zurlog/subset_wlabels huggingface dataset:
Title: a novel comparative study for detection of covid-19 on ct lung images using texture analysis machine learning and deep learning methods
Journal: Multimed Tools Appl
Published: 2020-10-13 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Pneumonia
Task: 2. Detection/Diagnosis | Modality: CT

Abstract: The Covid-19 virus outbreak that emerged in China at the end of 2019 caused a huge and devastating effect worldwide. In patients with severe symptoms of the disease, pneumonia develops due to Covid-19 virus. This causes intense involvement and damage in lungs. Although the emergence of the disease occurred a short time ago, many literature studies have been carried out in which these effects of the disease on the lungs were revealed by the help of lung CT imaging. In this study, 1.396 lung CT images in total (386 Covid-19 and 1.010 Non-Covid-19) were subjected to automatic classification. In this study, Convolutional Neural Network (CNN), one of the deep learning methods, was used which suggested automatic classification of CT images of lungs for early diagnosis of Covid-19 disease. In addition, k-Nearest Neighbors (k-NN) and Support Vector Machine (SVM) was used to compare the classification successes of deep learning with machine learning. Within the scope of the study, a 23-layer CNN architecture was designed and used as a classifier. Also, training and testing processes were performed for Alexnet and Mobilenetv2 CNN architectures as well. The classification results were also calculated for the case of increasing the number of images used in training for the first 23-layer CNN architecture by 5, 10, and 20 times using data augmentation methods. To reveal the effect of the change in the number of images in the training and test clusters on the results, two different training and testing processes, 2-fold and 10-fold cross-validation, were performed and the results of the study were calculated. As a result, thanks to these detailed calculations performed within the scope of the study, a comprehensive comparison of the success of the texture analysis method, machine learning, and deep learning methods in Covid-19 classification from CT images was made. The highest mean sensitivity, specificity, accuracy, F-1 score, and AUC values obtained as a result of the study were 0,9197, 0,9891, 0,9473, 0,9058, 0,9888; respectively for 2-fold cross-validation, and they were 0,9404, 0,9901, 0,9599, 0,9284, 0,9903; respectively for 10-fold cross-validation.
Title: covid-19-ct-cxr: a freely accessible and weakly labeled chest x-ray and ct image collection on covid-19 from biomedical literature
Journal: IEEE Trans Big Data
Published: 2021-05-18 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;COVID-19 Pandemic;Influenza, Human
Task: 2. Detection/Diagnosis | Modality: CT

Abstract: The latest threat to global health is the COVID-19 outbreak. Although there exist large datasets of chest X-rays (CXR) and computed tomography (CT) scans, few COVID-19 image collections are currently available due to patient privacy. At the same time, there is a rapid growth of COVID-19-relevant articles in the biomedical literature, including those that report findings on radiographs. Here, we present COVID-19-CT-CXR, a public database of COVID-19 CXR and CT images, which are automatically extracted from COVID-19-relevant articles from the PubMed Central Open Access (PMC-OA) Subset. We extracted figures, associated captions, and relevant figure descriptions in the article and separated compound figures into subfigures. Because a large portion of figures in COVID-19 articles are not CXR or CT, we designed a deep-learning model to distinguish them from other figure types and to classify them accordingly. The final database includes 1,327 CT and 263 CXR images (as of May 9, 2020) with their relevant text. To demonstrate the utility of COVID-19-CT-CXR, we conducted four case studies. We show that COVID-19-CT-CXR, when used as additional training data, is able to contribute to improved deep-learning (DL) performance for the classification of COVID-19 and non-COVID-19 CT. We collected CT images of influenza, another common infectious respiratory illness that may present similarly to COVID-19, and fine-tuned a baseline deep neural network to distinguish a diagnosis of COVID-19, influenza, or normal or other types of diseases on CT. We fine-tuned an unsupervised one-class classifier from non-COVID-19 CXR and performed anomaly detection to detect COVID-19 CXR. From text-mined captions and figure descriptions, we compared 15 clinical symptoms and 20 clinical findings of COVID-19 versus those of influenza to demonstrate the disease differences in the scientific publications. Our database is unique, as the figures are retrieved along with relevant text with fine-grained descriptions, and it can be extended easily in the future. We believe that our work is complementary to existing resources and hope that it will contribute to medical image analysis of the COVID-19 pandemic. The dataset, code, and DL models are publicly available at GitHub
