pt-sk/ml_research_abs huggingface dataset:
CARes-UNet: Content-aware residual UNet for lesion segmentation of COVID-19 from chest CT images.
Authors: XinhuaXu, YuhangWen, LuZhao, YiZhang, YoujunZhao, ZixuanTang, ZiduoYang, Calvin Yu-ChianChen
Journal: Medical physics

Coronavirus disease 2019 (COVID-19) has caused a serious global health crisis. It has been proven that the deep learning method has great potential to assist doctors in diagnosing COVID-19 by automatically segmenting the lesions in computed tomography (CT) slices. However, there are still several challenges restricting the application of these methods, including high variation in lesion characteristics and low contrast between lesion areas and healthy tissues. Moreover, the lack of high-quality labeled samples and large number of patients lead to the urgency to develop a high accuracy model, which performs well not only under supervision but also with semi-supervised methods.
We propose a content-aware lung infection segmentation deep residual network (content-aware residual UNet (CARes-UNet)) to segment the lesion areas of COVID-19 from the chest CT slices. In our CARes-UNet, the residual connection was used in the convolutional block, which alleviated the degradation problem during the training. Then, the content-aware upsampling modules were introduced to improve the performance of the model while reducing the computation cost. Moreover, to achieve faster convergence, an advanced optimizer named Ranger was utilized to update the model's parameters during training. Finally, we employed a semi-supervised segmentation framework to deal with the problem of lacking pixel-level labeled data.
We evaluated our approach using three public datasets with multiple metrics and compared its performance to several models. Our method outperforms other models in multiple indicators, for instance in terms of Dice coefficient on COVID-SemiSeg Dataset, CARes-UNet got the score 0.731, and semi-CARes-UNet further boosted it to 0.776. More ablation studies were done and validated the effectiveness of each key component of our proposed model.
Compared with the existing neural network methods applied to the COVID-19 lesion segmentation tasks, our CARes-UNet can gain more accurate segmentation results, and semi-CARes-UNet can further improve it using semi-supervised learning methods while presenting a possible way to solve the problem of lack of high-quality annotated samples. Our CARes-UNet and semi-CARes-UNet can be used in artificial intelligence-empowered computer-aided diagnosis system to improve diagnostic accuracy in this ongoing COVID-19 pandemic.
Densely connected attention network for diagnosing COVID-19 based on chest CT.
Authors: YuFu, PengXue, EnqingDong
Journal: Computers in biology and medicine

To fully enhance the feature extraction capabilities of deep learning models, so as to accurately diagnose coronavirus disease 2019 (COVID-19) based on chest CT images, a densely connected attention network (DenseANet) was constructed by utilizing the self-attention mechanism in deep learning.
During the construction of the DenseANet, we not only densely connected attention features within and between the feature extraction blocks with the same scale, but also densely connected attention features with different scales at the end of the deep model, thereby further enhancing the high-order features. In this way, as the depth of the deep model increases, the spatial attention features generated by different layers can be densely connected and gradually transferred to deeper layers. The DenseANet takes CT images of the lung fields segmented by an improved U-Net as inputs and outputs the probability of the patients suffering from COVID-19.
Compared with exiting attention networks, DenseANet can maximize the utilization of self-attention features at different depths in the model. A five-fold cross-validation experiment was performed on a dataset containing 2993 CT scans of 2121 patients, and experiments showed that the DenseANet can effectively locate the lung lesions of patients infected with SARS-CoV-2, and distinguish COVID-19, common pneumonia and normal controls with an average of 96.06% Acc and 0.989 AUC.
The DenseANet we proposed can generate strong attention features and achieve the best diagnosis results. In addition, the proposed method of densely connecting attention features can be easily extended to other advanced deep learning methods to improve their performance in related tasks.
Genetic-based adaptive momentum estimation for predicting mortality risk factors for COVID-19 patients using deep learning.
Authors: Sally MElghamrawy, Aboul EllaHassanien, Athanasios VVasilakos
Journal: International journal of imaging systems and technology

