pt-sk/ml_research_abs huggingface dataset:
COVID-19 detection from chest x-ray using MobileNet and residual separable convolution block.
Authors: V Santhosh KumarTangudu, JagadeeshKakarla, Isunuri BalaVenkateswarlu
Journal: Soft computing

A newly emerged coronavirus disease affects the social and economical life of the world. This virus mainly infects the respiratory system and spreads with airborne communication. Several countries witness the serious consequences of the COVID-19 pandemic. Early detection of COVID-19 infection is the critical step to survive a patient from death. The chest radiography examination is the fast and cost-effective way for COVID-19 detection. Several researchers have been motivated to automate COVID-19 detection and diagnosis process using chest x-ray images. However, existing models employ deep networks and are suffering from high training time. This work presents transfer learning and residual separable convolution block for COVID-19 detection. The proposed model utilizes pre-trained MobileNet for binary image classification. The proposed residual separable convolution block has improved the performance of basic MobileNet. Two publicly available datasets COVID5K, and COVIDRD have considered for the evaluation of the proposed model. Our proposed model exhibits superior performance than existing state-of-art and pre-trained models with 99% accuracy on both datasets. We have achieved similar performance on noisy datasets. Moreover, the proposed model outperforms existing pre-trained models with less training time and competitive performance than basic MobileNet. Further, our model is suitable for mobile applications as it uses fewer parameters and lesser training time.
COVID-19 CT image recognition algorithm based on transformer and CNN.
Authors: XiaoleFan, XiufangFeng, YunyunDong, HuichaoHou
Journal: Displays

Novel corona virus pneumonia (COVID-19) broke out in 2019, which had a great impact on the development of world economy and people's lives. As a new mainstream image processing method, deep learning network has been constructed to extract medical features from chest CT images, and has been used as a new detection method in clinical practice. However, due to the medical characteristics of COVID-19 CT images, the lesions are widely distributed and have many local features. Therefore, it is difficult to diagnose directly by using the existing deep learning model. According to the medical features of CT images in COVID-19, a parallel bi-branch model (Trans-CNN Net) based on Transformer module and Convolutional Neural Network module is proposed by making full use of the local feature extraction capability of Convolutional Neural Network and the global feature extraction advantage of Transformer. According to the principle of cross-fusion, a bi-directional feature fusion structure is designed, in which features extracted from two branches are fused bi-directionally, and the parallel structures of branches are fused by a feature fusion module, forming a model that can extract features of different scales. To verify the effect of network classification, the classification accuracy on COVIDx-CT dataset is 96.7%, which is obviously higher than that of typical CNN network (ResNet-152) (95.2%) and Transformer network (Deit-B) (75.8%). These results demonstrate accuracy is improved. This model also provides a new method for the diagnosis of COVID-19, and through the combination of deep learning and medical imaging, it promotes the development of real-time diagnosis of lung diseases caused by COVID-19 infection, which is helpful for reliable and rapid diagnosis, thus saving precious lives.
Feasibility study of multi-site split learning for privacy-preserving medical systems under data imbalance constraints in COVID-19, X-ray, and cholesterol dataset.
Authors: Yoo JeongHa, GusangLee, MinjaeYoo, SoyiJung, SeehwanYoo, JoongheonKim
Journal: Scientific reports

It seems as though progressively more people are in the race to upload content, data, and information online; and hospitals haven't neglected this trend either. Hospitals are now at the forefront for multi-site medical data sharing to provide ground-breaking advancements in the way health records are shared and patients are diagnosed. Sharing of medical data is essential in modern medical research. Yet, as with all data sharing technology, the challenge is to balance improved treatment with protecting patient's personal information. This paper provides a novel split learning algorithm coined the term, "multi-site split learning", which enables a secure transfer of medical data between multiple hospitals without fear of exposing personal data contained in patient records. It also explores the effects of varying the number of end-systems and the ratio of data-imbalance on the deep learning performance. A guideline for the most optimal configuration of split learning that ensures privacy of patient data whilst achieving performance is empirically given. We argue the benefits of our multi-site split learning algorithm, especially regarding the privacy preserving factor, using CT scans of COVID-19 patients, X-ray bone scans, and cholesterol level medical data.
A fuzzy-enhanced deep learning approach for early detection of Covid-19 pneumonia from portable chest X-ray images.
Authors: CosimoIeracitano, NadiaMammone, MarioVersaci, GiuseppeVarone, Abder-RahmanAli, AntonioArmentano, GraziaCalabrese, AnnaFerrarelli, LorenaTurano, CarmelaTebala, ZainHussain, ZakariyaSheikh, AzizSheikh, GiuseppeSceni, AmirHussain, Francesco CarloMorabito
Journal: Neurocomputing