Title: the usage of deep neural network improves distinguishing covid-19 from other suspected viral pneumonia by clinicians on chest ct: a real-world study
Journal: Eur Radiol
Published: 2020-12-30 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Pneumonia;Pneumonia, Viral
Task: 2. Detection/Diagnosis | Modality: CT

Abstract: Based on the current clinical routine, we aimed to develop a novel deep learning model to distinguish coronavirus disease 2019 (COVID-19) pneumonia from other types of pneumonia and validate it with a real-world dataset (RWD). A total of 563 chest CT scans of 380 patients (227/380 were diagnosed with COVID-19 pneumonia) from 5 hospitals were collected to train our deep learning (DL) model. Lung regions were extracted by U-net, then transformed and fed to pre-trained ResNet-50-based IDANNet (Identification and Analysis of New covid-19 Net) to produce a diagnostic probability. Fivefold cross-validation was employed to validate the application of our model. Another 318 scans of 316 patients (243/316 were diagnosed with COVID-19 pneumonia) from 2 other hospitals were enrolled prospectively as the RWDs to testify our DL model's performance and compared it with that from 3 experienced radiologists. A three-dimensional DL model was successfully established. The diagnostic threshold to differentiate COVID-19 and non-COVID-19 pneumonia was 0.685 with an AUC of 0.906 (95% CI: 0.886-0.913) in the internal validation group. In the RWD cohort, our model achieved an AUC of 0.868 (95% CI: 0.851-0.876) with the sensitivity of 0.811 and the specificity of 0.822, non-inferior to the performance of 3 experienced radiologists, suggesting promising clinical practical usage. The established DL model was able to achieve accurate identification of COVID-19 pneumonia from other suspected ones in the real-world situation, which could become a reliable tool in clinical routine. In an internal validation set, our DL model achieved the best performance to differentiate COVID-19 from non-COVID-19 pneumonia with a sensitivity of 0.836, a specificity of 0.800, and an AUC of 0.906 (95% CI: 0.886-0.913) when the threshold was set at 0.685. In the prospective RWD cohort, our DL diagnostic model achieved a sensitivity of 0.811, a specificity of 0.822, and AUC of 0.868 (95% CI: 0.851-0.876), non-inferior to the performance of 3 experienced radiologists. The attention heatmaps were fully generated by the model without additional manual annotation and the attention regions were highly aligned with the ROIs acquired by human radiologists for diagnosis.
Title: deep metric learning-based image retrieval system for chest radiograph and its clinical applications in covid-19
Journal: Med Image Anal
Published: 2021-03-13 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;COVID-19 Pandemic
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: In recent years, deep learning-based image analysis methods have been widely applied in computer-aided detection, diagnosis and prognosis, and has shown its value during the public health crisis of the novel coronavirus disease 2019 (COVID-19) pandemic. Chest radiograph (CXR) has been playing a crucial role in COVID-19 patient triaging, diagnosing and monitoring, particularly in the United States. Considering the mixed and unspecific signals in CXR, an image retrieval model of CXR that provides both similar images and associated clinical information can be more clinically meaningful than a direct image diagnostic model. In this work we develop a novel CXR image retrieval model based on deep metric learning. Unlike traditional diagnostic models which aim at learning the direct mapping from images to labels, the proposed model aims at learning the optimized embedding space of images, where images with the same labels and similar contents are pulled together. The proposed model utilizes multi-similarity loss with hard-mining sampling strategy and attention mechanism to learn the optimized embedding space, and provides similar images, the visualizations of disease-related attention maps and useful clinical information to assist clinical decisions. The model is trained and validated on an international multi-site COVID-19 dataset collected from 3 different sources. Experimental results of COVID-19 image retrieval and diagnosis tasks show that the proposed model can serve as a robust solution for CXR analysis and patient management for COVID-19. The model is also tested on its transferability on a different clinical decision support task for COVID-19, where the pre-trained model is applied to extract image features from a new dataset without any further training. The extracted features are then combined with COVID-19 patient's vitals, lab tests and medical histories to predict the possibility of airway intubation in 72 hours, which is strongly associated with patient prognosis, and is crucial for patient care and hospital resource planning. These results demonstrate our deep metric learning based image retrieval model is highly efficient in the CXR retrieval, diagnosis and prognosis, and thus has great clinical value for the treatment and management of COVID-19 patients.
