zurlog/subset_wlabels huggingface dataset:
Title: a comparison of deep machine learning algorithms in covid-19 disease diagnosis
Published: 2020-10-09 (Preprint, arXiv)
Condition: COVID-19
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: The aim of the work is to use deep neural network models for solving the problem of image recognition. These days, every human being is threatened by a harmful coronavirus disease, also called COVID-19 disease. The spread of coronavirus affects the economy of many countries in the world. To find COVID-19 patients early is very essential to avoid the spread and harm to society. Pathological tests and Chromatography (CT) scans are helpful for the diagnosis of COVID-19. However, these tests are having drawbacks such as a large number of false positives, and cost of these tests are so expensive. Hence, it requires finding an easy, accurate, and less expensive way for the detection of the harmful COVID-19 disease. Chest-x-ray can be useful for the detection of this disease. Therefore, in this work chest, x-ray images are used for the diagnosis of suspected COVID-19 patients using modern machine learning techniques. The analysis of the results is carried out and conclusions are made about the effectiveness of deep machine learning algorithms in image recognition problems.
Title: classification of covid-19 coronavirus pneumonia and healthy lungs in ct scans using q-deformed entropy and deep learning features
Journal: Entropy (Basel)
Published: 2020-12-09 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Pneumonia
Task: 2. Detection/Diagnosis | Modality: CT

Abstract: Many health systems over the world have collapsed due to limited capacity and a dramatic increase of suspected COVID-19 cases. What has emerged is the need for finding an efficient, quick and accurate method to mitigate the overloading of radiologists' efforts to diagnose the suspected cases. This study presents the combination of deep learning of extracted features with the Q-deformed entropy handcrafted features for discriminating between COVID-19 coronavirus, pneumonia and healthy computed tomography (CT) lung scans. In this study, pre-processing is used to reduce the effect of intensity variations between CT slices. Then histogram thresholding is used to isolate the background of the CT lung scan. Each CT lung scan undergoes a feature extraction which involves deep learning and a Q-deformed entropy algorithm. The obtained features are classified using a long short-term memory (LSTM) neural network classifier. Subsequently, combining all extracted features significantly improves the performance of the LSTM network to precisely discriminate between COVID-19, pneumonia and healthy cases. The maximum achieved accuracy for classifying the collected dataset comprising 321 patients is 99.68%.
Title: unveiling covid-19 from chest x-ray with deep learning: a hurdles race with small data
Journal: Int J Environ Res Public Health
Published: 2020-09-26 (Journal Article;Research Support, Non-U.S. Gov't, Peer reviewed (PubMed))
Condition: COVID-19
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: The possibility to use widespread and simple chest X-ray (CXR) imaging for early screening of COVID-19 patients is attracting much interest from both the clinical and the AI community. In this study we provide insights and also raise warnings on what is reasonable to expect by applying deep learning to COVID classification of CXR images. We provide a methodological guide and critical reading of an extensive set of statistical results that can be obtained using currently available datasets. In particular, we take the challenge posed by current small size COVID data and show how significant can be the bias introduced by transfer-learning using larger public non-COVID CXR datasets. We also contribute by providing results on a medium size COVID CXR dataset, just collected by one of the major emergency hospitals in Northern Italy during the peak of the COVID pandemic. These novel data allow us to contribute to validate the generalization capacity of preliminary results circulating in the scientific community. Our conclusions shed some light into the possibility to effectively discriminate COVID using CXR.
Title: exploration of interpretability techniques for deep covid-19 classification using chest x-ray images
Published: 2022-03-11 (Preprint, Research Square)
Condition: COVID-19
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: The outbreak of COVID-19 has shocked the entire world with its fairly rapid spread and has challenged different sectors. One of the most effective ways to limit its spread is the early and accurate diagnosis of infected patients. Medical imaging such as X-ray and Computed Tomography (CT) combined with the potential of Artificial Intelligence (AI) plays an essential role in supporting the medical staff in the diagnosis process. Thereby, five different deep learning models (ResNet18, ResNet34, InceptionV3, InceptionResNetV2, and DenseNet161) and their Ensemble have been used in this paper, to classify COVID-19, pneumoniae and healthy subjects using Chest X-Ray images. Multi-label classification was performed to predict multiple pathologies for each patient, if present. Foremost, the interpretability of each of the networks was thoroughly studied using techniques like occlusion, saliency, input X gradient, guided backpropagation, integrated gradients, and DeepLIFT. The mean Micro-F1 score of the models for COVID-19 classifications ranges from 0.66 to 0.875, and is 0.89 for the Ensemble of the network models. The qualitative results depicted the ResNets to be the most interpretable models.
