, specificity of 87.50%, sensitivity of 80%, and F1 value of 0.80 in the test set.
By using a machine learning algorithm that was composed of clinical and DL-segmentation-based radiological parameters and that was trained with a balanced data set, COVID-19 patients who may require intensive care could be successfully predicted.
Deep learning-based lesion subtyping and prediction of clinical outcomes in COVID-19 pneumonia using chest CT.
Authors: DavidBermejo-Peláez, RaúlSan José Estépar, MaríaFernández-Velilla, CarmeloPalacios Miras, GuillermoGallardo Madueño, MarianaBenegas, CarolinaGotera Rivera, SandraCuerpo, MiguelLuengo-Oroz, JacoboSellarés, MarceloSánchez, GorkaBastarrika, GermanPeces Barba, Luis MSeijo, María JLedesma-Carbayo
Journal: Scientific reports

The main objective of this work is to develop and evaluate an artificial intelligence system based on deep learning capable of automatically identifying, quantifying, and characterizing COVID-19 pneumonia patterns in order to assess disease severity and predict clinical outcomes, and to compare the prediction performance with respect to human reader severity assessment and whole lung radiomics. We propose a deep learning based scheme to automatically segment the different lesion subtypes in nonenhanced CT scans. The automatic lesion quantification was used to predict clinical outcomes. The proposed technique has been independently tested in a multicentric cohort of 103 patients, retrospectively collected between March and July of 2020. Segmentation of lesion subtypes was evaluated using both overlapping (Dice) and distance-based (Hausdorff and average surface) metrics, while the proposed system to predict clinically relevant outcomes was assessed using the area under the curve (AUC). Additionally, other metrics including sensitivity, specificity, positive predictive value and negative predictive value were estimated. 95% confidence intervals were properly calculated. The agreement between the automatic estimate of parenchymal damage (%) and the radiologists' severity scoring was strong, with a Spearman correlation coefficient (R) of 0.83. The automatic quantification of lesion subtypes was able to predict patient mortality, admission to the Intensive Care Units (ICU) and need for mechanical ventilation with an AUC of 0.87, 0.73 and 0.68 respectively. The proposed artificial intelligence system enabled a better prediction of those clinically relevant outcomes when compared to the radiologists' interpretation and to whole lung radiomics. In conclusion, deep learning lesion subtyping in COVID-19 pneumonia from noncontrast chest CT enables quantitative assessment of disease severity and better prediction of clinical outcomes with respect to whole lung radiomics or radiologists' severity score.
Towards an effective model for lung disease classification: Using Dense Capsule Nets for early classification of lung diseases.
Authors: FaizanKarim, Munam AliShah, Hasan AliKhattak, ZoobiaAmeer, UmarShoaib, Hafiz TayyabRauf, FadiAl-Turjman
Journal: Applied soft computing

Machine Learning and computer vision have been the frontiers of the war against the COVID-19 Pandemic. Radiology has vastly improved the diagnosis of diseases, especially lung diseases, through the early assessment of key disease factors. Chest X-rays have thus become among the commonly used radiological tests to detect and diagnose many lung diseases. However, the discovery of lung disease through X-rays is a significantly challenging task depending on the availability of skilled radiologists. There has been a recent increase in attention to the design of Convolution Neural Networks (CNN) models for lung disease classification. A considerable amount of training dataset is required for CNN to work, but the problem is that it cannot handle translation and rotation correctly as input. The recently proposed Capsule Networks (referred to as CapsNets) are new automated learning architecture that aims to overcome the shortcomings in CNN. CapsNets are vital for rotation and complex translation. They require much less training information, which applies to the processing of data sets from medical images, including radiological images of the chest X-rays. In this research, the adoption and integration of CapsNets into the problem of chest X-ray classification have been explored. The aim is to design a deep model using CapsNet that increases the accuracy of the classification problem involved. We have used convolution blocks that take input images and generate convolution layers used as input to capsule block. There are 12 capsule layers operated, and the output of each capsule is used as an input to the next convolution block. The process is repeated for all blocks. The experimental results show that the proposed architecture yields better results when compared with the existing CNN techniques by achieving a better area under the curve (AUC) average. Furthermore, DNet checks the best performance in the ChestXray-14 data set on traditional CNN, and it is validated that DNet performs better with a higher level of total depth.
Prior-aware autoencoders for lung pathology segmentation.
Authors: MehdiAstaraki, ÖrjanSmedby, ChunliangWang
Journal: Medical image analysis

