PCovNet: A presymptomatic COVID-19 detection framework using deep learning model using wearables data.
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ABSTRACT:
SUBMITTER: Abir FF
PROVIDER: S-EPMC9170596 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe COVID-19 pandemic has exposed the vulnerability of healthcare services worldwide, especially in underdeveloped countries. There is a clear need to develop novel computer-assisted diagnosis tools to provide rapid and cost-effective screening in places where massive traditional testing is not feasible. Lung ultrasound is a portable, easy to disinfect, low cost and non-invasive tool that can be used to identify lung diseases. Computer-assisted analysis of lung ultrasound imagery is a relatively recent approach that has shown great potential for diagnosing pulmonary conditions, being a viable alternative for screening and diagnosing COVID-19.ObjectiveTo evaluate and compare the performance of deep-learning techniques for detecting COVID-19 infections from lung ultrasound imagery.MethodsWe adapted different pre-trained deep learning architectures, including VGG19, InceptionV3, Xception, and ResNet50. We used the publicly available POCUS dataset comprising 3326 lung ultrasound frames of healthy, COVID-19, and pneumonia patients for training and fine-tuning. We conducted two experiments considering three classes (COVID-19, pneumonia, and healthy) and two classes (COVID-19 versus pneumonia and COVID-19 versus non-COVID-19) of predictive models. The obtained results were also compared with the POCOVID-net model. For performance evaluation, we calculated per-class classification metrics (Precision, Recall, and F1-score) and overall metrics (Accuracy, Balanced Accuracy, and Area Under the Receiver Operating Characteristic Curve). Lastly, we performed a statistical analysis of performance results using ANOVA and Friedman tests followed by post-hoc analysis using the Wilcoxon signed-rank test with the Holm's step-down correction.ResultsInceptionV3 network achieved the best average accuracy (89.1%), balanced accuracy (89.3%), and area under the receiver operating curve (97.1%) for COVID-19 detection from bacterial pneumonia and healthy lung ultrasound data. The ANOVA and Friedman tests found statistically significant performance differences between models for accuracy, balanced accuracy and area under the receiver operating curve. Post-hoc analysis showed statistically significant differences between the performance obtained with the InceptionV3-based model and POCOVID-net, VGG19-, and ResNet50-based models. No statistically significant differences were found in the performance obtained with InceptionV3- and Xception-based models.ConclusionsDeep learning techniques for computer-assisted analysis of lung ultrasound imagery provide a promising avenue for COVID-19 screening and diagnosis. Particularly, we found that the InceptionV3 network provides the most promising predictive results from all AI-based techniques evaluated in this work. InceptionV3- and Xception-based models can be used to further develop a viable computer-assisted screening tool for COVID-19 based on ultrasound imagery.
| S-EPMC8363024 | biostudies-literature
Project description:Even after scavenging the existence of mankind for the past year, the wrath of CoVID-19 is yet to die down. Countries like India are still getting haunted by the devastating conundrum, with coronavirus ripping through its citizens in the concurrent second wave. The surge of cases has prompted rapid intervention, with medical authorities pushing it to the limit to curve a roadblock to its aggressive growth. But, even after effortless work, human intervention remains slow and insufficient. Furthermore, relevant testing methodologies have shown weakness while detecting threats, with the recent growth of post-Covid complexities, thereby leaving a painful mark. This as such created a major requirement for technological advancements, which can cater to the mass. The growth of computational prowess in the past decade made the field of Deep Learning a major contributor in curving out algorithms to solve this. Adding to the excellent foundation of Deep Learning, this paper, proposes a novel CoWarriorNet model for rapid detection of CoVID-19, via chest X-ray images, which adds in an extra layer of precision and confirmation in the detection of cases in both pre-Covid and post-Covid conditions. The proposed classification model curves out an excellent accuracy of 97.8%, with the major eye-candy being the sensitivity rate of 0.99 when detecting CoVID-19 cases. This model introduces a new concept of Alpha Trimmed Average Pooling, which along with the novel architecture adds a subtle touch to its high efficiency, thereby giving a much-needed solution to the medical experts. The two-mouthed architecture provides the added benefit of a confidence score, deducing human aid in case of discrepancy.Supplementary informationThe online version contains supplementary material available at 10.1007/s00354-021-00143-1.
