pt-sk/ml_research_abs huggingface dataset:
Cov-caldas: A new COVID-19 chest X-Ray dataset from state of Caldas-Colombia.
Authors: Jesús AlejandroAlzate-Grisales, AlejandroMora-Rubio, Harold BrayanArteaga-Arteaga, Mario AlejandroBravo-Ortiz, DanielArias-Garzón, Luis HumbertoLópez-Murillo, EstebanMercado-Ruiz, Juan PabloVilla-Pulgarin, OscarCardona-Morales, SimonOrozco-Arias, FelipeBuitrago-Carmona, Maria JosePalancares-Sosa, FernandaMartínez-Rodríguez, Sonia HContreras-Ortiz, Jose ManuelSaborit-Torres, Joaquim ÁngelMontell Serrano, María MónicaRamirez-Sánchez, Mario AlfonsoSierra-Gaber, OscarJaramillo-Robledo, Mariade la Iglesia-Vayá, ReinelTabares-Soto
Journal: Scientific data

The emergence of COVID-19 as a global pandemic forced researchers worldwide in various disciplines to investigate and propose efficient strategies and/or technologies to prevent COVID-19 from further spreading. One of the main challenges to be overcome is the fast and efficient detection of COVID-19 using deep learning approaches and medical images such as Chest Computed Tomography (CT) and Chest X-ray images. In order to contribute to this challenge, a new dataset was collected in collaboration with "S.E.S Hospital Universitario de Caldas" ( https://hospitaldecaldas.com/ ) from Colombia and organized following the Medical Imaging Data Structure (MIDS) format. The dataset contains 7,307 chest X-ray images divided into 3,077 and 4,230 COVID-19 positive and negative images. Images were subjected to a selection and anonymization process to allow the scientific community to use them freely. Finally, different convolutional neural networks were used to perform technical validation. This dataset contributes to the scientific community by tackling significant limitations regarding data quality and availability for the detection of COVID-19.
Application of Machine Learning and Deep Learning Techniques for COVID-19 Screening Using Radiological Imaging: A Comprehensive Review.
Authors: AsifuzzamanLasker, Sk MdObaidullah, ChandanChakraborty, KaushikRoy
Journal: SN computer science

Lung, being one of the most important organs in human body, is often affected by various SARS diseases, among which COVID-19 has been found to be the most fatal disease in recent times. In fact, SARS-COVID 19 led to pandemic that spreads fast among the community causing respiratory problems. Under such situation, radiological imaging-based screening [mostly chest X-ray and computer tomography (CT) modalities] has been performed for rapid screening of the disease as it is a non-invasive approach. Due to scarcity of physician/chest specialist/expert doctors, technology-enabled disease screening techniques have been developed by several researchers with the help of artificial intelligence and machine learning (AI/ML). It can be remarkably observed that the researchers have introduced several AI/ML/DL (deep learning) algorithms for computer-assisted detection of COVID-19 using chest X-ray and CT images. In this paper, a comprehensive review has been conducted to summarize the works related to applications of AI/ML/DL for diagnostic prediction of COVID-19, mainly using X-ray and CT images. Following the PRISMA guidelines, total 265 articles have been selected out of 1715 published articles till the third quarter of 2021. Furthermore, this review summarizes and compares varieties of ML/DL techniques, various datasets, and their results using X-ray and CT imaging. A detailed discussion has been made on the novelty of the published works, along with advantages and limitations.
Rapid diagnosis of Covid-19 infections by a progressively growing GAN and CNN optimisation.
Authors: RutwikGulakala, BerndMarkert, MarcusStoffel
Journal: Computer methods and programs in biomedicine

