pt-sk/ml_research_abs huggingface dataset:
Automatic diagnosis of COVID-19 from CT images using CycleGAN and transfer learning.
Authors: NavidGhassemi, AfshinShoeibi, MarjaneKhodatars, JonathanHeras, AlirezaRahimi, AssefZare, Yu-DongZhang, Ram BilasPachori, J ManuelGorriz
Journal: Applied soft computing

The outbreak of the corona virus disease (COVID-19) has changed the lives of most people on Earth. Given the high prevalence of this disease, its correct diagnosis in order to quarantine patients is of the utmost importance in the steps of fighting this pandemic. Among the various modalities used for diagnosis, medical imaging, especially computed tomography (CT) imaging, has been the focus of many previous studies due to its accuracy and availability. In addition, automation of diagnostic methods can be of great help to physicians. In this paper, a method based on pre-trained deep neural networks is presented, which, by taking advantage of a cyclic generative adversarial net (CycleGAN) model for data augmentation, has reached state-of-the-art performance for the task at hand, i.e., 99.60% accuracy. Also, in order to evaluate the method, a dataset containing 3163 images from 189 patients has been collected and labeled by physicians. Unlike prior datasets, normal data have been collected from people suspected of having COVID-19 disease and not from data from other diseases, and this database is made available publicly. Moreover, the method's reliability is further evaluated by calibration metrics, and its decision is interpreted by Grad-CAM also to find suspicious regions as another output of the method and make its decisions trustworthy and explainable.
To segment or not to segment: COVID-19 detection for chest X-rays.
Authors: SaraAl Hajj Ibrahim, KhalilEl-Khatib
Journal: Informatics in medicine unlocked

Artificial intelligence (AI) has been integrated into most technologies we use. One of the most promising applications in AI is medical imaging. Research demonstrates that AI has improved the performance of most medical imaging analysis systems. Consequently, AI has become a fundamental element of the state of the art with improved outcomes across a variety of medical imaging applications. Moreover, it is believed that computer vision (CV) algorithms are highly effective for image analysis. Recent advances in CV facilitate the recognition of patterns in medical images. In this manner, we investigate CV segmentation techniques for COVID-19 analysis. We use different segmentation techniques, such as k-means, U-net, and flood fill, to extract the lung region from CXRs. Afterwards, we compare the effectiveness of these three segmentation approaches when applied to CXRs. Then, we use machine learning (ML) and deep learning (DL) models to identify COVID-19 lesion molecules in both healthy and pathological lung x-rays. We evaluate our ML and DL findings in the context of CV techniques. Our results indicate that the segmentation-related CV techniques do not exhibit comparable performance to DL and ML techniques. The most optimal AI algorithm yields an accuracy range of 0.92-0.94, whereas the addition of CV algorithms leads to a reduction in accuracy to approximately the range of 0.81-0.88. In addition, we test the performance of DL models under real-world noise, such as salt and pepper noise, which negatively impacts the overall performance.
CT medical image segmentation algorithm based on deep learning technology.
Authors: TongpingShen, FangliangHuang, XusongZhang
Journal: Mathematical biosciences and engineering : MBE

For the problems of blurred edges, uneven background distribution, and many noise interferences in medical image segmentation, we proposed a medical image segmentation algorithm based on deep neural network technology, which adopts a similar U-Net backbone structure and includes two parts: encoding and decoding. Firstly, the images are passed through the encoder path with residual and convolutional structures for image feature information extraction. We added the attention mechanism module to the network jump connection to address the problems of redundant network channel dimensions and low spatial perception of complex lesions. Finally, the medical image segmentation results are obtained using the decoder path with residual and convolutional structures. To verify the validity of the model in this paper, we conducted the corresponding comparative experimental analysis, and the experimental results show that the DICE and IOU of the proposed model are 0.7826, 0.9683, 0.8904, 0.8069, and 0.9462, 0.9537 for DRIVE, ISIC2018 and COVID-19 CT datasets, respectively. The segmentation accuracy is effectively improved for medical images with complex shapes and adhesions between lesions and normal tissues.
COV-MobNets: a mobile networks ensemble model for diagnosis of COVID-19 based on chest X-ray images.
Authors: Mohammad AmirEshraghi, AhmadAyatollahi, Shahriar BaradaranShokouhi
Journal: BMC medical imaging

