pt-sk/ml_research_abs huggingface dataset:
Non-contrast CT synthesis using patch-based cycle-consistent generative adversarial network (Cycle-GAN) for radiomics and deep learning in the era of COVID-19.
Authors: RezaKalantar, SumeetHindocha, BenjaminHunter, BhupinderSharma, NasirKhan, Dow-MuKoh, MerinaAhmed, Eric OAboagye, Richard WLee, Matthew DBlackledge
Journal: Scientific reports

Handcrafted and deep learning (DL) radiomics are popular techniques used to develop computed tomography (CT) imaging-based artificial intelligence models for COVID-19 research. However, contrast heterogeneity from real-world datasets may impair model performance. Contrast-homogenous datasets present a potential solution. We developed a 3D patch-based cycle-consistent generative adversarial network (cycle-GAN) to synthesize non-contrast images from contrast CTs, as a data homogenization tool. We used a multi-centre dataset of 2078 scans from 1,650 patients with COVID-19. Few studies have previously evaluated GAN-generated images with handcrafted radiomics, DL and human assessment tasks. We evaluated the performance of our cycle-GAN with these three approaches. In a modified Turing-test, human experts identified synthetic vs acquired images, with a false positive rate of 67% and Fleiss' Kappa 0.06, attesting to the photorealism of the synthetic images. However, on testing performance of machine learning classifiers with radiomic features, performance decreased with use of synthetic images. Marked percentage difference was noted in feature values between pre- and post-GAN non-contrast images. With DL classification, deterioration in performance was observed with synthetic images. Our results show that whilst GANs can produce images sufficient to pass human assessment, caution is advised before GAN-synthesized images are used in medical imaging applications.
Explainable COVID-19 Detection Based on Chest X-rays Using an End-to-End RegNet Architecture.
Authors: MohamedChetoui, Moulay AAkhloufi, El MostafaBouattane, JosephAbdulnour, StephaneRoux, Chantal D'AoustBernard
Journal: Viruses

COVID-19,which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is one of the worst pandemics in recent history. The identification of patients suspected to be infected with COVID-19 is becoming crucial to reduce its spread. We aimed to validate and test a deep learning model to detect COVID-19 based on chest X-rays. The recent deep convolutional neural network (CNN) RegNetX032 was adapted for detecting COVID-19 from chest X-ray (CXR) images using polymerase chain reaction (RT-PCR) as a reference. The model was customized and trained on five datasets containing more than 15,000 CXR images (including 4148COVID-19-positive cases) and then tested on 321 images (150 COVID-19-positive) from Montfort Hospital. Twenty percent of the data from the five datasets were used as validation data for hyperparameter optimization. Each CXR image was processed by the model to detect COVID-19. Multi-binary classifications were proposed, such as: COVID-19 vs. normal, COVID-19 + pneumonia vs. normal, and pneumonia vs. normal. The performance results were based on the area under the curve (AUC), sensitivity, and specificity. In addition, an explainability model was developed that demonstrated the high performance and high generalization degree of the proposed model in detecting and highlighting the signs of the disease. The fine-tuned RegNetX032 model achieved an overall accuracy score of 96.0%, with an AUC score of 99.1%. The model showed a superior sensitivity of 98.0% in detecting signs from CXR images of COVID-19 patients, and a specificity of 93.0% in detecting healthy CXR images. A second scenario compared COVID-19 + pneumonia vs. normal (healthy X-ray) patients. The model achieved an overall score of 99.1% (AUC) with a sensitivity of 96.0% and specificity of 93.0% on the Montfort dataset. For the validation set, the model achieved an average accuracy of 98.6%, an AUC score of 98.0%, a sensitivity of 98.0%, and a specificity of 96.0% for detection (COVID-19 patients vs. healthy patients). The second scenario compared COVID-19 + pneumonia vs. normal patients. The model achieved an overall score of 98.8% (AUC) with a sensitivity of 97.0% and a specificity of 96.0%. This robust deep learning model demonstrated excellent performance in detecting COVID-19 from chest X-rays. This model could be used to automate the detection of COVID-19 and improve decision making for patient triage and isolation in hospital settings. This could also be used as a complementary aid for radiologists or clinicians when differentiating to make smart decisions.
COVID-19 Severity Prediction from Chest X-ray Images Using an Anatomy-Aware Deep Learning Model.
Authors: Nusrat BintaNizam, Sadi MohammadSiddiquee, MahbubaShirin, Mohammed Imamul HassanBhuiyan, TaufiqHasan
Journal: Journal of digital imaging