The Covid-19 pandemic is the defining global health crisis of our time. Chest X-Rays (CXR) have been an important imaging modality for assisting in the diagnosis and management of hospitalised Covid-19 patients. However, their interpretation is time intensive for radiologists. Accurate computer aided systems can facilitate early diagnosis of Covid-19 and effective triaging. In this paper, we propose a fuzzy logic based deep learning (DL) approach to differentiate between CXR images of patients with Covid-19 pneumonia and with interstitial pneumonias not related to Covid-19. The developed model here, referred to as
COVID-19 diagnosis using state-of-the-art CNN architecture features and Bayesian Optimization.
Authors: Muhammet FatihAslan, KadirSabanci, AkifDurdu, Muhammed FahriUnlersen
Journal: Computers in biology and medicine

The coronavirus outbreak 2019, called COVID-19, which originated in Wuhan, negatively affected the lives of millions of people and many people died from this infection. To prevent the spread of the disease, which is still in effect, various restriction decisions have been taken all over the world. In addition, the number of COVID-19 tests has been increased to quarantine infected people. However, due to the problems encountered in the supply of RT-PCR tests and the ease of obtaining Computed Tomography and X-ray images, imaging-based methods have become very popular in the diagnosis of COVID-19. Therefore, studies using these images to classify COVID-19 have increased. This paper presents a classification method for computed tomography chest images in the COVID-19 Radiography Database using features extracted by popular Convolutional Neural Networks (CNN) models (AlexNet, ResNet18, ResNet50, Inceptionv3, Densenet201, Inceptionresnetv2, MobileNetv2, GoogleNet). The determination of hyperparameters of Machine Learning (ML) algorithms by Bayesian optimization, and ANN-based image segmentation are the two main contributions in this study. First of all, lung segmentation is performed automatically from the raw image with Artificial Neural Networks (ANNs). To ensure data diversity, data augmentation is applied to the COVID-19 classes, which are fewer than the other two classes. Then these images are applied as input to five different CNN models. The features extracted from each CNN model are given as input to four different ML algorithms, namely Support Vector Machine (SVM), k-Nearest Neighbors (k-NN), Naive Bayes (NB), and Decision Tree (DT) for classification. To achieve the most successful classification accuracy, the hyperparameters of each ML algorithm are determined using Bayesian optimization. With the classification made using these hyperparameters, the highest success is obtained as 96.29% with the DenseNet201 model and SVM algorithm. The Sensitivity, Precision, Specificity, MCC, and F1-Score metric values for this structure are 0.9642, 0.9642, 0.9812, 0.9641 and 0.9453, respectively. These results showed that ML methods with the most optimum hyperparameters can produce successful results.
Efficient and visualizable convolutional neural networks for COVID-19 classification using Chest CT.
Authors: AkshGarg, SanaSalehi, Marianna LaRocca, RachaelGarner, DominiqueDuncan
Journal: Expert systems with applications