Title: automated methods for detection and classification pneumonia based on x-ray images using deep learning
Published: 2020-03-31 (Preprint, arXiv)
Condition: COVID-19;Pneumonia
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: Recently, researchers, specialists, and companies around the world are rolling out deep learning and image processing-based systems that can fastly process hundreds of X-Ray and computed tomography (CT) images to accelerate the diagnosis of pneumonia such as SARS, COVID-19, and aid in its containment. Medical images analysis is one of the most promising research areas, it provides facilities for diagnosis and making decisions of a number of diseases such as MERS, COVID-19. In this paper, we present a comparison of recent Deep Convolutional Neural Network (DCNN) architectures for automatic binary classification of pneumonia images based fined tuned versions of (VGG16, VGG19, DenseNet201, Inception_ResNet_V2, Inception_V3, Resnet50, MobileNet_V2 and Xception). The proposed work has been tested using chest X-Ray and CT dataset which contains 5856 images (4273 pneumonia and 1583 normal). As result we can conclude that fine-tuned version of Resnet50, MobileNet_V2 and Inception_Resnet_V2 show highly satisfactory performance with rate of increase in training and validation accuracy (more than 96% of accuracy). Unlike CNN, Xception, VGG16, VGG19, Inception_V3 and DenseNet201 display low performance (more than 84% accuracy).
Title: deep learning-based decision-tree classifier for covid-19 diagnosis from chest x-ray imaging
Journal: Front Med (Lausanne)
Published: 2020-08-08 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Pneumonia;Tuberculosis
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: The global pandemic of coronavirus disease 2019 (COVID-19) has resulted in an increased demand for testing, diagnosis, and treatment. Reverse transcription polymerase chain reaction (RT-PCR) is the definitive test for the diagnosis of COVID-19; however, chest X-ray radiography (CXR) is a fast, effective, and affordable test that identifies the possible COVID-19-related pneumonia. This study investigates the feasibility of using a deep learning-based decision-tree classifier for detecting COVID-19 from CXR images. The proposed classifier comprises three binary decision trees, each trained by a deep learning model with convolution neural network based on the PyTorch frame. The first decision tree classifies the CXR images as normal or abnormal. The second tree identifies the abnormal images that contain signs of tuberculosis, whereas the third does the same for COVID-19. The accuracies of the first and second decision trees are 98 and 80%, respectively, whereas the average accuracy of the third decision tree is 95%. The proposed deep learning-based decision-tree classifier may be used in pre-screening patients to conduct triage and fast-track decision making before RT-PCR results are available.
Title: an artificial intelligence system for predicting the deterioration of covid-19 patients in the emergency department
Journal: NPJ Digit Med
Published: 2021-05-14 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;COVID-19 Pandemic
Task: 4. Prognosis/Treatment | Modality: X-Ray

Abstract: During the coronavirus disease 2019 (COVID-19) pandemic, rapid and accurate triage of patients at the emergency department is critical to inform decision-making. We propose a data-driven approach for automatic prediction of deterioration risk using a deep neural network that learns from chest X-ray images and a gradient boosting model that learns from routine clinical variables. Our AI prognosis system, trained using data from 3661 patients, achieves an area under the receiver operating characteristic curve (AUC) of 0.786 (95% CI: 0.745-0.830) when predicting deterioration within 96 hours. The deep neural network extracts informative areas of chest X-ray images to assist clinicians in interpreting the predictions and performs comparably to two radiologists in a reader study. In order to verify performance in a real clinical setting, we silently deployed a preliminary version of the deep neural network at New York University Langone Health during the first wave of the pandemic, which produced accurate predictions in real-time. In summary, our findings demonstrate the potential of the proposed system for assisting front-line physicians in the triage of COVID-19 patients.