The medical profession is facing an excessive workload, which has led to the development of various Computer-Aided Diagnosis (CAD) systems as well as Mobile-Aid Diagnosis (MAD) systems. These technologies enhance the speed and accuracy of diagnoses, particularly in areas with limited resources or remote regions during the pandemic. The primary purpose of this research is to predict and diagnose COVID-19 infection from chest X-ray images by developing a mobile-friendly deep learning framework, which has the potential for deployment in portable devices such as mobile or tablet, especially in situations where the workload of radiology specialists may be high. Moreover, this could improve the accuracy and transparency of population screening to assist radiologists during the pandemic.
In this study, the Mobile Networks ensemble model called COV-MobNets is proposed to classify positive COVID-19 X-ray images from negative ones and can have an assistant role in diagnosing COVID-19. The proposed model is an ensemble model, combining two lightweight and mobile-friendly models: MobileViT based on transformer structure and MobileNetV3 based on Convolutional Neural Network. Hence, COV-MobNets can extract the features of chest X-ray images in two different methods to achieve better and more accurate results. In addition, data augmentation techniques were applied to the dataset to avoid overfitting during the training process. The COVIDx-CXR-3 benchmark dataset was used for training and evaluation.
The classification accuracy of the improved MobileViT and MobileNetV3 models on the test set has reached 92.5% and 97%, respectively, while the accuracy of the proposed model (COV-MobNets) has reached 97.75%. The sensitivity and specificity of the proposed model have also reached 98.5% and 97%, respectively. Experimental comparison proves the result is more accurate and balanced than other methods.
The proposed method can distinguish between positive and negative COVID-19 cases more accurately and quickly. The proposed method proves that utilizing two automatic feature extractors with different structures as an overall framework of COVID-19 diagnosis can lead to improved performance, enhanced accuracy, and better generalization to new or unseen data. As a result, the proposed framework in this study can be used as an effective method for computer-aided diagnosis and mobile-aided diagnosis of COVID-19. The code is available publicly for open access at https://github.com/MAmirEshraghi/COV-MobNets .
A genetic programming-based convolutional deep learning algorithm for identifying COVID-19 cases via X-ray images.
Authors: Mohammad Hassan TayaraniNajaran
Journal: Artificial intelligence in medicine

Evolutionary algorithms have been successfully employed to find the best structure for many learning algorithms including neural networks. Due to their flexibility and promising results, Convolutional Neural Networks (CNNs) have found their application in many image processing applications. The structure of CNNs greatly affects the performance of these algorithms both in terms of accuracy and computational cost, thus, finding the best architecture for these networks is a crucial task before they are employed. In this paper, we develop a genetic programming approach for the optimization of CNN structure in diagnosing COVID-19 cases via X-ray images. A graph representation for CNN architecture is proposed and evolutionary operators including crossover and mutation are specifically designed for the proposed representation. The proposed architecture of CNNs is defined by two sets of parameters, one is the skeleton which determines the arrangement of the convolutional and pooling operators and their connections and one is the numerical parameters of the operators which determine the properties of these operators like filter size and kernel size. The proposed algorithm in this paper optimizes the skeleton and the numerical parameters of the CNN architectures in a co-evolutionary scheme. The proposed algorithm is used to identify covid-19 cases via X-ray images.
Artificial Intelligence-assisted quantification of COVID-19 pneumonia burden from computed tomography improves prediction of adverse outcomes over visual scoring systems.
Authors: KajetanGrodecki, AdityaKillekar, JuditSimon, AndrewLin, SebastienCadet, PriscillaMcElhinney, CatoChan, Michelle CWilliams, Barry DPressman, PeterJulien, DebiaoLi, PeterChen, NicolaGaibazzi, UditThakur, ElisabettaMancini, CeciliaAgalbato, JiroMunechika, HidenariMatsumoto, RobertoMene, GianfrancoParati, FrancoCernigliaro, NiteshNerlekar, CamillaTorlasco, GianlucaPontone, PalMaurovich-Horvat, Piotr JSlomka, DaminiDey
Journal: The British journal of radiology

