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1.
Front Public Health ; 9: 768278, 2021.
Article in English | MEDLINE | ID: covidwho-1518580

ABSTRACT

Objective: COVID-19 is a sort of infectious disease caused by a new strain of coronavirus. This study aims to develop a more accurate COVID-19 diagnosis system. Methods: First, the n-conv module (nCM) is introduced. Then we built a 12-layer convolutional neural network (12l-CNN) as the backbone network. Afterwards, PatchShuffle was introduced to integrate with 12l-CNN as a regularization term of the loss function. Our model was named PSCNN. Moreover, multiple-way data augmentation and Grad-CAM are employed to avoid overfitting and locating lung lesions. Results: The mean and standard variation values of the seven measures of our model were 95.28 ± 1.03 (sensitivity), 95.78 ± 0.87 (specificity), 95.76 ± 0.86 (precision), 95.53 ± 0.83 (accuracy), 95.52 ± 0.83 (F1 score), 91.7 ± 1.65 (MCC), and 95.52 ± 0.83 (FMI). Conclusion: Our PSCNN is better than 10 state-of-the-art models. Further, we validate the optimal hyperparameters in our model and demonstrate the effectiveness of PatchShuffle.


Subject(s)
COVID-19 , Deep Learning , COVID-19 Testing , Humans , Neural Networks, Computer , SARS-CoV-2
2.
PLoS One ; 16(9): e0256630, 2021.
Article in English | MEDLINE | ID: covidwho-1518353

ABSTRACT

Pneumonia is a respiratory infection caused by bacteria or viruses; it affects many individuals, especially in developing and underdeveloped nations, where high levels of pollution, unhygienic living conditions, and overcrowding are relatively common, together with inadequate medical infrastructure. Pneumonia causes pleural effusion, a condition in which fluids fill the lung, causing respiratory difficulty. Early diagnosis of pneumonia is crucial to ensure curative treatment and increase survival rates. Chest X-ray imaging is the most frequently used method for diagnosing pneumonia. However, the examination of chest X-rays is a challenging task and is prone to subjective variability. In this study, we developed a computer-aided diagnosis system for automatic pneumonia detection using chest X-ray images. We employed deep transfer learning to handle the scarcity of available data and designed an ensemble of three convolutional neural network models: GoogLeNet, ResNet-18, and DenseNet-121. A weighted average ensemble technique was adopted, wherein the weights assigned to the base learners were determined using a novel approach. The scores of four standard evaluation metrics, precision, recall, f1-score, and the area under the curve, are fused to form the weight vector, which in studies in the literature was frequently set experimentally, a method that is prone to error. The proposed approach was evaluated on two publicly available pneumonia X-ray datasets, provided by Kermany et al. and the Radiological Society of North America (RSNA), respectively, using a five-fold cross-validation scheme. The proposed method achieved accuracy rates of 98.81% and 86.85% and sensitivity rates of 98.80% and 87.02% on the Kermany and RSNA datasets, respectively. The results were superior to those of state-of-the-art methods and our method performed better than the widely used ensemble techniques. Statistical analyses on the datasets using McNemar's and ANOVA tests showed the robustness of the approach. The codes for the proposed work are available at https://github.com/Rohit-Kundu/Ensemble-Pneumonia-Detection.


Subject(s)
COVID-19/diagnosis , Early Diagnosis , Pneumonia/diagnosis , Thorax/diagnostic imaging , COVID-19/diagnostic imaging , COVID-19/virology , Deep Learning , Humans , Lung/diagnostic imaging , Lung/pathology , Neural Networks, Computer , North America , Pneumonia/diagnostic imaging , SARS-CoV-2/isolation & purification , SARS-CoV-2/pathogenicity , Thorax/pathology , X-Rays
3.
Comput Intell Neurosci ; 2021: 9615034, 2021.
Article in English | MEDLINE | ID: covidwho-1518184