| S-EPMC8639408 | biostudies-literature
Project description:Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data
| PRJEB31789 | ENA
Project description:Radiological methodologies, such as chest x-rays and CT, are widely employed to help diagnose and monitor COVID-19 disease. COVID-19 displays certain radiological patterns easily detectable by X-rays of the chest. Therefore, radiologists can investigate these patterns for detecting coronavirus disease. However, this task is time-consuming and needs lots of trial and error. One of the main solutions to resolve this issue is to apply intelligent techniques such as deep learning (DL) models to automatically analyze the chest X-rays. Nevertheless, fine-tuning of architecture and hyperparameters of DL models is a complex and time-consuming procedure. In this paper, we propose an effective method to detect COVID-19 disease by applying convolutional neural network (CNN) to the chest X-ray images. To improve the accuracy of the proposed method, the last Softmax CNN layer is replaced with a K -nearest neighbors (KNN) classifier which takes into account the agreement of the neighborhood labeling. Moreover, we develop a novel evolutionary algorithm by improving the basic version of competitive swarm optimizer. To this end, three powerful evolutionary operators: Cauchy Mutation (CM), Evolutionary Boundary Constraint Handling (EBCH), and tent chaotic map are incorporated into the search process of the proposed evolutionary algorithm to speed up its convergence and make an excellent balance between exploration and exploitation phases. Then, the proposed evolutionary algorithm is used to automatically achieve the optimal values of CNN's hyperparameters leading to a significant improvement in the classification accuracy of the proposed method. Comprehensive comparative results reveal that compared with current models in the literature, the proposed method performs significantly more efficient.
| S-EPMC8966159 | biostudies-literature
Project description:The lethal novel coronavirus disease 2019 (COVID-19) pandemic is affecting the health of the global population severely, and a huge number of people may have to be screened in the future. There is a need for effective and reliable systems that perform automatic detection and mass screening of COVID-19 as a quick alternative diagnostic option to control its spread. A robust deep learning-based system is proposed to detect the COVID-19 using chest X-ray images. Infected patient's chest X-ray images reveal numerous opacities (denser, confluent, and more profuse) in comparison to healthy lungs images which are used by a deep learning algorithm to generate a model to facilitate an accurate diagnostics for multi-class classification (COVID vs. normal vs. bacterial pneumonia vs. viral pneumonia) and binary classification (COVID-19 vs. non-COVID). COVID-19 positive images have been used for training and model performance assessment from several hospitals of India and also from countries like Australia, Belgium, Canada, China, Egypt, Germany, Iran, Israel, Italy, Korea, Spain, Taiwan, USA, and Vietnam. The data were divided into training, validation and test sets. The average test accuracy of 97.11 ± 2.71% was achieved for multi-class (COVID vs. normal vs. pneumonia) and 99.81% for binary classification (COVID-19 vs. non-COVID). The proposed model performs rapid disease detection in 0.137 s per image in a system equipped with a GPU and can reduce the workload of radiologists by classifying thousands of images on a single click to generate a probabilistic report in real-time.
| S-EPMC7837255 | biostudies-literature
Project description:There have been more than 2.2 million confirmed cases and over 120 000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. However, there is currently a lack of proven effective medications against COVID-19. Drug repurposing offers a promising route for the development of prevention and treatment strategies for COVID-19. This study reports an integrative, network-based deep-learning methodology to identify repurposable drugs for COVID-19 (termed CoV-KGE). Specifically, we built a comprehensive knowledge graph that includes 15 million edges across 39 types of relationships connecting drugs, diseases, proteins/genes, pathways, and expression from a large scientific corpus of 24 million PubMed publications. Using Amazon's AWS computing resources and a network-based, deep-learning framework, we identified 41 repurposable drugs (including dexamethasone, indomethacin, niclosamide, and toremifene) whose therapeutic associations with COVID-19 were validated by transcriptomic and proteomics data in SARS-CoV-2-infected human cells and data from ongoing clinical trials. Whereas this study by no means recommends specific drugs, it demonstrates a powerful deep-learning methodology to prioritize existing drugs for further investigation, which holds the potential to accelerate therapeutic development for COVID-19.
| S-EPMC7384389 | biostudies-literature
Project description:Purpose: To construct a deep learning knowledge distillation framework exploring the utilization of MRI alone or combing with distilled Arthroscopy information for meniscus tear detection. Methods: A database of 199 paired knee Arthroscopy-MRI exams was used to develop a multimodal teacher network and an MRI-based student network, which used residual neural networks architectures. A knowledge distillation framework comprising the multimodal teacher network T and the monomodal student network S was proposed. We optimized the loss functions of mean squared error (MSE) and cross-entropy (CE) to enable the student network S to learn arthroscopic information from the teacher network T through our deep learning knowledge distillation framework, ultimately resulting in a distilled student network S T. A coronal proton density (PD)-weighted fat-suppressed MRI sequence was used in this study. Fivefold cross-validation was employed, and the accuracy, sensitivity, specificity, F1-score, receiver operating characteristic (ROC) curves and area under the receiver operating characteristic curve (AUC) were used to evaluate the medial and lateral meniscal tears detection performance of the models, including the undistilled student model S, the distilled student model S T and the teacher model T. Results: The AUCs of the undistilled student model S, the distilled student model S T, the teacher model T for medial meniscus (MM) tear detection and lateral meniscus (LM) tear detection are 0.773/0.672, 0.792/0.751 and 0.834/0.746, respectively. The distilled student model S T had higher AUCs than the undistilled model S. After undergoing knowledge distillation processing, the distilled student model demonstrated promising results, with accuracy (0.764/0.734), sensitivity (0.838/0.661), and F1-score (0.680/0.754) for both medial and lateral tear detection better than the undistilled one with accuracy (0.734/0.648), sensitivity (0.733/0.607), and F1-score (0.620/0.673). Conclusion: Through the knowledge distillation framework, the student model S based on MRI benefited from the multimodal teacher model T and achieved an improved meniscus tear detection performance.