We aimed to evaluate the effectiveness of utilizing artificial intelligence (AI) to quantify the extent of pneumonia from chest computed tomography (CT) scans, and to determine its ability to predict clinical deterioration or mortality in patients admitted to the hospital with COVID-19in comparison to semi-quantitative visual scoring systems.
A deep-learning algorithm was utilized to quantify the pneumonia burden, while semi-quantitative pneumonia severity scores were estimated through visual means. The primary outcomewas clinical deterioration, the composite endpoint including admission to the intensive care unit, need for invasive mechanical ventilation, or vasopressor therapy, as well as in-hospital death.
The final population comprised 743 patients (mean age 65  ±  17 years, 55% men), of whom 175 (23.5%) experienced clinical deterioration or death. The area under the receiver operating characteristic curve (AUC) for predicting the primary outcome was significantly higher for AI-assisted quantitative pneumonia burden (0.739, 
Utilizing AI-assisted quantification of pneumonia burden from chest CT scans offers a more accurate prediction of clinical deterioration in patients with COVID-19 compared to semi-quantitative severity scores, while requiring only a fraction of the analysis time.
Quantitative pneumonia burden assessed using AI demonstrated higher performance for predicting clinical deterioration compared to current semi-quantitative scoring systems. Such an AI system has the potential to be applied for image-based triage of COVID-19 patients in clinical practice.
A transformer-based representation-learning model with unified processing of multimodal input for clinical diagnostics.
Authors: Hong-YuZhou, YizhouYu, ChengdiWang, ShuZhang, YuanxuGao, JiaPan, JunShao, GuangmingLu, KangZhang, WeiminLi
Journal: Nature biomedical engineering

During the diagnostic process, clinicians leverage multimodal information, such as the chief complaint, medical images and laboratory test results. Deep-learning models for aiding diagnosis have yet to meet this requirement of leveraging multimodal information. Here we report a transformer-based representation-learning model as a clinical diagnostic aid that processes multimodal input in a unified manner. Rather than learning modality-specific features, the model leverages embedding layers to convert images and unstructured and structured text into visual tokens and text tokens, and uses bidirectional blocks with intramodal and intermodal attention to learn holistic representations of radiographs, the unstructured chief complaint and clinical history, and structured clinical information such as laboratory test results and patient demographic information. The unified model outperformed an image-only model and non-unified multimodal diagnosis models in the identification of pulmonary disease (by 12% and 9%, respectively) and in the prediction of adverse clinical outcomes in patients with COVID-19 (by 29% and 7%, respectively). Unified multimodal transformer-based models may help streamline the triaging of patients and facilitate the clinical decision-making process.
Remora Namib Beetle Optimization Enabled Deep Learning for Severity of COVID-19 Lung Infection Identification and Classification Using CT Images.
Authors: AmgothuShanthi, SrinivasKoppu
Journal: Sensors (Basel, Switzerland)