ABSTRACT

Fake news is challenging to detect due to mixing accurate and inaccurate information from reliable and unreliable sources. Social media is a data source that is not trustworthy all the time, especially in the COVID-19 outbreak. During the COVID-19 epidemic, fake news is widely spread. The best way to deal with this is early detection. Accordingly, in this work, we have proposed a hybrid deep learning model that uses convolutional neural network (CNN) and long short-term memory (LSTM) to detect COVID-19 fake news. The proposed model consists of some layers: an embedding layer, a convolutional layer, a pooling layer, an LSTM layer, a flatten layer, a dense layer, and an output layer. For experimental results, three COVID-19 fake news datasets are used to evaluate six machine learning models, two deep learning models, and our proposed model. The machine learning models are DT, KNN, LR, RF, SVM, and NB, while the deep learning models are CNN and LSTM. Also, four matrices are used to validate the results: accuracy, precision, recall, and F1-measure. The conducted experiments show that the proposed model outperforms the six machine learning models and the two deep learning models. Consequently, the proposed system is capable of detecting the fake news of COVID-19 significantly.


Subject(s)
COVID-19 , Deep Learning , Humans , Machine Learning , Neural Networks, Computer , SARS-CoV-2
4.
Sensors (Basel) ; 21(21)2021 Oct 25.
Article in English | MEDLINE | ID: covidwho-1512559

ABSTRACT

Wearable technologies are known to improve our quality of life. Among the various wearable devices, shoes are non-intrusive, lightweight, and can be used for outdoor activities. In this study, we estimated the energy consumption and heart rate in an environment (i.e., running on a treadmill) using smart shoes equipped with triaxial acceleration, triaxial gyroscope, and four-point pressure sensors. The proposed model uses the latest deep learning architecture which does not require any separate preprocessing. Moreover, it is possible to select the optimal sensor using a channel-wise attention mechanism to weigh the sensors depending on their contributions to the estimation of energy expenditure (EE) and heart rate (HR). The performance of the proposed model was evaluated using the root mean squared error (RMSE), mean absolute error (MAE), and coefficient of determination (R2). Moreover, the RMSE was 1.05 ± 0.15, MAE 0.83 ± 0.12 and R2 0.922 ± 0.005 in EE estimation. On the other hand, and RMSE was 7.87 ± 1.12, MAE 6.21 ± 0.86, and R2 0.897 ± 0.017 in HR estimation. In both estimations, the most effective sensor was the z axis of the accelerometer and gyroscope sensors. Through these results, it is demonstrated that the proposed model could contribute to the improvement of the performance of both EE and HR estimations by effectively selecting the optimal sensors during the active movements of participants.


Subject(s)
Deep Learning , Shoes , Energy Metabolism , Heart Rate , Humans , Quality of Life
5.
BMC Bioinformatics ; 22(Suppl 5): 147, 2021 Nov 08.
Article in English | MEDLINE | ID: covidwho-1505775

ABSTRACT

BACKGROUND: To classify chest computed tomography (CT) images as positive or negative for coronavirus disease 2019 (COVID-19) quickly and accurately, researchers attempted to develop effective models by using medical images. RESULTS: A convolutional neural network (CNN) ensemble model was developed for classifying chest CT images as positive or negative for COVID-19. To classify chest CT images acquired from COVID-19 patients, the proposed COVID19-CNN ensemble model combines the use of multiple trained CNN models with a majority voting strategy. The CNN models were trained to classify chest CT images by transfer learning from well-known pre-trained CNN models and by applying their algorithm hyperparameters as appropriate. The combination of algorithm hyperparameters for a pre-trained CNN model was determined by uniform experimental design. The chest CT images (405 from COVID-19 patients and 397 from healthy patients) used for training and performance testing of the COVID19-CNN ensemble model were obtained from an earlier study by Hu in 2020. Experiments showed that, the COVID19-CNN ensemble model achieved 96.7% accuracy in classifying CT images as COVID-19 positive or negative, which was superior to the accuracies obtained by the individual trained CNN models. Other performance measures (i.e., precision, recall, specificity, and F1-score) obtained bythe COVID19-CNN ensemble model were higher than those obtained by individual trained CNN models. CONCLUSIONS: The COVID19-CNN ensemble model had superior accuracy and excellent capability in classifying chest CT images as COVID-19 positive or negative.