Title: evaluation of contemporary convolutional neural network architectures for detecting covid-19 from chest radiographs
Published: 2020-06-30 (Preprint, arXiv)
Condition: COVID-19;COVID-19 Pandemic;Infections;Plague
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: Interpreting chest radiograph, a.ka. chest x-ray, images is a necessary and crucial diagnostic tool used by medical professionals to detect and identify many diseases that may plague a patient. Although the images themselves contain a wealth of valuable information, their usefulness may be limited by how well they are interpreted, especially when the reviewing radiologist may be fatigued or when or an experienced radiologist is unavailable. Research in the use of deep learning models to analyze chest radiographs yielded impressive results where, in some instances, the models outperformed practicing radiologists. Amidst the COVID-19 pandemic, researchers have explored and proposed the use of said deep models to detect COVID-19 infections from radiographs as a possible way to help ease the strain on medical resources. In this study, we train and evaluate three model architectures, proposed for chest radiograph analysis, under varying conditions, find issues that discount the impressive model performances proposed by contemporary studies on this subject, and propose methodologies to train models that yield more reliable results.. Code, scripts, pre-trained models, and visualizations are available at GitHub
Title: covid-19 detection using deep learning models to exploit social mimic optimization and structured chest x-ray images using fuzzy color and stacking approaches
Journal: Comput Biol Med
Published: 2020-06-23 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Pneumonia;Respiratory Tract Infections
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: Coronavirus causes a wide variety of respiratory infections and it is an RNA-type virus that can infect both humans and animal species. It often causes pneumonia in humans. Artificial intelligence models have been helpful for successful analyses in the biomedical field. In this study, Coronavirus was detected using a deep learning model, which is a sub-branch of artificial intelligence. Our dataset consists of three classes namely: coronavirus, pneumonia, and normal X-ray imagery. In this study, the data classes were restructured using the Fuzzy Color technique as a preprocessing step and the images that were structured with the original images were stacked. In the next step, the stacked dataset was trained with deep learning models (MobileNetV2, SqueezeNet) and the feature sets obtained by the models were processed using the Social Mimic optimization method. Thereafter, efficient features were combined and classified using Support Vector Machines (SVM). The overall classification rate obtained with the proposed approach was 99.27%. With the proposed approach in this study, it is evident that the model can efficiently contribute to the detection of COVID-19 disease.
Title: gasnet: weakly-supervised framework for covid-19 lesion segmentation
Published: 2020-10-19 (Preprint, arXiv)
Condition: COVID-19
Task: Segmentation-only | Modality: CT

Abstract: Segmentation of infected areas in chest CT volumes is of great significance for further diagnosis and treatment of COVID-19 patients. Due to the complex shapes and varied appearances of lesions, a large number of voxel-level labeled samples are generally required to train a lesion segmentation network, which is a main bottleneck for developing deep learning based medical image segmentation algorithms. In this paper, we propose a weakly-supervised lesion segmentation framework by embedding the Generative Adversarial training process into the Segmentation Network, which is called GASNet. GASNet is optimized to segment the lesion areas of a COVID-19 CT by the segmenter, and to replace the abnormal appearance with a generated normal appearance by the generator, so that the restored CT volumes are indistinguishable from healthy CT volumes by the discriminator. GASNet is supervised by chest CT volumes of many healthy and COVID-19 subjects without voxel-level annotations. Experiments on three public databases show that when using as few as one voxel-level labeled sample, the performance of GASNet is comparable to fully-supervised segmentation algorithms trained on dozens of voxel-level labeled samples.
Title: mantiscovid: rapid x-ray chest radiograph and mortality rate evaluation with artificial intelligence for covid-19
Published: 2020-05-08 (Preprint, medRxiv)
Condition: COVID-19;Infections
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: The novel coronavirus pandemic has negative impacts over the health, economy and well-being of the global population. This negative effect is growing with the high spreading rate of the virus. The most critical step to prevent the spreading of the virus is pre-screening and early diagnosis of the individuals. This results in quaranteeing the patients not to effect the healthy population. COVID-19 is the name of the disease caused by the novel coronavirus. It has a high infection rate and it is urgent to diagnose many patients as we can to prevent the spread of the virus at the early stage. Rapid diagnostic tools development is urgent to save lives. MantisCOVID is a cloud-based pre-diagnosis tool to be accessed from the internet. This tool delivers a rapid screening test by analyzing the X-ray Chest Radiograph scans via Artificial Intelligence (AI) and it also evaluates the mortality rate of patients with the synthesis of the patient’s history with the machine learning methods. This study reveals the methods used over the platform and evaluation of the algorithms via open datasets.
Title: covid-19 deep learning prediction model using publicly available radiologist-adjudicated chest x-ray images as training data: preliminary findings
Journal: Int J Biomed Imaging
Published: 2020-08-28 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: The key component in deep learning research is the availability of training data sets. With a limited number of publicly available COVID-19 chest X-ray images, the generalization and robustness of deep learning models to detect COVID-19 cases developed based on these images are questionable. We aimed to use thousands of readily available chest radiograph images with clinical findings associated with COVID-19 as a training data set, mutually exclusive from the images with confirmed COVID-19 cases, which will be used as the testing data set. We used a deep learning model based on the ResNet-101 convolutional neural network architecture, which was pretrained to recognize objects from a million of images and then retrained to detect abnormality in chest X-ray images. The performance of the model in terms of area under the receiver operating curve, sensitivity, specificity, and accuracy was 0.82, 77.3%, 71.8%, and 71.9%, respectively. The strength of this study lies in the use of labels that have a strong clinical association with COVID-19 cases and the use of mutually exclusive publicly available data for training, validation, and testing.