| S-EPMC10825958 | biostudies-literature
Project description:BackgroundArtificial intelligence technologies in classification/detection of COVID-19 positive cases suffer from generalizability. Moreover, accessing and preparing another large dataset is not always feasible and time-consuming. Several studies have combined smaller COVID-19 CT datasets into "supersets" to maximize the number of training samples. This study aims to assess generalizability by splitting datasets into different portions based on 3D CT images using deep learning.MethodTwo large datasets, including 1110 3D CT images, were split into five segments of 20% each. Each dataset's first 20% segment was separated as a holdout test set. 3D-CNN training was performed with the remaining 80% from each dataset. Two small external datasets were also used to independently evaluate the trained models.ResultsThe total combination of 80% of each dataset has an accuracy of 91% on Iranmehr and 83% on Moscow holdout test datasets. Results indicated that 80% of the primary datasets are adequate for fully training a model. The additional fine-tuning using 40% of a secondary dataset helps the model generalize to a third, unseen dataset. The highest accuracy achieved through transfer learning was 85% on LDCT dataset and 83% on Iranmehr holdout test sets when retrained on 80% of Iranmehr dataset.ConclusionWhile the total combination of both datasets produced the best results, different combinations and transfer learning still produced generalizable results. Adopting the proposed methodology may help to obtain satisfactory results in the case of limited external datasets.
| S-EPMC8971071 | biostudies-literature
Project description:Detecting COVID-19 at an early stage is essential to reduce the mortality risk of the patients. In this study, a cascaded system is proposed to segment the lung, detect, localize, and quantify COVID-19 infections from computed tomography images. An extensive set of experiments were performed using Encoder-Decoder Convolutional Neural Networks (ED-CNNs), UNet, and Feature Pyramid Network (FPN), with different backbone (encoder) structures using the variants of DenseNet and ResNet. The conducted experiments for lung region segmentation showed a Dice Similarity Coefficient (DSC) of 97.19% and Intersection over Union (IoU) of 95.10% using U-Net model with the DenseNet 161 encoder. Furthermore, the proposed system achieved an elegant performance for COVID-19 infection segmentation with a DSC of 94.13% and IoU of 91.85% using the FPN with DenseNet201 encoder. The proposed system can reliably localize infections of various shapes and sizes, especially small infection regions, which are rarely considered in recent studies. Moreover, the proposed system achieved high COVID-19 detection performance with 99.64% sensitivity and 98.72% specificity. Finally, the system was able to discriminate between different severity levels of COVID-19 infection over a dataset of 1110 subjects with sensitivity values of 98.3%, 71.2%, 77.8%, and 100% for mild, moderate, severe, and critical, respectively.
| S-EPMC8155971 | biostudies-literature
Project description:Emotion states recognition using wireless signals is an emerging area of research that has an impact on neuroscientific studies of human behaviour and well-being monitoring. Currently, standoff emotion detection is mostly reliant on the analysis of facial expressions and/or eye movements acquired from optical or video cameras. Meanwhile, although they have been widely accepted for recognizing human emotions from the multimodal data, machine learning approaches have been mostly restricted to subject dependent analyses which lack of generality. In this paper, we report an experimental study which collects heartbeat and breathing signals of 15 participants from radio frequency (RF) reflections off the body followed by novel noise filtering techniques. We propose a novel deep neural network (DNN) architecture based on the fusion of raw RF data and the processed RF signal for classifying and visualising various emotion states. The proposed model achieves high classification accuracy of 71.67% for independent subjects with 0.71, 0.72 and 0.71 precision, recall and F1-score values respectively. We have compared our results with those obtained from five different classical ML algorithms and it is established that deep learning offers a superior performance even with limited amount of raw RF and post processed time-sequence data. The deep learning model has also been validated by comparing our results with those from ECG signals. Our results indicate that using wireless signals for stand-by emotion state detection is a better alternative to other technologies with high accuracy and have much wider applications in future studies of behavioural sciences.
| S-EPMC7857608 | biostudies-literature