The mortality risk factors for coronavirus disease (COVID-19) must be early predicted, especially for severe cases, to provide intensive care before they develop to critically ill immediately. This paper aims to develop an optimized convolution neural network (CNN) for predicting mortality risk factors for COVID-19 patients. The proposed model supports two types of input data clinical variables and the computed tomography (CT) scans. The features are extracted from the optimized CNN phase and then applied to the classification phase. The CNN model's hyperparameters were optimized using a proposed genetic-based adaptive momentum estimation (GB-ADAM) algorithm. The GB-ADAM algorithm employs the genetic algorithm (GA) to optimize Adam optimizer's configuration parameters, consequently improving the classification accuracy. The model is validated using three recent cohorts from New York, Mexico, and Wuhan, consisting of 3055, 7497,504 patients, respectively. The results indicated that the most significant mortality risk factors are: CD
A novel and efficient deep learning approach for COVID-19 detection using X-ray imaging modality.
Authors: PrashantBhardwaj, AmanpreetKaur
Journal: International journal of imaging systems and technology

With the exponential growth of COVID-19 cases, medical practitioners are searching for accurate and quick automated detection methods to prevent Covid from spreading while trying to reduce the computational requirement of devices. In this research article, a deep learning Convolutional Neural Network (CNN) based accurate and efficient ensemble model using deep learning is being proposed with 2161 COVID-19, 2022 pneumonia, and 5863 normal chest X-ray images that has been collected from previous publications and other online resources. To improve the detection accuracy contrast enhancement and image normalization have been done to produce better quality images at the pre-processing level. Further data augmentation methods are used by creating modified versions of images in the dataset to train the four efficient CNN models (Inceptionv3, DenseNet121, Xception, InceptionResNetv2) Experimental results provide 98.33% accuracy for binary class and 92.36% for multiclass. The performance evaluation metrics reveal that this tool can be very helpful for early disease diagnosis.
A Novel Multicolor-thresholding Auto-detection Method to Detect the Location and Severity of Inflammation in Confirmed SARS-COV-2 Cases using Chest X-Ray Images.
Authors: Mohammed SAlqahtani, Mohamed AAbbas, Ali MAlqahtani, Mohammad YAlshahrani, Abdulhadi JAlkulib, Magbool AAlelyani, Awad MAlmarhaby
Journal: Current medical imaging

Since late 2019, Coronavirus Disease 2019 (COVID-19) has spread around the world. It has been determined that the disease is very contagious and can cause Acute Respiratory Distress (ARD). Medical imaging has the potential to help identify, detect, and quantify the severity of this infection. This work seeks to develop a novel auto-detection technique for verified COVID-19 cases that can detect aberrant alterations in traditional X-ray pictures.
Nineteen separately colored layers were created from X-ray scans of patients diagnosed with COVID-19. Each layer represents objects that have a similar contrast and can be represented by a single color. In a single layer, objects with similar contrasts are formed. A single color image was created by extracting all the objects from all the layers. The prototype model could recognize a wide range of abnormal changes in the image texture based on color differentiation. This was true even when the contrast values of the detected unclear abnormalities varied slightly.
The results indicate that the proposed novel method is 91% accurate in detecting and grading COVID-19 lung infections compared to the opinions of three experienced radiologists evaluating chest X-ray images. Additionally, the method can be used to determine the infection site and severity of the disease by categorizing X-rays into five severity levels.
By comparing affected tissue to healthy tissue, the proposed COVID-19 auto-detection method can identify locations and indicate the severity of the disease, as well as predict where the disease may spread.
Classification of Lung Disease in Children by Using Lung Ultrasound Images and Deep Convolutional Neural Network.
Authors: SilviaMagrelli, PieroValentini, CristinaDe Rose, RosaMorello, DaniloBuonsenso
Journal: Frontiers in physiology