Segmentation of lung pathology in Computed Tomography (CT) images is of great importance for lung disease screening. However, the presence of different types of lung pathologies with a wide range of heterogeneities in size, shape, location, and texture, on one side, and their visual similarity with respect to surrounding tissues, on the other side, make it challenging to perform reliable automatic lesion segmentation. To leverage segmentation performance, we propose a deep learning framework comprising a Normal Appearance Autoencoder (NAA) model to learn the distribution of healthy lung regions and reconstruct pathology-free images from the corresponding pathological inputs by replacing the pathological regions with the characteristics of healthy tissues. Detected regions that represent prior information regarding the shape and location of pathologies are then integrated into a segmentation network to guide the attention of the model into more meaningful delineations. The proposed pipeline was tested on three types of lung pathologies, including pulmonary nodules, Non-Small Cell Lung Cancer (NSCLC), and Covid-19 lesion on five comprehensive datasets. The results show the superiority of the proposed prior model, which outperformed the baseline segmentation models in all the cases with significant margins. On average, adding the prior model improved the Dice coefficient for the segmentation of lung nodules by 0.038, NSCLCs by 0.101, and Covid-19 lesions by 0.041. We conclude that the proposed NAA model produces reliable prior knowledge regarding the lung pathologies, and integrating such knowledge into a prior segmentation network leads to more accurate delineations.
An interpretable multi-task system for clinically applicable COVID-19 diagnosis using CXR.
Authors: YanZhuang, Md FashiarRahman, YuxinWen, MichaelPokojovy, PeterMcCaffrey, AlexanderVo, EricWalser, ScottMoen, HonglunXu, Tzu-Liang BillTseng
Journal: Journal of X-ray science and technology

With the emergence of continuously mutating variants of coronavirus, it is urgent to develop a deep learning model for automatic COVID-19 diagnosis at early stages from chest X-ray images. Since laboratory testing is time-consuming and requires trained laboratory personal, diagnosis using chest X-ray (CXR) is a befitting option.
In this study, we proposed an interpretable multi-task system for automatic lung detection and COVID-19 screening in chest X-rays to find an alternate method of testing which are reliable, fast and easily accessible, and able to generate interpretable predictions that are strongly correlated with radiological findings.
The proposed system consists of image preprocessing and an unsupervised machine learning (UML) algorithm for lung region detection, as well as a truncated CNN model based on deep transfer learning (DTL) to classify chest X-rays into three classes of COVID-19, pneumonia, and normal. The Grad-CAM technique was applied to create class-specific heatmap images in order to establish trust in the medical AI system.
Experiments were performed with 15,884 frontal CXR images to show that the proposed system achieves an accuracy of 91.94% in a test dataset with 2,680 images including a sensitivity of 94.48% on COVID-19 cases, a specificity of 88.46% on normal cases, and a precision of 88.01% on pneumonia cases. Our system also produced state-of-the-art outcomes with a sensitivity of 97.40% on public test data and 88.23% on a previously unseen clinical data (1,000 cases) for binary classification of COVID-19-positive and COVID-19-negative films.
Our automatic computerized evaluation for grading lung infections exhibited sensitivity comparable to that of radiologist interpretation in clinical applicability. Therefore, the proposed solution can be used as one element of patient evaluation along with gold-standard clinical and laboratory testing.
An Analysis of New Feature Extraction Methods Based on Machine Learning Methods for Classification Radiological Images.
Authors: Firoozeh AbolhasaniZadeh, Mohammadreza VazifehArdalani, Ali RezaeiSalehi, RozaJalali Farahani, MandanaHashemi, Adil HusseinMohammed
Journal: Computational intelligence and neuroscience

The lungs are COVID-19's most important focus, as it induces inflammatory changes in the lungs that can lead to respiratory insufficiency. Reducing the supply of oxygen to human cells negatively impacts humans, and multiorgan failure with a high mortality rate may, in certain circumstances, occur. Radiological pulmonary evaluation is a vital part of patient therapy for the critically ill patient with COVID-19. The evaluation of radiological imagery is a specialized activity that requires a radiologist. Artificial intelligence to display radiological images is one of the essential topics. Using a deep machine learning technique to identify morphological differences in the lungs of COVID-19-infected patients could yield promising results on digital images of chest X-rays. Minor differences in digital images that are not detectable or apparent to the human eye may be detected using computer vision algorithms. This paper uses machine learning methods to diagnose COVID-19 on chest X-rays, and the findings have been very promising. The dataset includes COVID-19-enhanced X-ray images for disease detection using chest X-ray images. The data were gathered from two publicly accessible datasets. The feature extractions are done using the gray level co-occurrence matrix methods.
Multiclass Classification of Chest X-Ray Images for the Prediction of COVID-19 Using Capsule Network.
Authors: MahmoudRagab, SamahAlshehri, Nabil AAlhakamy, Romany FMansour, DeepikaKoundal
Journal: Computational intelligence and neuroscience