Coronavirus disease 2019 (COVID-19) has seen a crucial outburst for both females and males worldwide. Automatic lung infection detection from medical imaging modalities provides high potential for increasing the treatment for patients to tackle COVID-19 disease. COVID-19 detection from lung CT images is a rapid way of diagnosing patients. However, identifying the occurrence of infectious tissues and segmenting this from CT images implies several challenges. Therefore, efficient techniques termed as Remora Namib Beetle Optimization_ Deep Quantum Neural Network (RNBO_DQNN) and RNBO_Deep Neuro Fuzzy Network (RNBO_DNFN) are introduced for the identification as well as classification of COVID-19 lung infection. Here, the pre-processing of lung CT images is performed utilizing an adaptive Wiener filter, whereas lung lobe segmentation is performed employing the Pyramid Scene Parsing Network (PSP-Net). Afterwards, feature extraction is carried out wherein features are extracted for the classification phase. In the first level of classification, DQNN is utilized, tuned by RNBO. Furthermore, RNBO is designed by merging the Remora Optimization Algorithm (ROA) and Namib Beetle Optimization (NBO). If a classified output is COVID-19, then the second-level classification is executed using DNFN for further classification. Additionally, DNFN is also trained by employing the newly proposed RNBO. Furthermore, the devised RNBO_DNFN achieved maximum testing accuracy, with TNR and TPR obtaining values of 89.4%, 89.5% and 87.5%.
A Review Paper about Deep Learning for Medical Image Analysis.
Authors: BagherSistaninejhad, HabibRasi, ParisaNayeri
Journal: Computational and mathematical methods in medicine

Medical imaging refers to the process of obtaining images of internal organs for therapeutic purposes such as discovering or studying diseases. The primary objective of medical image analysis is to improve the efficacy of clinical research and treatment options. Deep learning has revamped medical image analysis, yielding excellent results in image processing tasks such as registration, segmentation, feature extraction, and classification. The prime motivations for this are the availability of computational resources and the resurgence of deep convolutional neural networks. Deep learning techniques are good at observing hidden patterns in images and supporting clinicians in achieving diagnostic perfection. It has proven to be the most effective method for organ segmentation, cancer detection, disease categorization, and computer-assisted diagnosis. Many deep learning approaches have been published to analyze medical images for various diagnostic purposes. In this paper, we review the work exploiting current state-of-the-art deep learning approaches in medical image processing. We begin the survey by providing a synopsis of research works in medical imaging based on convolutional neural networks. Second, we discuss popular pretrained models and general adversarial networks that aid in improving convolutional networks' performance. Finally, to ease direct evaluation, we compile the performance metrics of deep learning models focusing on COVID-19 detection and child bone age prediction.
Deep learning framework for rapid and accurate respiratory COVID-19 prediction using chest X-ray images.
Authors: Chiagoziem CUkwuoma, DongshengCai, Md Belal BinHeyat, OlusolaBamisile, HumphreyAdun, ZaidAl-Huda, Mugahed AAl-Antari
Journal: Journal of King Saud University. Computer and information sciences

COVID-19 is a contagious disease that affects the human respiratory system. Infected individuals may develop serious illnesses, and complications may result in death. Using medical images to detect COVID-19 from essentially identical thoracic anomalies is challenging because it is time-consuming, laborious, and prone to human error. This study proposes an end-to-end deep-learning framework based on deep feature concatenation and a Multi-head Self-attention network. Feature concatenation involves fine-tuning the pre-trained backbone models of DenseNet, VGG-16, and InceptionV3, which are trained on a large-scale ImageNet, whereas a Multi-head Self-attention network is adopted for performance gain. End-to-end training and evaluation procedures are conducted using the COVID-19_Radiography_Dataset for binary and multi-classification scenarios. The proposed model achieved overall accuracies (96.33% and 98.67%) and F1_scores (92.68% and 98.67%) for multi and binary classification scenarios, respectively. In addition, this study highlights the difference in accuracy (98.0% vs. 96.33%) and F_1 score (97.34% vs. 95.10%) when compared with feature concatenation against the highest individual model performance. Furthermore, a virtual representation of the saliency maps of the employed attention mechanism focusing on the abnormal regions is presented using explainable artificial intelligence (XAI) technology. The proposed framework provided better COVID-19 prediction results outperforming other recent deep learning models using the same dataset.
POLCOVID: a multicenter multiclass chest X-ray database (Poland, 2020-2021).
Authors: AleksandraSuwalska, JoannaTobiasz, WojciechPrazuch, MarekSocha, PawelFoszner, DamianPiotrowski, KatarzynaGruszczynska, MagdalenaSliwinska, JerzyWalecki, TadeuszPopiela, GrzegorzPrzybylski, MateuszNowak, PiotrFiedor, MalgorzataPawlowska, RobertFlisiak, KrzysztofSimon, GabrielaZapolska, BarbaraGizycka, EdytaSzurowska, NoneNone, MichalMarczyk, AndrzejCieszanowski, JoannaPolanska
Journal: Scientific data