With coronavirus disease 2019 (COVID-19) cases rising rapidly, deep learning has emerged as a promising diagnosis technique. However, identifying the most accurate models to characterize COVID-19 patients is challenging because comparing results obtained with different types of data and acquisition processes is non-trivial. In this paper we designed, evaluated, and compared the performance of 20 convolutional neutral networks in classifying patients as COVID-19 positive, healthy, or suffering from other pulmonary lung infections based on chest computed tomography (CT) scans, serving as the first to consider the EfficientNet family for COVID-19 diagnosis and employ intermediate activation maps for visualizing model performance. All models are trained and evaluated in Python using 4173 chest CT images from the dataset entitled "A COVID multiclass dataset of CT scans," with 2168, 758, and 1247 images of patients that are COVID-19 positive, healthy, or suffering from other pulmonary infections, respectively. EfficientNet-B5 was identified as the best model with an F1 score of 0.9769 ± 0.0046, accuracy of 0.9759 ± 0.0048, sensitivity of 0.9788 ± 0.0055, specificity of 0.9730 ± 0.0057, and precision of 0.9751 ± 0.0051. On an alternate 2-class dataset, EfficientNetB5 obtained an accuracy of 0.9845 ± 0.0109, F1 score of 0.9599 ± 0.0251, sensitivity of 0.9682 ± 0.0099, specificity of 0.9883 ± 0.0150, and precision of 0.9526 ± 0.0523. Intermediate activation maps and Gradient-weighted Class Activation Mappings offered human-interpretable evidence of the model's perception of ground-class opacities and consolidations, hinting towards a promising use-case of artificial intelligence-assisted radiology tools. With a prediction speed of under 0.1 s on GPUs and 0.5 s on CPUs, our proposed model offers a rapid, scalable, and accurate diagnostic for COVID-19.
SAM: Self-augmentation mechanism for COVID-19 detection using chest X-ray images.
Authors: UsmanMuhammad, Md ZiaulHoque, MouradOussalah, AnjaKeskinarkaus, TapioSeppänen, PinakiSarder
Journal: Knowledge-based systems

COVID-19 is a rapidly spreading viral disease and has affected over 100 countries worldwide. The numbers of casualties and cases of infection have escalated particularly in countries with weakened healthcare systems. Recently, reverse transcription-polymerase chain reaction (RT-PCR) is the test of choice for diagnosing COVID-19. However, current evidence suggests that COVID-19 infected patients are mostly stimulated from a lung infection after coming in contact with this virus. Therefore, chest X-ray (i.e., radiography) and chest CT can be a surrogate in some countries where PCR is not readily available. This has forced the scientific community to detect COVID-19 infection from X-ray images and recently proposed machine learning methods offer great promise for fast and accurate detection. Deep learning with convolutional neural networks (CNNs) has been successfully applied to radiological imaging for improving the accuracy of diagnosis. However, the performance remains limited due to the lack of representative X-ray images available in public benchmark datasets. To alleviate this issue, we propose a self-augmentation mechanism for data augmentation in the feature space rather than in the data space using reconstruction independent component analysis (RICA). Specifically, a unified architecture is proposed which contains a deep convolutional neural network (CNN), a feature augmentation mechanism, and a bidirectional LSTM (BiLSTM). The CNN provides the high-level features extracted at the pooling layer where the augmentation mechanism chooses the most relevant features and generates low-dimensional augmented features. Finally, BiLSTM is used to classify the processed sequential information. We conducted experiments on three publicly available databases to show that the proposed approach achieves the state-of-the-art results with accuracy of 97%, 84% and 98%. Explainability analysis has been carried out using feature visualization through PCA projection and t-SNE plots.
Contour-enhanced attention CNN for CT-based COVID-19 segmentation.
Authors: RKarthik, RMenaka, HariharanM, DaehanWon
Journal: Pattern recognition

Accurate detection of COVID-19 is one of the challenging research topics in today's healthcare sector to control the coronavirus pandemic. Automatic data-powered insights for COVID-19 localization from medical imaging modality like chest CT scan tremendously augment clinical care assistance. In this research, a Contour-aware Attention Decoder CNN has been proposed to precisely segment COVID-19 infected tissues in a very effective way. It introduces a novel attention scheme to extract boundary, shape cues from CT contours and leverage these features in refining the infected areas. For every decoded pixel, the attention module harvests contextual information in its spatial neighborhood from the contour feature maps. As a result of incorporating such rich structural details into decoding via dense attention, the CNN is able to capture even intricate morphological details. The decoder is also augmented with a Cross Context Attention Fusion Upsampling to robustly reconstruct deep semantic features back to high-resolution segmentation map. It employs a novel pixel-precise attention model that draws relevant encoder features to aid in effective upsampling. The proposed CNN was evaluated on 3D scans from MosMedData and Jun Ma benchmarked datasets. It achieved state-of-the-art performance with a high dice similarity coefficient of 85.43% and a recall of 88.10%.
COVID-19 detection in CT and CXR images using deep learning models.
Authors: InesChouat, AmiraEchtioui, RafikKhemakhem, WassimZouch, MohamedGhorbel, Ahmed BenHamida
Journal: Biogerontology