Covid-19 infections are spreading around the globe since December 2019. Several diagnostic methods were developed based on biological investigations and the success of each method depends on the accuracy of identifying Covid infections. However, access to diagnostic tools can be limited, depending on geographic region and the diagnosis duration plays an important role in treating Covid-19. Since the virus causes pneumonia, its presence can also be detected using medical imaging by Radiologists. Hospitals with X-ray capabilities are widely distributed all over the world, so a method for diagnosing Covid-19 from chest X-rays would present itself. Studies have shown promising results in automatically detecting Covid-19 from medical images using supervised Artificial neural network (ANN) algorithms. The major drawback of supervised learning algorithms is that they require huge amounts of data to train. Also, the radiology equipment is not computationally efficient for deep neural networks. Therefore, we aim to develop a Generative Adversarial Network (GAN) based image augmentation to optimize the performance of custom, light, Convolutional networks used for the classification of Chest X-rays (CXR).
A Progressively Growing Generative Adversarial Network (PGGAN) is used to generate synthetic and augmented data to supplement the dataset. We propose two novel CNN architectures to perform the Multi-class classification of Covid-19, healthy and pneumonia affected Chest X-rays. Comparisons have been drawn to the state of the art models and transfer learning methods to evaluate the superiority of the networks. All the models are trained using enhanced and augmented X-ray images and are compared based on classification metrics.
The proposed models had extremely high classification metrics with proposed Architectures having test accuracy of 98.78% and 99.2% respectively while having 40% lesser training parameters than their state of the art counterpart.
In the present study, a method based on artificial intelligence is proposed, leading to a rapid diagnostic tool for Covid infections based on Generative Adversarial Network (GAN) and Convolutional Neural Networks (CNN). The benefit will be a high accuracy of detection with up to 99% hit rate, a rapid diagnosis, and an accessible Covid identification method by chest X-ray images.
COVID-DSNet: A novel deep convolutional neural network for detection of coronavirus (SARS-CoV-2) cases from CT and Chest X-Ray images.
Authors: Hatice CatalReis, VeyselTurk
Journal: Artificial intelligence in medicine

COVID-19 (SARS-CoV-2), which causes acute respiratory syndrome, is a contagious and deadly disease that has devastating effects on society and human life. COVID-19 can cause serious complications, especially in patients with pre-existing chronic health problems such as diabetes, hypertension, lung cancer, weakened immune systems, and the elderly. The most critical step in the fight against COVID-19 is the rapid diagnosis of infected patients. Computed Tomography (CT), chest X-ray (CXR), and RT-PCR diagnostic kits are frequently used to diagnose the disease. However, due to difficulties such as the inadequacy of RT-PCR test kits and false negative (FN) results in the early stages of the disease, the time-consuming examination of medical images obtained from CT and CXR imaging techniques by specialists/doctors, and the increasing workload on specialists, it is challenging to detect COVID-19. Therefore, researchers have suggested searching for new methods in COVID- 19 detection. In analysis studies with CT and CXR radiography images, it was determined that COVID-19-infected patients experienced abnormalities related to COVID-19. The anomalies observed here are the primary motivation for artificial intelligence researchers to develop COVID-19 detection applications with deep convolutional neural networks. Here, convolutional neural network-based deep learning algorithms from artificial intelligence technologies with high discrimination capabilities can be considered as an alternative approach in the disease detection process. This study proposes a deep convolutional neural network, COVID-DSNet, to diagnose typical pneumonia (bacterial, viral) and COVID-19 diseases from CT, CXR, hybrid CT + CXR images. In the multi-classification study with the CT dataset, 97.60 % accuracy and 97.60 % sensitivity values were obtained from the COVID-DSNet model, and 100 %, 96.30 %, and 96.58 % sensitivity values were obtained in the detection of typical, common pneumonia and COVID-19, respectively. The proposed model is an economical, practical deep learning network that data scientists can benefit from and develop. Although it is not a definitive solution in disease diagnosis, it may help experts as it produces successful results in detecting pneumonia and COVID-19.
Classification and visual explanation for COVID-19 pneumonia from CT images using triple learning.
Authors: SotaKato, MasahiroOda, KensakuMori, AkinobuShimizu, YoshitoOtake, MasahiroHashimoto, ToshiakiAkashi, KazuhiroHotta
Journal: Scientific reports

This study presents a novel framework for classifying and visualizing pneumonia induced by COVID-19 from CT images. Although many image classification methods using deep learning have been proposed, in the case of medical image fields, standard classification methods are unable to be used in some cases because the medical images that belong to the same category vary depending on the progression of the symptoms and the size of the inflamed area. In addition, it is essential that the models used be transparent and explainable, allowing health care providers to trust the models and avoid mistakes. In this study, we propose a classification method using contrastive learning and an attention mechanism. Contrastive learning is able to close the distance for images of the same category and generate a better feature space for classification. An attention mechanism is able to emphasize an important area in the image and visualize the location related to classification. Through experiments conducted on two-types of classification using a three-fold cross validation, we confirmed that the classification accuracy was significantly improved; in addition, a detailed visual explanation was achieved comparison with conventional methods.
A lightweight network for COVID-19 detection in X-ray images.
Authors: YongShi, AndaTang, YangXiao, LingfengNiu
Journal: Methods (San Diego, Calif.)