Title: classification of the covid-19 infected patients using densenet201 based deep transfer learning
Journal: J Biomol Struct Dyn
Published: 2020-07-04 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19
Task: 2. Detection/Diagnosis | Modality: CT

Abstract: Deep learning models are widely used in the automatic analysis of radiological images. These techniques can train the weights of networks on large datasets as well as fine tuning the weights of pre-trained networks on small datasets. Due to the small COVID-19 dataset available, the pre-trained neural networks can be used for diagnosis of coronavirus. However, these techniques applied on chest CT image is very limited till now. Hence, the main aim of this paper to use the pre-trained deep learning architectures as an automated tool to detection and diagnosis of COVID-19 in chest CT. A DenseNet201 based deep transfer learning (DTL) is proposed to classify the patients as COVID infected or not i.e. COVID-19 or COVID . The proposed model is utilized to extract features by using its own learned weights on the ImageNet dataset along with a convolutional neural structure. Extensive experiments are performed to evaluate the performance of the propose DTL model on COVID-19 chest CT scan images. Comparative analyses reveal that the proposed DTL based COVID-19 classification model outperforms the competitive approaches.Communicated by Ramaswamy H. Sarma.
Title: emcnet: automated covid-19 diagnosis from x-ray images using convolutional neural network and ensemble of machine learning classifiers
Journal: Inform Med Unlocked
Published: 2020-12-29 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: Recently, coronavirus disease (COVID-19) has caused a serious effect on the healthcare system and the overall global economy. Doctors, researchers, and experts are focusing on alternative ways for the rapid detection of COVID-19, such as the development of automatic COVID-19 detection systems. In this paper, an automated detection scheme named EMCNet was proposed to identify COVID-19 patients by evaluating chest X-ray images. A convolutional neural network was developed focusing on the simplicity of the model to extract deep and high-level features from X-ray images of patients infected with COVID-19. With the extracted features, binary machine learning classifiers (random forest, support vector machine, decision tree, and AdaBoost) were developed for the detection of COVID-19. Finally, these classifiers' outputs were combined to develop an ensemble of classifiers, which ensures better results for the dataset of various sizes and resolutions. In comparison with other recent deep learning-based systems, EMCNet showed better performance with 98.91% accuracy, 100% precision, 97.82% recall, and 98.89% F1-score. The system could maintain its great importance on the automatic detection of COVID-19 through instant detection and low false negative rate.
Title: classification of covid-19 patients from chest ct images using multi-objective differential evolution-based convolutional neural networks
Journal: Eur J Clin Microbiol Infect Dis
Published: 2020-04-28 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Infections
Task: 2. Detection/Diagnosis | Modality: CT

Abstract: Early classification of 2019 novel coronavirus disease (COVID-19) is essential for disease cure and control. Compared with reverse-transcription polymerase chain reaction (RT-PCR), chest computed tomography (CT) imaging may be a significantly more trustworthy, useful, and rapid technique to classify and evaluate COVID-19, specifically in the epidemic region. Almost all hospitals have CT imaging machines; therefore, the chest CT images can be utilized for early classification of COVID-19 patients. However, the chest CT-based COVID-19 classification involves a radiology expert and considerable time, which is valuable when COVID-19 infection is growing at rapid rate. Therefore, an automated analysis of chest CT images is desirable to save the medical professionals' precious time. In this paper, a convolutional neural networks (CNN) is used to classify the COVID-19-infected patients as infected (+ve) or not (-ve). Additionally, the initial parameters of CNN are tuned using multi-objective differential evolution (MODE). Extensive experiments are performed by considering the proposed and the competitive machine learning techniques on the chest CT images. Extensive analysis shows that the proposed model can classify the chest CT images at a good accuracy rate.
Title: a light cnn for detecting covid-19 from ct scans of the chest
Journal: Pattern Recognit Lett
Published: 2020-10-13 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Pneumonia
Task: 2. Detection/Diagnosis | Modality: CT

Abstract: Computer Tomography (CT) imaging of the chest is a valid diagnosis tool to detect COVID-19 promptly and to control the spread of the disease. In this work we propose a light Convolutional Neural Network (CNN) design, based on the model of the SqueezeNet, for the efficient discrimination of COVID-19 CT images with respect to other community-acquired pneumonia and/or healthy CT images. The architecture allows to an accuracy of 85.03% with an improvement of about 3.2% in the first dataset arrangement and of about 2.1% in the second dataset arrangement. The obtained gain, though of low entity, can be really important in medical diagnosis and, in particular, for Covid-19 scenario. Also the average classification time on a high-end workstation, 1.25 s, is very competitive with respect to that of more complex CNN designs, 13.41 s, witch require pre-processing. The proposed CNN can be executed on medium-end laptop without GPU acceleration in 7.81 s: this is impossible for methods requiring GPU acceleration. The performance of the method can be further improved with efficient pre-processing strategies for witch GPU acceleration is not necessary.