The COVID-19 pandemic has been adversely affecting the patient management systems in hospitals around the world. Radiological imaging, especially chest x-ray and lung Computed Tomography (CT) scans, plays a vital role in the severity analysis of hospitalized COVID-19 patients. However, with an increasing number of patients and a lack of skilled radiologists, automated assessment of COVID-19 severity using medical image analysis has become increasingly important. Chest x-ray (CXR) imaging plays a significant role in assessing the severity of pneumonia, especially in low-resource hospitals, and is the most frequently used diagnostic imaging in the world. Previous methods that automatically predict the severity of COVID-19 pneumonia mainly focus on feature pooling from pre-trained CXR models without explicitly considering the underlying human anatomical attributes. This paper proposes an anatomy-aware (AA) deep learning model that learns the generic features from x-ray images considering the underlying anatomical information. Utilizing a pre-trained model and lung segmentation masks, the model generates a feature vector including disease-level features and lung involvement scores. We have used four different open-source datasets, along with an in-house annotated test set for training and evaluation of the proposed method. The proposed method improves the geographical extent score by 11% in terms of mean squared error (MSE) while preserving the benchmark result in lung opacity score. The results demonstrate the effectiveness of the proposed AA model in COVID-19 severity prediction from chest X-ray images. The algorithm can be used in low-resource setting hospitals for COVID-19 severity prediction, especially where there is a lack of skilled radiologists.
Deep learning-based technique for lesions segmentation in CT scan images for COVID-19 prediction.
Authors: MounaAfif, RiadhAyachi, YahiaSaid, MohamedAtri
Journal: Multimedia tools and applications

Since 2019, COVID-19 disease caused significant damage and it has become a serious health issue in the worldwide. The number of infected and confirmed cases is increasing day by day. Different hospitals and countries around the world to this day are not equipped enough to treat these cases and stop this pandemic evolution. Lung and chest X-ray images (e.g., radiography images) and chest CT images are the most effective imaging techniques to analyze and diagnose the COVID-19 related problems. Deep learning-based techniques have recently shown good performance in computer vision and healthcare fields. We propose developing a new deep learning-based application for COVID-19 segmentation and analysis in this work. The proposed system is developed based on the context aggregation neural network. This network consists of three main modules: the context fuse model (CFM), attention mix module (AMM) and a residual convolutional module (RCM). The developed system can detect two main COVID-19-related regions: ground glass opacity and consolidation area in CT images. Generally, these lesions are often related to common pneumonia and COVID 19 cases. Training and testing experiments have been conducted using the COVID-x-CT dataset. Based on the obtained results, the developed system demonstrated better and more competitive results compared to state-of-the-art performances. The numerical findings demonstrate the effectiveness of the proposed work by outperforming other works in terms of accuracy by a factor of over 96.23%.
MediNet: transfer learning approach with MediNet medical visual database.
Authors: Hatice CatalReis, VeyselTurk, KouroshKhoshelham, SerhatKaya
Journal: Multimedia tools and applications