The Novel Coronavirus 2019 (COVID-19) is a global pandemic which has a devastating impact. Due to its quick transmission, a prominent challenge in confronting this pandemic is the rapid diagnosis. Currently, the commonly-used diagnosis is the specific molecular tests aided with the medical imaging modalities such as chest X-ray (CXR). However, with the large demand, the diagnoses of CXR are time-consuming and laborious. Deep learning is promising for automatically diagnosing COVID-19 to ease the burden on medical systems. At present, the most applied neural networks are large, which hardly satisfy the rapid yet inexpensive requirements of COVID-19 detection. To reduce huge computation and memory demands, in this paper, we focus on implementing lightweight networks for COVID-19 detection in CXR. Concretely, we first augment data based on clinical visual features of CXR from expertise. Then, according to the fact that all the input data are CXR, we design a targeted four-layer network with either 11 × 11 or 3 × 3 kernels to recognize regional features and detail features. A pruning criterion based on the weights importance is also proposed to further prune the network. Experiments on a public COVID-19 dataset validate the effectiveness and efficiency of the proposed method.
Radiomorphological signs and clinical severity of SARS-CoV-2 lineage B.1.1.7.
Authors: JuditSimon, KajetanGrodecki, SebastianCadet, AdityaKillekar, PiotrSlomka, Samuel JamesZara, EmeseZsarnóczay, ChiaraNardocci, NorbertNagy, KatalinKristóf, BarnaVásárhelyi, VeronikaMüller, BélaMerkely, DaminiDey, PálMaurovich-Horvat
Journal: BJR open

We aimed to assess the differences in the severity and chest-CT radiomorphological signs of SARS-CoV-2 B.1.1.7 and non-B.1.1.7 variants.
We collected clinical data of consecutive patients with laboratory-confirmed COVID-19 and chest-CT imaging who were admitted to the Emergency Department between September 1- November 13, 2020 (non-B.1.1.7 cases) and March 1-March 18, 2021 (B.1.1.7 cases). We also examined the differences in the severity and radiomorphological features associated with COVID-19 pneumonia. Total pneumonia burden (%), mean attenuation of ground-glass opacities and consolidation were quantified using deep-learning research software.
The final population comprised 500 B.1.1.7 and 500 non-B.1.1.7 cases. Patients with B.1.1.7 infection were younger (58.5 ± 15.6 vs 64.8 ± 17.3; 
Despite B.1.1.7 patients were younger and had fewer comorbidities, they experienced more severe disease than non-B.1.1.7 patients, however, the risk of death was the same between the two groups.
Our study provides data on deep-learning based quantitative lung lesion burden and clinical outcomes of patients infected by B.1.1.7 VOC. Our findings might serve as a model for later investigations, as new variants are emerging across the globe.
3D CT-Inclusive Deep-Learning Model to Predict Mortality, ICU Admittance, and Intubation in COVID-19 Patients.
Authors: AlbertoDi Napoli, EmanuelaTagliente, LucaPasquini, EnricaCipriano, FilomenaPietrantonio, PiermariaOrtis, SimonaCurti, AlessandroBoellis, TeseoStefanini, AntonioBernardini, ChiaraAngeletti, Sofia ChiatamoneRanieri, PaolaFranchi, Ioan PaulVoicu, CarloCapotondi, AntonioNapolitano
Journal: Journal of digital imaging