Bronchiolitis is the most common cause of hospitalization of children in the first year of life and pneumonia is the leading cause of infant mortality worldwide. Lung ultrasound technology (LUS) is a novel imaging diagnostic tool for the early detection of respiratory distress and offers several advantages due to its low-cost, relative safety, portability, and easy repeatability. More precise and efficient diagnostic and therapeutic strategies are needed. Deep-learning-based computer-aided diagnosis (CADx) systems, using chest X-ray images, have recently demonstrated their potential as a screening tool for pulmonary disease (such as COVID-19 pneumonia). We present the first computer-aided diagnostic scheme for LUS images of pulmonary diseases in children. In this study, we trained from scratch four state-of-the-art deep-learning models (VGG19, Xception, Inception-v3 and Inception-ResNet-v2) for detecting children with bronchiolitis and pneumonia. In our experiments we used a data set consisting of 5,907 images from 33 healthy infants, 3,286 images from 22 infants with bronchiolitis, and 4,769 images from 7 children suffering from bacterial pneumonia. Using four-fold cross-validation, we implemented one binary classification (healthy vs. bronchiolitis) and one three-class classification (healthy vs. bronchiolitis vs. bacterial pneumonia) out of three classes. Affine transformations were applied for data augmentation. Hyperparameters were optimized for the learning rate, dropout regularization, batch size, and epoch iteration. The Inception-ResNet-v2 model provides the highest classification performance, when compared with the other models used on test sets: for healthy vs. bronchiolitis, it provides 97.75% accuracy, 97.75% sensitivity, and 97% specificity whereas for healthy vs. bronchiolitis vs. bacterial pneumonia, the Inception-v3 model provides the best results with 91.5% accuracy, 91.5% sensitivity, and 95.86% specificity. We performed a gradient-weighted class activation mapping (Grad-CAM) visualization and the results were qualitatively evaluated by a pediatrician expert in LUS imaging: heatmaps highlight areas containing diagnostic-relevant LUS imaging-artifacts, e.g., A-, B-, pleural-lines, and consolidations. These complex patterns are automatically learnt from the data, thus avoiding hand-crafted features usage. By using LUS imaging, the proposed framework might aid in the development of an accessible and rapid decision support-method for diagnosing pulmonary diseases in children using LUS imaging.
Novel ensemble of optimized CNN and dynamic selection techniques for accurate Covid-19 screening using chest CT images.
Authors: SameenaPathan, P CSiddalingaswamy, PreethamKumar, ManoharaPai M M, TanweerAli, U RajendraAcharya
Journal: Computers in biology and medicine

The world is significantly affected by infectious coronavirus disease (covid-19). Timely prognosis and treatment are important to control the spread of this infection. Unreliable screening systems and limited number of clinical facilities are the major hurdles in controlling the spread of covid-19. Nowadays, many automated detection systems based on deep learning techniques using computed tomography (CT) images have been proposed to detect covid-19. However, these systems have the following drawbacks: (i) limited data problem poses a major hindrance to train the deep neural network model to provide accurate diagnosis, (ii) random choice of hyperparameters of Convolutional Neural Network (CNN) significantly affects the classification performance, since the hyperparameters have to be application dependent and, (iii) the generalization ability using CNN classification is usually not validated. To address the aforementioned issues, we propose two models: (i) based on a transfer learning approach, and (ii) using novel strategy to optimize the CNN hyperparameters using Whale optimization-based BAT algorithm + AdaBoost classifier built using dynamic ensemble selection techniques. According to our second method depending on the characteristics of test sample, the classifier is chosen, thereby reducing the risk of overfitting and simultaneously produced promising results. Our proposed methodologies are developed using 746 CT images. Our method obtained a sensitivity, specificity, accuracy, F-1 score, and precision of 0.98, 0.97, 0.98, 0.98, and 0.98, respectively with five-fold cross-validation strategy. Our developed prototype is ready to be tested with huge chest CT images database before its real-world application.
A multi-scale gated multi-head attention depthwise separable CNN model for recognizing COVID-19.
Authors: GengHong, XiaoyanChen, JianyongChen, MiaoZhang, YumengRen, XinyuZhang
Journal: Scientific reports