Title: systematic review of artificial intelligence techniques in the detection and classification of covid-19 medical images in terms of evaluation and benchmarking: taxonomy analysis challenges future solutions and methodological aspects
Journal: J Infect Public Health
Published: 2020-07-11 (Journal Article;Systematic Review, Peer reviewed (PubMed))
Condition: COVID-19
Task: Review | Modality: Multimodal

Abstract: This study presents a systematic review of artificial intelligence (AI) techniques used in the detection and classification of coronavirus disease 2019 (COVID-19) medical images in terms of evaluation and benchmarking. Five reliable databases, namely, IEEE Xplore, Web of Science, PubMed, ScienceDirect and Scopus were used to obtain relevant studies of the given topic. Several filtering and scanning stages were performed according to the inclusion/exclusion criteria to screen the 36 studies obtained; however, only 11 studies met the criteria. Taxonomy was performed, and the 11 studies were classified on the basis of two categories, namely, review and research studies. Then, a deep analysis and critical review were performed to highlight the challenges and critical gaps outlined in the academic literature of the given subject. Results showed that no relevant study evaluated and benchmarked AI techniques utilised in classification tasks (i.e. binary, multi-class, multi-labelled and hierarchical classifications) of COVID-19 medical images. In case evaluation and benchmarking will be conducted, three future challenges will be encountered, namely, multiple evaluation criteria within each classification task, trade-off amongst criteria and importance of these criteria. According to the discussed future challenges, the process of evaluation and benchmarking AI techniques used in the classification of COVID-19 medical images considered multi-complex attribute problems. Thus, adopting multi-criteria decision analysis (MCDA) is an essential and effective approach to tackle the problem complexity. Moreover, this study proposes a detailed methodology for the evaluation and benchmarking of AI techniques used in all classification tasks of COVID-19 medical images as future directions; such methodology is presented on the basis of three sequential phases. Firstly, the identification procedure for the construction of four decision matrices, namely, binary, multi-class, multi-labelled and hierarchical, is presented on the basis of the intersection of evaluation criteria of each classification task and AI classification techniques. Secondly, the development of the MCDA approach for benchmarking AI classification techniques is provided on the basis of the integrated analytic hierarchy process and VlseKriterijumska Optimizacija I Kompromisno Resenje methods. Lastly, objective and subjective validation procedures are described to validate the proposed benchmarking solutions.
Title: a systematic review on the use of ai and ml for fighting the covid-19 pandemic
Journal: IEEE Trans Artif Intell
Published: 2021-03-01 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;COVID-19 Pandemic
Task: Review | Modality: Multimodal

Abstract: Artificial intelligence (AI) and machine learning (ML) have caused a paradigm shift in healthcare that can be used for decision support and forecasting by exploring medical data. Recent studies have shown that AI and ML can be used to fight COVID-19. The objective of this article is to summarize the recent AI- and ML-based studies that have addressed the pandemic. From an initial set of 634 articles, a total of 49 articles were finally selected through an inclusion-exclusion process. In this article, we have explored the objectives of the existing studies (i.e., the role of AI/ML in fighting the COVID-19 pandemic); the context of the studies (i.e., whether it was focused on a specific country-context or with a global perspective; the type and volume of the dataset; and the methodology, algorithms, and techniques adopted in the prediction or diagnosis processes). We have mapped the algorithms and techniques with the data type by highlighting their prediction/classification accuracy. From our analysis, we categorized the objectives of the studies into four groups: disease detection, epidemic forecasting, sustainable development, and disease diagnosis. We observed that most of these studies used deep learning algorithms on image-data, more specifically on chest X-rays and CT scans. We have identified six future research opportunities that we have summarized in this paper. Artificial intelligence (AI) and machine learning (ML) methods have been widely used to assist in the fight against COVID-19 pandemic. A very few in-depth literature reviews have been conducted to synthesize the knowledge and identify future research agenda including a previously published review on data science for COVID-19 in this article. In this article, we synthesized reviewed recent literature that focuses on the usages and applications of AI and ML to fight against COVID-19. We have identified seven future research directions that would guide researchers to conduct future research. The most significant of these are: develop new treatment options, explore the contextual effect and variation in research outcomes, support the health care workforce, and explore the effect and variation in research outcomes based on different types of data.