The outbreak of the SARS-CoV-2 pandemic has put healthcare systems worldwide to their limits, resulting in increased waiting time for diagnosis and required medical assistance. With chest radiographs (CXR) being one of the most common COVID-19 diagnosis methods, many artificial intelligence tools for image-based COVID-19 detection have been developed, often trained on a small number of images from COVID-19-positive patients. Thus, the need for high-quality and well-annotated CXR image databases increased. This paper introduces POLCOVID dataset, containing chest X-ray (CXR) images of patients with COVID-19 or other-type pneumonia, and healthy individuals gathered from 15 Polish hospitals. The original radiographs are accompanied by the preprocessed images limited to the lung area and the corresponding lung masks obtained with the segmentation model. Moreover, the manually created lung masks are provided for a part of POLCOVID dataset and the other four publicly available CXR image collections. POLCOVID dataset can help in pneumonia or COVID-19 diagnosis, while the set of matched images and lung masks may serve for the development of lung segmentation solutions.
Harnessing Machine Learning in Early COVID-19 Detection and Prognosis: A Comprehensive Systematic Review.
Authors: RufaidahDabbagh, AmrJamal, Jakir HossainBhuiyan Masud, Maher ATiti, Yasser SAmer, AfnanKhayat, Taha SAlhazmi, LayalHneiny, Fatmah ABaothman, MetabAlkubeyyer, Samina AKhan, Mohamad-HaniTemsah
Journal: Cureus

During the early phase of the COVID-19 pandemic, reverse transcriptase-polymerase chain reaction (RT-PCR) testing faced limitations, prompting the exploration of machine learning (ML) alternatives for diagnosis and prognosis. Providing a comprehensive appraisal of such decision support systems and their use in COVID-19 management can aid the medical community in making informed decisions during the risk assessment of their patients, especially in low-resource settings. Therefore, the objective of this study was to systematically review the studies that predicted the diagnosis of COVID-19 or the severity of the disease using ML. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA), we conducted a literature search of MEDLINE (OVID), Scopus, EMBASE, and IEEE Xplore from January 1 to June 31, 2020. The outcomes were COVID-19 diagnosis or prognostic measures such as death, need for mechanical ventilation, admission, and acute respiratory distress syndrome. We included peer-reviewed observational studies, clinical trials, research letters, case series, and reports. We extracted data about the study's country, setting, sample size, data source, dataset, diagnostic or prognostic outcomes, prediction measures, type of ML model, and measures of diagnostic accuracy. Bias was assessed using the Prediction model Risk Of Bias ASsessment Tool (PROBAST). This study was registered in the International Prospective Register of Systematic Reviews (PROSPERO), with the number CRD42020197109. The final records included for data extraction were 66. Forty-three (64%) studies used secondary data. The majority of studies were from Chinese authors (30%). Most of the literature (79%) relied on chest imaging for prediction, while the remainder used various laboratory indicators, including hematological, biochemical, and immunological markers. Thirteen studies explored predicting COVID-19 severity, while the rest predicted diagnosis. Seventy percent of the articles used deep learning models, while 30% used traditional ML algorithms. Most studies reported high sensitivity, specificity, and accuracy for the ML models (exceeding 90%). The overall concern about the risk of bias was "unclear" in 56% of the studies. This was mainly due to concerns about selection bias. ML may help identify COVID-19 patients in the early phase of the pandemic, particularly in the context of chest imaging. Although these studies reflect that these ML models exhibit high accuracy, the novelty of these models and the biases in dataset selection make using them as a replacement for the clinicians' cognitive decision-making questionable. Continued research is needed to enhance the robustness and reliability of ML systems in COVID-19 diagnosis and prognosis.