Infectious diseases pose a threat to human life and could affect the whole world in a very short time. Corona-2019 virus disease (COVID-19) is an example of such harmful diseases. COVID-19 is a pandemic of an emerging infectious disease, called coronavirus disease 2019 or COVID-19, caused by the coronavirus SARS-CoV-2, which first appeared in December 2019 in Wuhan, China, before spreading around the world on a very large scale. The continued rise in the number of positive COVID-19 cases has disrupted the health care system in many countries, creating a lot of stress for governing bodies around the world, hence the need for a rapid way to identify cases of this disease. Medical imaging is a widely accepted technique for early detection and diagnosis of the disease which includes different techniques such as Chest X-ray (CXR), Computed Tomography (CT) scan, etc. In this paper, we propose a methodology to investigate the potential of deep transfer learning in building a classifier to detect COVID-19 positive patients using CT scan and CXR images. Data augmentation technique is used to increase the size of the training dataset in order to solve overfitting and enhance generalization ability of the model. Our contribution consists of a comprehensive evaluation of a series of pre-trained deep neural networks: ResNet50, InceptionV3, VGGNet-19, and Xception, using data augmentation technique. The findings proved that deep learning is effective at detecting COVID-19 cases. From the results of the experiments it was found that by considering each modality separately, the VGGNet-19 model outperforms the other three models proposed by using the CT image dataset where it achieved  88.5% precision, 86% recall, 86.5% F1-score, and 87% accuracy while the refined Xception version gave the highest precision, recall, F1-score, and accuracy values which equal 98% using CXR images dataset. On the other hand, and by applying the average of the two modalities X-ray and CT, VGG-19 presents the best score which is 90.5% for the accuracy and the F1-score, 90.3% for the recall while the precision is 91.5%. These results enables to automatize the process of analyzing chest CT scans and X-ray images with high accuracy and can be used in cases where RT-PCR testing and materials are limited.
Using a Deep Learning Model to Explore the Impact of Clinical Data on COVID-19 Diagnosis Using Chest X-ray.
Authors: Irfan UllahKhan, NidaAslam, TalhaAnwar, Hind SAlsaif, Sara Mhd BacharChrouf, Norah AAlzahrani, Fatimah AhmedAlamoudi, Mariam Moataz AlyKamaleldin, Khaled BassamAwary
Journal: Sensors (Basel, Switzerland)

The coronavirus pandemic (COVID-19) is disrupting the entire world; its rapid global spread threatens to affect millions of people. Accurate and timely diagnosis of COVID-19 is essential to control the spread and alleviate risk. Due to the promising results achieved by integrating machine learning (ML), particularly deep learning (DL), in automating the multiple disease diagnosis process. In the current study, a model based on deep learning was proposed for the automated diagnosis of COVID-19 using chest X-ray images (CXR) and clinical data of the patient. The aim of this study is to investigate the effects of integrating clinical patient data with the CXR for automated COVID-19 diagnosis. The proposed model used data collected from King Fahad University Hospital, Dammam, KSA, which consists of 270 patient records. The experiments were carried out first with clinical data, second with the CXR, and finally with clinical data and CXR. The fusion technique was used to combine the clinical features and features extracted from images. The study found that integrating clinical data with the CXR improves diagnostic accuracy. Using the clinical data and the CXR, the model achieved an accuracy of 0.970, a recall of 0.986, a precision of 0.978, and an F-score of 0.982. Further validation was performed by comparing the performance of the proposed system with the diagnosis of an expert. Additionally, the results have shown that the proposed system can be used as a tool that can help the doctors in COVID-19 diagnosis.
Automated detection of COVID-19 through convolutional neural network using chest x-ray images.
Authors: RubinaSarki, KhandakarAhmed, HuaWang, YanchunZhang, KateWang
Journal: PloS one