Title: machine learning automatically detects covid-19 using chest cts in a large multicenter cohort
Journal: Eur Radiol
Published: 2021-05-03 (Journal Article;Multicenter Study, Peer reviewed (PubMed))
Condition: COVID-19;Lung Diseases;Pneumonia;Pneumonia, Interstitial
Task: 2. Detection/Diagnosis | Modality: CT

Abstract: To investigate machine learning classifiers and interpretable models using chest CT for detection of COVID-19 and differentiation from other pneumonias, interstitial lung disease (ILD) and normal CTs. Our retrospective multi-institutional study obtained 2446 chest CTs from 16 institutions (including 1161 COVID-19 patients). Training/validation/testing cohorts included 1011/50/100 COVID-19, 388/16/33 ILD, 189/16/33 other pneumonias, and 559/17/34 normal (no pathologies) CTs. A metric-based approach for the classification of COVID-19 used interpretable features, relying on logistic regression and random forests. A deep learning-based classifier differentiated COVID-19 via 3D features extracted directly from CT attenuation and probability distribution of airspace opacities. Most discriminative features of COVID-19 are the percentage of airspace opacity and peripheral and basal predominant opacities, concordant with the typical characterization of COVID-19 in the literature. Unsupervised hierarchical clustering compares feature distribution across COVID-19 and control cohorts. The metrics-based classifier achieved AUC = 0.83, sensitivity = 0.74, and specificity = 0.79 versus respectively 0.93, 0.90, and 0.83 for the DL-based classifier. Most of ambiguity comes from non-COVID-19 pneumonia with manifestations that overlap with COVID-19, as well as mild COVID-19 cases. Non-COVID-19 classification performance is 91% for ILD, 64% for other pneumonias, and 94% for no pathologies, which demonstrates the robustness of our method against different compositions of control groups. Our new method accurately discriminates COVID-19 from other types of pneumonia, ILD, and CTs with no pathologies, using quantitative imaging features derived from chest CT, while balancing interpretability of results and classification performance and, therefore, may be useful to facilitate diagnosis of COVID-19. Unsupervised clustering reveals the key tomographic features including percent airspace opacity and peripheral and basal opacities most typical of COVID-19 relative to control groups. COVID-19-positive CTs were compared with COVID-19-negative chest CTs (including a balanced distribution of non-COVID-19 pneumonia, ILD, and no pathologies). Classification accuracies for COVID-19, pneumonia, ILD, and CT scans with no pathologies are respectively 90%, 64%, 91%, and 94%. Our deep learning (DL)-based classification method demonstrates an AUC of 0.93 (sensitivity 90%, specificity 83%). Machine learning methods applied to quantitative chest CT metrics can therefore improve diagnostic accuracy in suspected COVID-19, particularly in resource-constrained environments.