It is critical to establish a reliable method for detecting people infected with COVID-19 since the pandemic has numerous harmful consequences worldwide. If the patient is infected with COVID-19, a chest X-ray can be used to determine this. In this work, an X-ray showing a COVID-19 infection is classified by the capsule neural network model we trained to recognise. 6310 chest X-ray pictures were used to train the models, separated into three categories: normal, pneumonia, and COVID-19. This work is considered an improved deep learning model for the classification of COVID-19 disease through X-ray images. Viewpoint invariance, fewer parameters, and better generalisation are some of the advantages of CapsNet compared with the classic convolutional neural network (CNN) models. The proposed model has achieved an accuracy greater than 95% during the model's training, which is better than the other state-of-the-art algorithms. Furthermore, to aid in detecting COVID-19 in a chest X-ray, the model could provide extra information.
COVLIAS 1.0
Authors: Jasjit SSuri, SushantAgarwal, Gian LucaChabert, AlessandroCarriero, AlessioPaschè, Pietro S CDanna, LucaSaba, ArminMehmedović, GavinoFaa, Inder MSingh, MonikaTurk, Paramjit SChadha, Amer MJohri, Narendra NKhanna, SophieMavrogeni, John RLaird, GyanPareek, MartinMiner, David WSobel, AntonellaBalestrieri, Petros PSfikakis, GeorgeTsoulfas, Athanasios DProtogerou, Durga PrasannaMisra, VikasAgarwal, George DKitas, Jagjit STeji, MustafaAl-Maini, Surinder KDhanjil, AndrewNicolaides, AdityaSharma, VijayRathore, MostafaFatemi, AzraAlizad, Pudukode RKrishnan, FerencNagy, ZoltanRuzsa, Mostafa MFouda, SubbaramNaidu, KlaudijaViskovic, Manudeep KKalra
Journal: Diagnostics (Basel, Switzerland)

Background: COVID-19 is a disease with multiple variants, and is quickly spreading throughout the world. It is crucial to identify patients who are suspected of having COVID-19 early, because the vaccine is not readily available in certain parts of the world. Methodology: Lung computed tomography (CT) imaging can be used to diagnose COVID-19 as an alternative to the RT-PCR test in some cases. The occurrence of ground-glass opacities in the lung region is a characteristic of COVID-19 in chest CT scans, and these are daunting to locate and segment manually. The proposed study consists of a combination of solo deep learning (DL) and hybrid DL (HDL) models to tackle the lesion location and segmentation more quickly. One DL and four HDL models—namely, PSPNet, VGG-SegNet, ResNet-SegNet, VGG-UNet, and ResNet-UNet—were trained by an expert radiologist. The training scheme adopted a fivefold cross-validation strategy on a cohort of 3000 images selected from a set of 40 COVID-19-positive individuals. Results: The proposed variability study uses tracings from two trained radiologists as part of the validation. Five artificial intelligence (AI) models were benchmarked against MedSeg. The best AI model, ResNet-UNet, was superior to MedSeg by 9% and 15% for Dice and Jaccard, respectively, when compared against MD 1, and by 4% and 8%, respectively, when compared against MD 2. Statistical tests—namely, the Mann−Whitney test, paired t-test, and Wilcoxon test—demonstrated its stability and reliability, with p < 0.0001. The online system for each slice was <1 s. Conclusions: The AI models reliably located and segmented COVID-19 lesions in CT scans. The COVLIAS 1.0Lesion lesion locator passed the intervariability test.
Towards robust diagnosis of COVID-19 using vision self-attention transformer.
Authors: FoziaMehboob, AbdulRauf, RichardJiang, Abdul Khader JilaniSaudagar, Khalid MahmoodMalik, Muhammad BadruddinKhan, Mozaherul Hoque AbdulHasnat, AbdullahAlTameem, MohammedAlKhathami
Journal: Scientific reports

The outbreak of COVID-19, since its appearance, has affected about 200 countries and endangered millions of lives. COVID-19 is extremely contagious disease, and it can quickly incapacitate the healthcare systems if infected cases are not handled timely. Several Conventional Neural Networks (CNN) based techniques have been developed to diagnose the COVID-19. These techniques require a large, labelled dataset to train the algorithm fully, but there are not too many labelled datasets. To mitigate this problem and facilitate the diagnosis of COVID-19, we developed a self-attention transformer-based approach having self-attention mechanism using CT slices. The architecture of transformer can exploit the ample unlabelled datasets using pre-training. The paper aims to compare the performances of self-attention transformer-based approach with CNN and Ensemble classifiers for diagnosis of COVID-19 using binary Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and multi-class Hybrid-learning for UnbiaSed predicTion of COVID-19 (HUST-19) CT scan dataset. To perform this comparison, we have tested Deep learning-based classifiers and ensemble classifiers with proposed approach using CT scan images. Proposed approach is more effective in detection of COVID-19 with an accuracy of 99.7% on multi-class HUST-19, whereas 98% on binary class SARS-CoV-2 dataset. Cross corpus evaluation achieves accuracy of 93% by training the model with Hust19 dataset and testing using Brazilian COVID dataset.