Coronavirus 2019 (COVID-19) is a new acute respiratory disease that has spread rapidly throughout the world. In this paper, a lightweight convolutional neural network (CNN) model named multi-scale gated multi-head attention depthwise separable CNN (MGMADS-CNN) is proposed, which is based on attention mechanism and depthwise separable convolution. A multi-scale gated multi-head attention mechanism is designed to extract effective feature information from the COVID-19 X-ray and CT images for classification. Moreover, the depthwise separable convolution layers are adopted as MGMADS-CNN's backbone to reduce the model size and parameters. The LeNet-5, AlexNet, GoogLeNet, ResNet, VGGNet-16, and three MGMADS-CNN models are trained, validated and tested with tenfold cross-validation on X-ray and CT images. The results show that MGMADS-CNN with three attention layers (MGMADS-3) has achieved accuracy of 96.75% on X-ray images and 98.25% on CT images. The specificity and sensitivity are 98.06% and 96.6% on X-ray images, and 98.17% and 98.05% on CT images. The size of MGMADS-3 model is only 43.6 M bytes. In addition, the detection speed of MGMADS-3 on X-ray images and CT images are 6.09 ms and 4.23 ms for per image, respectively. It is proved that the MGMADS-3 can detect and classify COVID-19 faster with higher accuracy and efficiency.
Recognition of COVID-19 from CT Scans Using Two-Stage Deep-Learning-Based Approach: CNR-IEMN.
Authors: FaresBougourzi, RiccardoContino, CosimoDistante, AbdelmalikTaleb-Ahmed
Journal: Sensors (Basel, Switzerland)

Since the appearance of the COVID-19 pandemic (at the end of 2019, Wuhan, China), the recognition of COVID-19 with medical imaging has become an active research topic for the machine learning and computer vision community. This paper is based on the results obtained from the 2021 COVID-19 SPGC challenge, which aims to classify volumetric CT scans into normal, COVID-19, or community-acquired pneumonia (Cap) classes. To this end, we proposed a deep-learning-based approach (CNR-IEMN) that consists of two main stages. In the first stage, we trained four deep learning architectures with a multi-tasks strategy for slice-level classification. In the second stage, we used the previously trained models with an XG-boost classifier to classify the whole CT scan into normal, COVID-19, or Cap classes. Our approach achieved a good result on the validation set, with an overall accuracy of 87.75% and 96.36%, 52.63%, and 95.83% sensitivities for COVID-19, Cap, and normal, respectively. On the other hand, our approach achieved fifth place on the three test datasets of SPGC in the COVID-19 challenge, where our approach achieved the best result for COVID-19 sensitivity. In addition, our approach achieved second place on two of the three testing sets.
On the Use of Deep Learning for Imaging-Based COVID-19 Detection Using Chest X-rays.
Authors: Gabriel IluebeOkolo, StamosKatsigiannis, TurkeAlthobaiti, NaeemRamzan
Journal: Sensors (Basel, Switzerland)

The global COVID-19 pandemic that started in 2019 and created major disruptions around the world demonstrated the imperative need for quick, inexpensive, accessible and reliable diagnostic methods that would allow the detection of infected individuals with minimal resources. Radiography, and more specifically, chest radiography, is a relatively inexpensive medical imaging modality that can potentially offer a solution for the diagnosis of COVID-19 cases. In this work, we examined eleven deep convolutional neural network architectures for the task of classifying chest X-ray images as belonging to healthy individuals, individuals with COVID-19 or individuals with viral pneumonia. All the examined networks are established architectures that have been proven to be efficient in image classification tasks, and we evaluated three different adjustments to modify the architectures for the task at hand by expanding them with additional layers. The proposed approaches were evaluated for all the examined architectures on a dataset with real chest X-ray images, reaching the highest classification accuracy of 98.04% and the highest F1-score of 98.22% for the best-performing setting.
AIforCOVID: Predicting the clinical outcomes in patients with COVID-19 applying AI to chest-X-rays. An Italian multicentre study.
Authors: PaoloSoda, Natascha ClaudiaD'Amico, JacopoTessadori, GiovanniValbusa, ValerioGuarrasi, ChandraBortolotto, Muhammad UsmanAkbar, RosaSicilia, ErmannoCordelli, DeborahFazzini, MichaelaCellina, GiancarloOliva, GiovanniCallea, SilviaPanella, MaurizioCariati, DilettaCozzi, VittorioMiele, ElviraStellato, GianpaoloCarrafiello, GiuliaCastorani, AnnalisaSimeone, LorenzoPreda, GiulioIannello, AlessioDel Bue, FabioTedoldi, MarcoAlí, DiegoSona, SergioPapa
Journal: Medical image analysis