Title: diagnosis of coronavirus disease 2019 pneumonia by using chest radiography: value of artificial intelligence
Journal: Radiology
Published: 2020-09-25 (Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't, Peer reviewed (PubMed))
Condition: COVID-19;Pneumonia;Severe Acute Respiratory Syndrome
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: Background Radiologists are proficient in differentiating between chest radiographs with and without symptoms of pneumonia but have found it more challenging to differentiate coronavirus disease 2019 (COVID-19) pneumonia from non-COVID-19 pneumonia on chest radiographs. Purpose To develop an artificial intelligence algorithm to differentiate COVID-19 pneumonia from other causes of abnormalities at chest radiography. In this retrospective study, a deep neural network, CV19-Net, was trained, validated, and tested on chest radiographs in patients with and without COVID-19 pneumonia. For the chest radiographs positive for COVID-19, patients with reverse transcription polymerase chain reaction results positive for severe acute respiratory syndrome coronavirus 2 with findings positive for pneumonia between February 1, 2020, and May 30, 2020, were included. For the non-COVID-19 chest radiographs, patients with pneumonia who underwent chest radiography between October 1, 2019, and December 31, 2019, were included. Area under the receiver operating characteristic curve (AUC), sensitivity, and specificity were calculated to characterize diagnostic performance. To benchmark the performance of CV19-Net, a randomly sampled test data set composed of 500 chest radiographs in 500 patients was evaluated by the CV19-Net and three experienced thoracic radiologists. Results A total of 2060 patients (5806 chest radiographs; mean age, 62 years ; 1059 men) with COVID-19 pneumonia and 3148 patients (5300 chest radiographs; mean age, 64 years ; 1578 men) with non-COVID-19 pneumonia were included and split into training and validation and test data sets. For the test set, CV19-Net achieved an AUC of 0.92 (95% CI: 0.91, 0.93). This corresponded to a sensitivity of 88% (95% CI: 87, 89) and a specificity of 79% (95% CI: 77, 80) by using a high-sensitivity operating threshold, or a sensitivity of 78% (95% CI: 77, 79) and a specificity of 89% (95% CI: 88, 90) by using a high-specificity operating threshold. For the 500 sampled chest radiographs, CV19-Net achieved an AUC of 0.94 (95% CI: 0.93, 0.96) compared with an AUC of 0.85 (95% CI: 0.81, 0.88) achieved by radiologists. Conclusion CV19-Net was able to differentiate coronavirus disease 2019-related pneumonia from other types of pneumonia, with performance exceeding that of experienced thoracic radiologists.
Title: development of a quantitative segmentation model to assess the effect of comorbidity on patients with covid-19
Journal: Eur J Med Res
Published: 2020-10-14 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Diabetes Mellitus;Pneumonia
Task: Segmentation-only | Modality: CT

Abstract: The coronavirus disease 2019 (COVID-19) has brought a global disaster. Quantitative lesions may provide the radiological evidence of the severity of pneumonia and further to assess the effect of comorbidity on patients with COVID-19. 294 patients with COVID-19 were enrolled from February, 24, 2020 to June, 1, 2020 from six centers. Multi-task Unet network was used to segment the whole lung and lesions from chest CT images. This deep learning method was pre-trained in 650 CT images (550 in primary dataset and 100 in test dataset) with COVID-19 or community-acquired pneumonia and Dice coefficients in test dataset were calculated. 50 CT scans of 50 patients (15 with comorbidity and 35 without comorbidity) were random selected to mark lesions manually. The results will be compared with the automatic segmentation model. Eight quantitative parameters were calculated based on the segmentation results to evaluate the effect of comorbidity on patients with COVID-19. Quantitative segmentation model was proved to be effective and accurate with all Dice coefficients more than 0.85 and all accuracies more than 0.95. Of the 294 patients, 52 patients were reported having at least one comorbidity; 14 having more than one comorbidity. Patients with any comorbidity were older (P < 0.001), had longer incubation period (P < 0.001), were more likely to have abnormal laboratory findings (P < 0.05), and be in severity status (P < 0.001). More lesions (including larger volume of lesion, consolidation, and ground-glass opacity) were shown in patients with any comorbidity than patients without comorbidity (all P < 0.001). More lesions were found on CT images in patients with more comorbidities. The median volumes of lesion, consolidation, and ground-glass opacity in diabetes mellitus group were largest among the groups with single comorbidity that had the incidence rate of top three. Multi-task Unet network can make quantitative CT analysis of lesions to assess the effect of comorbidity on patients with COVID-19, further to provide the radiological evidence of the severity of pneumonia. More lesions (including GGO and consolidation) were found in CT images of cases with comorbidity. The more comorbidities patients have, the more lesions CT images show.