The rapid development of machine learning has increased interest in the use of deep learning methods in medical research. Deep learning in the medical field is used in disease detection and classification problems in the clinical decision-making process. Large amounts of labeled datasets are often required to train deep neural networks; however, in the medical field, the lack of a sufficient number of images in datasets and the difficulties encountered during data collection are among the main problems. In this study, we propose MediNet, a new 10-class visual dataset consisting of Rontgen (X-ray), Computed Tomography (CT), Magnetic Resonance Imaging (MRI), Ultrasound, and Histopathological images such as calcaneal normal, calcaneal tumor, colon benign colon adenocarcinoma, brain normal, brain tumor, breast benign, breast malignant, chest normal, chest pneumonia. AlexNet, VGG19-BN, Inception V3, DenseNet 121, ResNet 101, EfficientNet B0, Nested-LSTM + CNN, and proposed RdiNet deep learning algorithms are used in the transfer learning for pre-training and classification application. Transfer learning aims to apply previously learned knowledge in a new task. Seven algorithms were trained with the MediNet dataset, and the models obtained from these algorithms, namely feature vectors, were recorded. Pre-training models were used for classification studies on chest X-ray images, diabetic retinopathy, and Covid-19 datasets with the transfer learning technique. In performance measurement, an accuracy of 94.84% was obtained in the traditional classification study for the InceptionV3 model in the classification study performed on the Chest X-Ray Images dataset, and the accuracy was increased 98.71% after the transfer learning technique was applied. In the Covid-19 dataset, the classification success of the DenseNet121 model before pre-trained was 88%, while the performance after the transfer application with MediNet was 92%. In the Diabetic retinopathy dataset, the classification success of the Nested-LSTM + CNN model before pre-trained was 79.35%, while the classification success was 81.52% after the transfer application with MediNet. The comparison of results obtained from experimental studies observed that the proposed method produced more successful results.
COVID-19 prediction based on hybrid Inception V3 with VGG16 using chest X-ray images.
Authors: KSrinivas, RGagana Sri, KPravallika, KNishitha, Subba RaoPolamuri
Journal: Multimedia tools and applications

The Corona Virus was first started in the Wuhan city, China in December of 2019. It belongs to the Coronaviridae family, which can infect both animals and humans. The diagnosis of coronavirus disease-2019 (COVID-19) is typically detected by Serology, Genetic Real-Time reverse transcription-Polymerase Chain Reaction (RT-PCR), and Antigen testing. These testing methods have limitations like limited sensitivity, high cost, and long turn-around time. It is necessary to develop an automatic detection system for COVID-19 prediction. Chest X-ray is a lower-cost process in comparison to chest Computed tomography (CT). Deep learning is the best fruitful technique of machine learning, which provides useful investigation for learning and screening a large amount of chest X-ray images with COVID-19 and normal. There are many deep learning methods for prediction, but these methods have a few limitations like overfitting, misclassification, and false predictions for poor-quality chest X-rays. In order to overcome these limitations, the novel hybrid model called "Inception V3 with VGG16 (Visual Geometry Group)" is proposed for the prediction of COVID-19 using chest X-rays. It is a combination of two deep learning models, Inception V3 and VGG16 (IV3-VGG). To build the hybrid model, collected 243 images from the COVID-19 Radiography Database. Out of 243 X-rays, 121 are COVID-19 positive and 122 are normal images. The hybrid model is divided into two modules namely pre-processing and the IV3-VGG. In the dataset, some of the images with different sizes and different color intensities are identified and pre-processed. The second module i.e., IV3-VGG consists of four blocks. The first block is considered for VGG-16 and blocks 2 and 3 are considered for Inception V3 networks and final block 4 consists of four layers namely Avg pooling, dropout, fully connected, and Softmax layers. The experimental results show that the IV3-VGG model achieves the highest accuracy of 98% compared to the existing five prominent deep learning models such as Inception V3, VGG16, ResNet50, DenseNet121, and MobileNet.
Deep efficient-nets with transfer learning assisted detection of COVID-19 using chest X-ray radiology imaging.
Authors: HibaMzoughi, InesNjeh, Mohamed BenSlima, AhmedBenHamida
Journal: Multimedia tools and applications