Chest CT is a useful initial exam in patients with coronavirus disease 2019 (COVID-19) for assessing lung damage. AI-powered predictive models could be useful to better allocate resources in the midst of the pandemic. Our aim was to build a deep-learning (DL) model for COVID-19 outcome prediction inclusive of 3D chest CT images acquired at hospital admission. This retrospective multicentric study included 1051 patients (mean age 69, SD = 15) who presented to the emergency department of three different institutions between 20th March 2020 and 20th January 2021 with COVID-19 confirmed by real-time reverse transcriptase polymerase chain reaction (RT-PCR). Chest CT at hospital admission were evaluated by a 3D residual neural network algorithm. Training, internal validation, and external validation groups included 608, 153, and 290 patients, respectively. Images, clinical, and laboratory data were fed into different customizations of a dense neural network to choose the best performing architecture for the prediction of mortality, intubation, and intensive care unit (ICU) admission. The AI model tested on CT and clinical features displayed accuracy, sensitivity, specificity, and ROC-AUC, respectively, of 91.7%, 90.5%, 92.4%, and 95% for the prediction of patient's mortality; 91.3%, 91.5%, 89.8%, and 95% for intubation; and 89.6%, 90.2%, 86.5%, and 94% for ICU admission (internal validation) in the testing cohort. The performance was lower in the validation cohort for mortality (71.7%, 55.6%, 74.8%, 72%), intubation (72.6%, 74.7%, 45.7%, 64%), and ICU admission (74.7%, 77%, 46%, 70%) prediction. The addition of the available laboratory data led to an increase in sensitivity for patient's mortality (66%) and specificity for intubation and ICU admission (50%, 52%, respectively), while the other metrics maintained similar performance results. We present a deep-learning model to predict mortality, ICU admittance, and intubation in COVID-19 patients. KEY POINTS: • 3D CT-based deep learning model predicted the internal validation set with high accuracy, sensibility and specificity (> 90%) mortality, ICU admittance, and intubation in COVID-19 patients. • The model slightly increased prediction results when laboratory data were added to the analysis, despite data imbalance. However, the model accuracy dropped when CT images were not considered in the analysis, implying an important role of CT in predicting outcomes.
Automatic detection of Covid-19 from chest X-ray and lung computed tomography images using deep neural networks and transfer learning.
Authors: Linh TDuong, Phuong TNguyen, LudovicoIovino, MicheleFlammini
Journal: Applied soft computing

The world has been undergoing the most ever unprecedented circumstances caused by the coronavirus pandemic, which is having a devastating global effect in different aspects of life. Since there are not effective antiviral treatments for Covid-19 yet, it is crucial to early detect and monitor the progression of the disease, thereby helping to reduce mortality. While different measures are being used to combat the virus, medical imaging techniques have been examined to support doctors in diagnosing the disease. In this paper, we present a practical solution for the detection of Covid-19 from chest X-ray (CXR) and lung computed tomography (LCT) images, exploiting cutting-edge Machine Learning techniques. As the main classification engine, we make use of EfficientNet and MixNet, two recently developed families of deep neural networks. Furthermore, to make the training more effective and efficient, we apply three transfer learning algorithms. The ultimate aim is to build a reliable expert system to detect Covid-19 from different sources of images, making it be a multi-purpose AI diagnosing system. We validated our proposed approach using four real-world datasets. The first two are CXR datasets consist of 15,000 and 17,905 images, respectively. The other two are LCT datasets with 2,482 and 411,528 images, respectively. The five-fold cross-validation methodology was used to evaluate the approach, where the dataset is split into five parts, and accordingly the evaluation is conducted in five rounds. By each evaluation, four parts are combined to form the training data, and the remaining one is used for testing. We obtained an encouraging prediction performance for all the considered datasets. In all the configurations, the obtained accuracy is always larger than 95.0%. Compared to various existing studies, our approach yields a substantial performance gain. Moreover, such an improvement is statistically significant.
Mentoring within the medical radiation sciences - Establishing a national program.
Authors: AllieTonks, FranziskaJerjen
Journal: Journal of medical imaging and radiation sciences