The COVID-19 epidemic has a catastrophic impact on global well-being and public health. More than 27 million confirmed cases have been reported worldwide until now. Due to the growing number of confirmed cases, and challenges to the variations of the COVID-19, timely and accurate classification of healthy and infected patients is essential to control and treat COVID-19. We aim to develop a deep learning-based system for the persuasive classification and reliable detection of COVID-19 using chest radiography. Firstly, we evaluate the performance of various state-of-the-art convolutional neural networks (CNNs) proposed over recent years for medical image classification. Secondly, we develop and train CNN from scratch. In both cases, we use a public X-Ray dataset for training and validation purposes. For transfer learning, we obtain 100% accuracy for binary classification (i.e., Normal/COVID-19) and 87.50% accuracy for tertiary classification (Normal/COVID-19/Pneumonia). With the CNN trained from scratch, we achieve 93.75% accuracy for tertiary classification. In the case of transfer learning, the classification accuracy drops with the increased number of classes. The results are demonstrated by comprehensive receiver operating characteristics (ROC) and confusion metric analysis with 10-fold cross-validation.
COVID-19 detection using chest X-ray images based on a developed deep neural network.
Authors: ZohrehMousavi, NahalShahini, SobhanSheykhivand, SinaMojtahedi, AfroozArshadi
Journal: SLAS technology

Currently, a new coronavirus called COVID-19 is the biggest challenge of the human at 21st century. Now, the spread of this virus is such that mortality has risen strongly in all cities of countries. Therefore, it is necessary to think of a solution to handle the disease by fast and timely diagnosis. This paper proposes a method that uses chest X-ray imagery to divide 2-4 classes into 7 different Scenarios, including Bacterial, Viral, Healthy, and COVID-19 classes. The aim of this study is to propose a method that uses chest X-ray imagery to divide 2-4 classes into 7 different Scenarios, including Bacterial, Viral, Healthy, and COVID-19 classes.
6 different databases from chest X-ray imagery that have been widely used in recent studies have been gathered for this aim. A Convolutional Neural Network-Long Short Time Memory model is designed and developed to extract features from raw data hierarchically. In order to make more realistic assumptions and use the Proposed Method in the practical field, white Gaussian noise is added to the raw chest X-ray imagery. Additionally, the proposed network is tested and investigated not only on 6 expressed databases but also on two additional databases.
On the test set, the proposed network achieved an accuracy of more than 90% for all Scenarios excluding Scenario V, i.e. Healthy against the COVID-19 against the Viral, and also achieved 99% accuracy for separating the COVID-19 from the Healthy group. The results showed that the proposed network is robust to noise up to 1 dB. It is worth noting that the proposed network for two additional databases, which were only used as test databases, also achieved more than 90% accuracy. In addition, in comparison to the state-of-the-art pneumonia detection approaches, the final results obtained from the proposed network is so promising.
The proposed network is effective in detecting COVID-19 and other lung infectious diseases using chest X-ray imagery and can thus assist radiologists in making rapid and accurate detections.
Deep Learning-Based Four-Region Lung Segmentation in Chest Radiography for COVID-19 Diagnosis.
Authors: Young-GonKim, KyungsangKim, DufanWu, HuiRen, Won YoungTak, Soo YoungPark, Yu RimLee, Min KyuKang, Jung GilPark, Byung SeokKim, Woo JinChung, Mannudeep KKalra, QuanzhengLi
Journal: Diagnostics (Basel, Switzerland)

Imaging plays an important role in assessing the severity of COVID-19 pneumonia. Recent COVID-19 research indicates that the disease progress propagates from the bottom of the lungs to the top. However, chest radiography (CXR) cannot directly provide a quantitative metric of radiographic opacities, and existing AI-assisted CXR analysis methods do not quantify the regional severity. In this paper, to assist the regional analysis, we developed a fully automated framework using deep learning-based four-region segmentation and detection models to assist the quantification of COVID-19 pneumonia. Specifically, a segmentation model is first applied to separate left and right lungs, and then a detection network of the carina and left hilum is used to separate upper and lower lungs. To improve the segmentation performance, an ensemble strategy with five models is exploited. We evaluated the clinical relevance of the proposed method compared with the radiographic assessment of the quality of lung edema (RALE) annotated by physicians. Mean intensities of segmented four regions indicate a positive correlation to the regional extent and density scores of pulmonary opacities based on the RALE. Therefore, the proposed method can accurately assist the quantification of regional pulmonary opacities of COVID-19 pneumonia patients.