Corona Virus (COVID-19) could be considered as one of the most devastating pandemics of the twenty-first century. The effective and the rapid screening of infected patients could reduce the mortality and even the contagion rate. Chest X-ray radiology could be designed as one of the effective screening techniques for COVID-19 exploration. In this paper, we propose an advanced approach based on deep learning architecture to automatic and effective screening techniques dedicated to the COVID-19 exploration through chest X-ray (CXR) imaging. Despite the success of state-of-the-art deep learning-based models for COVID-19 detection, they might suffer from several problems such as the huge memory and the computational requirement, the overfitting effect, and the high variance. To alleviate these issues, we investigate the Transfer Learning to the Efficient-Nets models. Next, we fine-tuned the whole network to select the optimal hyperparameters. Furthermore, in the preprocessing step, we consider an intensity-normalization method succeeded by some data augmentation techniques to solve the imbalanced dataset classes' issues. The proposed approach has presented a good performance in detecting patients attained by COVID-19 achieving an accuracy rate of 99.0% and 98% respectively using training and testing datasets. A comparative study over a publicly available dataset with the recently published deep-learning-based architectures could attest the proposed approach's performance.
Bio-medical imaging (X-ray, CT, ultrasound, ECG), genome sequences applications of deep neural network and machine learning in diagnosis, detection, classification, and segmentation of COVID-19: a Meta-analysis & systematic review.
Authors: Yogesh HBhosale, K SridharPatnaik
Journal: Multimedia tools and applications

This review investigates how Deep Machine Learning (DML) has dealt with the Covid-19 epidemic and provides recommendations for future Covid-19 research. Despite the fact that vaccines for this epidemic have been developed, DL methods have proven to be a valuable asset in radiologists' arsenals for the automated assessment of Covid-19. This detailed review debates the techniques and applications developed for Covid-19 findings using DL systems. It also provides insights into notable datasets used to train neural networks, data partitioning, and various performance measurement metrics. The PRISMA taxonomy has been formed based on pretrained(45 systems) and hybrid/custom(17 systems) models with radiography modalities. A total of 62 systems with respect to X-ray(32), CT(19), ultrasound(7), ECG(2), and genome sequence(2) based modalities as taxonomy are selected from the studied articles. We originate by valuing the present phase of DL and conclude with significant limitations. The restrictions contain incomprehensibility, simplification measures, learning from incomplete labeled data, and data secrecy. Moreover, DML can be utilized to detect and classify Covid-19 from other COPD illnesses. The proposed literature review has found many DL-based systems to fight against Covid19. We expect this article will assist in speeding up the procedure of DL for Covid-19 researchers, including medical, radiology technicians, and data engineers.
Deep Learning Based COVID-19 Detection via Hard Voting Ensemble Method.
Authors: Asaad QasimShareef, SeferKurnaz
Journal: Wireless personal communications

Healthcare systems throughout the world are under a great deal of strain because to the continuing COVID-19 epidemic, making early and precise diagnosis critical for limiting the virus's propagation and efficiently treating victims. The utilization of medical imaging methods like X-rays can help to speed up the diagnosis procedure. Which can offer valuable insights into the virus's existence in the lungs. We present a unique ensemble approach to identify COVID-19 using X-ray pictures (X-ray-PIC) in this paper. The suggested approach, based on hard voting, combines the confidence scores of three classic deep learning models: CNN, VGG16, and DenseNet. We also apply transfer learning to enhance performance on small medical image datasets. Experiments indicate that the suggested strategy outperforms current techniques with a 97% accuracy, a 96% precision, a 100% recall, and a 98% F1-score.These results demonstrate the effectiveness of using ensemble approaches and COVID-19 transfer-learning diagnosis using X-ray-PIC, which could greatly aid in early detection and reducing the burden on global health systems.
ResNetFed: Federated Deep Learning Architecture for Privacy-Preserving Pneumonia Detection from COVID-19 Chest Radiographs.
Authors: PascalRiedel, Reinholdvon Schwerin, DanielSchaudt, AlexanderHafner, ChristianSpäte
Journal: Journal of healthcare informatics research