Subject(s)
COVID-19 , Deep Learning , Humans , Neural Networks, Computer , Research Design , SARS-CoV-2 , Tomography, X-Ray Computed
6.
Igaku Butsuri ; 41(3): 82-86, 2021.
Article in Japanese | MEDLINE | ID: covidwho-1505586

ABSTRACT

The intra- and inter-observer variability in diagnosis of thoracic CT images may affect the diagnosis of COVID-19. Therefore, several studies have been reported to develop artificial intelligence (AI) approaches using deep learning (DL) and radiomics technologies. The difference between them is automatic feature extraction (DL) and hand-crafted one (radiomics). The advantages of the AI-based imaging approaches for the COVID-19 are fast throughput, non-invasion, quantification, and integration of PCR results, CT findings, and clinical information. To the best of my knowledge, three types of the AI approaches have been studied: detection, severity differentiation, and prognosis prediction of COVID-19. AI technologies on assessment of severity/prediction of prognosis for COVID-19 may be more crucial than detection of COVID-19 pneumonia after COVID-19 becomes one of common diseases.


Subject(s)
COVID-19 , Deep Learning , Artificial Intelligence , Humans , SARS-CoV-2 , Tomography, X-Ray Computed
7.
Sci Rep ; 11(1): 21564, 2021 11 03.
Article in English | MEDLINE | ID: covidwho-1500504

ABSTRACT

The Coronavirus has spread across the world and infected millions of people, causing devastating damage to the public health and global economies. To mitigate the impact of the coronavirus a reliable, fast, and accurate diagnostic system should be promptly implemented. In this study, we propose EpistoNet, a decision tree-based ensemble model using two mixtures of discriminative experts to classify COVID-19 lung infection from chest X-ray images. To optimize the architecture and hyper-parameters of the designed neural networks, we employed Epistocracy algorithm, a recently proposed hyper-heuristic evolutionary method. Using 2500 chest X-ray images consisting of 1250 COVID-19 and 1250 non-COVID-19 cases, we left out 500 images for testing and partitioned the remaining 2000 images into 5 different clusters using K-means clustering algorithm. We trained multiple deep convolutional neural networks on each cluster to help build a mixture of strong discriminative experts from the top-performing models supervised by a gating network. The final ensemble model obtained 95% accuracy on COVID-19 images and 93% accuracy on non-COVID-19. The experimental results show that EpistoNet can accurately, and reliably be used to detect COVID-19 infection in the chest X-ray images, and Epistocracy algorithm can be effectively used to optimize the hyper-parameters of the proposed models.


Subject(s)
COVID-19 , Deep Learning , Image Processing, Computer-Assisted , Radiography, Thoracic
8.
PLoS One ; 16(10): e0259179, 2021.
Article in English | MEDLINE | ID: covidwho-1496531

ABSTRACT

This paper focuses on the application of deep learning (DL) in the diagnosis of coronavirus disease (COVID-19). The novelty of this work is in the introduction of optimized InceptionResNetV2 for COVID-19 (CO-IRv2) method. A part of the CO-IRv2 scheme is derived from the concepts of InceptionNet and ResNet with hyperparameter tuning, while the remaining part is a new architecture consisting of a global average pooling layer, batch normalization, dense layers, and dropout layers. The proposed CO-IRv2 is applied to a new dataset of 2481 computed tomography (CT) images formed by collecting two independent datasets. Data resizing and normalization are performed, and the evaluation is run up to 25 epochs. Various performance metrics, including precision, recall, accuracy, F1-score, area under the receiver operating characteristics (AUC) curve are used as performance metrics. The effectiveness of three optimizers known as Adam, Nadam and RMSProp are evaluated in classifying suspected COVID-19 patients and normal people. Results show that for CO-IRv2 and for CT images, the obtained accuracies of Adam, Nadam and RMSProp optimizers are 94.97%, 96.18% and 96.18%, respectively. Furthermore, it is shown here that for the case of CT images, CO-IRv2 with Nadam optimizer has better performance than existing DL algorithms in the diagnosis of COVID-19 patients. Finally, CO-IRv2 is applied to an X-ray dataset of 1662 images resulting in a classification accuracy of 99.40%.