The aim of this study was to compare the accuracy and performance of 12 pre-trained deep learning models for classifying covid-19 and normal chest X-ray images from Kaggle.
a desktop computer with an Intel CPU i9-10900 2.80GHz and NVIDIA GPU GeForce RTX2070 SUPER, Anaconda3 software with 12 pre-trained models including VGG16, VGG19, DenseNet121, DenseNet169, DenseNet201, RestNet50V2, RestNet101V2, RestNet152V2, InceptionRestnetV2, InceptionV3, XceptionV1 and MobileNetV2, covid-19 and normal chest X-ray from Kaggle website.
the images were divided into three sets of train, test, and validation sets using a ratio of 70:20:10, respectively. The performance was recorded for each pre-train model with hyperparameters of epoch, batch size, and learning rate as 16, 16 and 0.0001 respectively. The prediction results of each model were recorded and compared.
from the results of all 12 pre-trained deep learning model, five models that have highest validation accuracy were DenseNet169, DenseNet201, InceptionV3, DenseNet121 and InceptionRestNetV2, respectively.
The top-5 highest accuracy models for classifying the COVID-19 were DenseNet169, DenseNet201, InceptionV3, DenseNet121 and InceptionRestnetV2 with accuracies of 95.4%, 95.07%, 94.73%, 94.51% and 93.61% respectively.
Optimal Ensemble learning model for COVID-19 detection using chest X-ray images.
Authors: SBalasubramaniam, KSatheesh Kumar
Journal: Biomedical signal processing and control

COVID-19 pandemic is the main outbreak in the world, which has shown a bad impact on people's lives in more than 150 countries. The major steps in fighting COVID-19 are identifying the affected patients as early as possible and locating them with special care. Images from radiology and radiography are among the most effective tools for determining a patient's ailment. Recent studies have shown detailed abnormalities of affected patients with COVID-19 in the chest radiograms. The purpose of this work is to present a COVID-19 detection system with three key steps: "(i) preprocessing, (ii) Feature extraction, (iii) Classification." Originally, the input image is given to the preprocessing step as its input, extracting the deep features and texture features from the preprocessed image. Particularly, it extracts the deep features by inceptionv3. Then, the features like proposed Local Vector Patterns (LVP) and Local Binary Pattern (LBP) are extracted from the preprocessed image. Moreover, the extracted features are subjected to the proposed ensemble model based classification phase, including Support Vector Machine (SVM), Convolutional Neural Network (CNN), Optimized Neural Network (NN), and Random Forest (RF). A novel Self Adaptive Kill Herd Optimization (SAKHO) approach is used to properly tune the weight of NN to improve classification accuracy and precision. The performance of the proposed method is then compared to the performance of the conventional approaches using a variety of metrics, including recall, FNR, MCC, FDR, Thread score, FPR, precision, FOR, accuracy, specificity, NPV, FMS, and sensitivity, accordingly.
Deep Learning-Based Computer-Aided Diagnosis (CAD): Applications for Medical Image Datasets.
Authors: Yezi AliKadhim, Muhammad UmerKhan, AlokMishra
Journal: Sensors (Basel, Switzerland)

Computer-aided diagnosis (CAD) has proved to be an effective and accurate method for diagnostic prediction over the years. This article focuses on the development of an automated CAD system with the intent to perform diagnosis as accurately as possible. Deep learning methods have been able to produce impressive results on medical image datasets. This study employs deep learning methods in conjunction with meta-heuristic algorithms and supervised machine-learning algorithms to perform an accurate diagnosis. Pre-trained convolutional neural networks (CNNs) or auto-encoder are used for feature extraction, whereas feature selection is performed using an ant colony optimization (ACO) algorithm. Ant colony optimization helps to search for the best optimal features while reducing the amount of data. Lastly, diagnosis prediction (classification) is achieved using learnable classifiers. The novel framework for the extraction and selection of features is based on deep learning, auto-encoder, and ACO. The performance of the proposed approach is evaluated using two medical image datasets: chest X-ray (CXR) and magnetic resonance imaging (MRI) for the prediction of the existence of COVID-19 and brain tumors. Accuracy is used as the main measure to compare the performance of the proposed approach with existing state-of-the-art methods. The proposed system achieves an average accuracy of 99.61% and 99.18%, outperforming all other methods in diagnosing the presence of COVID-19 and brain tumors, respectively. Based on the achieved results, it can be claimed that physicians or radiologists can confidently utilize the proposed approach for diagnosing COVID-19 patients and patients with specific brain tumors.