Personal health data is subject to privacy regulations, making it challenging to apply centralized data-driven methods in healthcare, where personalized training data is frequently used. Federated Learning (FL) promises to provide a decentralized solution to this problem. In FL, siloed data is used for the model training to ensure data privacy. In this paper, we investigate the viability of the federated approach using the detection of COVID-19 pneumonia as a use case. 1411 individual chest radiographs, sourced from the public data repository COVIDx8 are used. The dataset contains radiographs of 753 normal lung findings and 658 COVID-19 related pneumonias. We partition the data unevenly across five separate data silos in order to reflect a typical FL scenario. For the binary image classification analysis of these radiographs, we propose
Pathological changes or technical artefacts? The problem of the heterogenous databases in COVID-19 CXR image analysis.
Authors: MarekSocha, WojciechPrażuch, AleksandraSuwalska, PawełFoszner, JoannaTobiasz, JerzyJaroszewicz, KatarzynaGruszczynska, MagdalenaSliwinska, MateuszNowak, BarbaraGizycka, GabrielaZapolska, TadeuszPopiela, GrzegorzPrzybylski, PiotrFiedor, MalgorzataPawlowska, RobertFlisiak, KrzysztofSimon, JerzyWalecki, AndrzejCieszanowski, EdytaSzurowska, MichalMarczyk, JoannaPolanska, NoneNone
Journal: Computer methods and programs in biomedicine

When the COVID-19 pandemic commenced in 2020, scientists assisted medical specialists with diagnostic algorithm development. One scientific research area related to COVID-19 diagnosis was medical imaging and its potential to support molecular tests. Unfortunately, several systems reported high accuracy in development but did not fare well in clinical application. The reason was poor generalization, a long-standing issue in AI development. Researchers found many causes of this issue and decided to refer to them as confounders, meaning a set of artefacts and methodological errors associated with the method. We aim to contribute to this steed by highlighting an undiscussed confounder related to image resolution.
20 216 chest X-ray images (CXR) from worldwide centres were analyzed. The CXRs were bijectively projected into the 2D domain by performing Uniform Manifold Approximation and Projection (UMAP) embedding on the radiomic features (rUMAP) or CNN-based neural features (nUMAP) from the pre-last layer of the pre-trained classification neural network. Additional 44 339 thorax CXRs were used for validation. The comprehensive analysis of the multimodality of the density distribution in rUMAP/nUMAP domains and its relation to the original image properties was used to identify the main confounders.
nUMAP revealed a hidden bias of neural networks towards the image resolution, which the regular up-sampling procedure cannot compensate for. The issue appears regardless of the network architecture and is not observed in a high-resolution dataset. The impact of the resolution heterogeneity can be partially diminished by applying advanced deep-learning-based super-resolution networks.
rUMAP and nUMAP are great tools for image homogeneity analysis and bias discovery, as demonstrated by applying them to COVID-19 image data. Nonetheless, nUMAP could be applied to any type of data for which a deep neural network could be constructed. Advanced image super-resolution solutions are needed to reduce the impact of the resolution diversity on the classification network decision.
LayNet-A multi-layer architecture to handle imbalance in medical imaging data.
Authors: JayJani, JayDoshi, IshitaKheria, KarishniMehta, ChetashriBhadane, RuhinaKarani
Journal: Computers in biology and medicine

In an imbalanced dataset, a machine learning classifier using traditional imbalance handling methods may achieve good accuracy, but in highly imbalanced datasets, it may over-predict the majority class and ignore the minority class. In the medical domain, failing to correctly estimate the minority class might lead to a false negative, which is concerning in cases of life-threatening illnesses and infectious diseases like Covid-19. Currently, classification in deep learning has a single layered architecture where a neural network is employed. This paper proposes a multilayer design entitled LayNet to address this issue. LayNet aims to lessen the class imbalance by dividing the classes among layers and achieving a balanced class distribution at each layer. To ensure that all the classes are being classified, minor classes are combined to form a single new 'hybrid' class at higher layers. The final layer has no hybrid class and only singleton(distinct) classes. Each layer of the architecture includes a separate model that determines if an input belongs to one class or a hybrid class. If it fits into the hybrid class, it advances to the following layer, which is further categorized within the hybrid class. The method to divide the classes into various architectural levels is also introduced in this paper. The Ocular Disease Intelligent Recognition Dataset, Covid-19 Radiography Dataset, and Retinal OCT Dataset are used to evaluate this methodology. The LayNet architecture performs better on these datasets when the results of the traditional single-layer architecture and the proposed multilayered architecture are compared.