Recent epidemiological data report that worldwide more than 53 million people have been infected by SARS-CoV-2, resulting in 1.3 million deaths. The disease has been spreading very rapidly and few months after the identification of the first infected, shortage of hospital resources quickly became a problem. In this work we investigate whether artificial intelligence working with chest X-ray (CXR) scans and clinical data can be used as a possible tool for the early identification of patients at risk of severe outcome, like intensive care or death. Indeed, further to induce lower radiation dose than computed tomography (CT), CXR is a simpler and faster radiological technique, being also more widespread. In this respect, we present three approaches that use features extracted from CXR images, either handcrafted or automatically learnt by convolutional neuronal networks, which are then integrated with the clinical data. As a further contribution, this work introduces a repository that collects data from 820 patients enrolled in six Italian hospitals in spring 2020 during the first COVID-19 emergency. The dataset includes CXR images, several clinical attributes and clinical outcomes. Exhaustive evaluation shows promising performance both in 10-fold and leave-one-centre-out cross-validation, suggesting that clinical data and images have the potential to provide useful information for the management of patients and hospital resources.
Pneumonia detection in chest X-ray images using an ensemble of deep learning models.
Authors: RohitKundu, RitachetaDas, Zong WooGeem, Gi-TaeHan, RamSarkar
Journal: PloS one

Pneumonia is a respiratory infection caused by bacteria or viruses; it affects many individuals, especially in developing and underdeveloped nations, where high levels of pollution, unhygienic living conditions, and overcrowding are relatively common, together with inadequate medical infrastructure. Pneumonia causes pleural effusion, a condition in which fluids fill the lung, causing respiratory difficulty. Early diagnosis of pneumonia is crucial to ensure curative treatment and increase survival rates. Chest X-ray imaging is the most frequently used method for diagnosing pneumonia. However, the examination of chest X-rays is a challenging task and is prone to subjective variability. In this study, we developed a computer-aided diagnosis system for automatic pneumonia detection using chest X-ray images. We employed deep transfer learning to handle the scarcity of available data and designed an ensemble of three convolutional neural network models: GoogLeNet, ResNet-18, and DenseNet-121. A weighted average ensemble technique was adopted, wherein the weights assigned to the base learners were determined using a novel approach. The scores of four standard evaluation metrics, precision, recall, f1-score, and the area under the curve, are fused to form the weight vector, which in studies in the literature was frequently set experimentally, a method that is prone to error. The proposed approach was evaluated on two publicly available pneumonia X-ray datasets, provided by Kermany et al. and the Radiological Society of North America (RSNA), respectively, using a five-fold cross-validation scheme. The proposed method achieved accuracy rates of 98.81% and 86.85% and sensitivity rates of 98.80% and 87.02% on the Kermany and RSNA datasets, respectively. The results were superior to those of state-of-the-art methods and our method performed better than the widely used ensemble techniques. Statistical analyses on the datasets using McNemar's and ANOVA tests showed the robustness of the approach. The codes for the proposed work are available at https://github.com/Rohit-Kundu/Ensemble-Pneumonia-Detection.
Cardiovascular CT and MRI in 2020: Review of Key Articles.
Authors: Gaurav SGulsin, NiallMcVeigh, Jonathon ALeipsic, Jonathan DDodd
Journal: Radiology

Despite the global coronavirus pandemic, cardiovascular imaging continued to evolve throughout 2020. It was an important year for cardiac CT and MRI, with increasing prominence in cardiovascular research, use in clinical decision making, and in guidelines. This review summarizes key publications in 2020 relevant to current and future clinical practice. In cardiac CT, these have again predominated in assessment of patients with chest pain and structural heart diseases, although more refined CT techniques, such as quantitative plaque analysis and CT perfusion, are also maturing. In cardiac MRI, the major developments have been in patients with cardiomyopathy and myocarditis, although coronary artery disease applications remain well represented. Deep learning applications in cardiovascular imaging have continued to advance in both CT and MRI, and these are now closer than ever to routine clinical adoption. Perhaps most important has been the rapid deployment of MRI in enhancing understanding of the impact of COVID-19 infection on the heart. Although this review focuses primarily on articles published in