Subject(s)
COVID-19/classification , COVID-19/diagnostic imaging , Image Processing, Computer-Assisted/methods , Algorithms , COVID-19/metabolism , Data Accuracy , Deep Learning , Humans , Neural Networks, Computer , ROC Curve , Radiography/methods , SARS-CoV-2/pathogenicity , Sensitivity and Specificity , Tomography, X-Ray Computed/methods
9.
Comput Intell Neurosci ; 2021: 2158184, 2021.
Article in English | MEDLINE | ID: covidwho-1495704

ABSTRACT

COVID-19 has claimed several human lives to this date. People are dying not only because of physical infection of the virus but also because of mental illness, which is linked to people's sentiments and psychologies. People's written texts/posts scattered on the web could help understand their psychology and the state they are in during this pandemic. In this paper, we analyze people's sentiment based on the classification of tweets collected from the social media platform, Twitter, in Nepal. For this, we, first, propose to use three different feature extraction methods-fastText-based (ft), domain-specific (ds), and domain-agnostic (da)-for the representation of tweets. Among these three methods, two methods ("ds" and "da") are the novel methods used in this study. Second, we propose three different convolution neural networks (CNNs) to implement the proposed features. Last, we ensemble such three CNNs models using ensemble CNN, which works in an end-to-end manner, to achieve the end results. For the evaluation of the proposed feature extraction methods and CNN models, we prepare a Nepali Twitter sentiment dataset, called NepCOV19Tweets, with 3 classes (positive, neutral, and negative). The experimental results on such dataset show that our proposed feature extraction methods possess the discriminating characteristics for the sentiment classification. Moreover, the proposed CNN models impart robust and stable performance on the proposed features. Also, our dataset can be used as a benchmark to study the COVID-19-related sentiment analysis in the Nepali language.


Subject(s)
COVID-19 , Deep Learning , Humans , Language , Pandemics , SARS-CoV-2
10.
J Infect Public Health ; 14(10): 1435-1445, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1492291

ABSTRACT

BACKGROUND: COVID-19 diagnosis in symptomatic patients is an important factor for arranging the necessary lifesaving facilities like ICU care and ventilator support. For this purpose, we designed a computer-aided diagnosis and severity detection method by using transfer learning and a back propagation neural network. METHOD: To increase the learning capability, we used data augmentation. Most of the previously done works in this area concentrate on private datasets, but we used two publicly available datasets. The first section diagnose COVID-19 from the input CT image using the transfer learning of the pre-trained network ResNet-50. We used ResNet-50 and DenseNet-201 pre-trained networks for feature extraction and trained a back propagation neural network to classify it into High, Medium, and Low severity. RESULTS: The proposed method for COVID-19 diagnosis gave an accuracy of 98.5% compared with the state-of-the-art methods. The experimental evaluation shows that combining the ResNet-50 and DenseNet-201 features gave more accurate results with the test data. The proposed system for COVID-19 severity detection gave better average classification accuracy of 97.84% compared with the state-of-the-art methods. This enables medical practitioners to identify the resources and treatment plans correctly. CONCLUSIONS: This work is useful in the medical field as a first-line severity risk detection that is helpful for medical personnel to plan patient care and assess the need for ICU facilities and ventilator support. A computer-aided system that is helpful to make a care plan for the huge amount of patient inflow each day is sure to be an asset in these turbulent times.


Subject(s)
COVID-19 , Deep Learning , COVID-19 Testing , Humans , Neural Networks, Computer , SARS-CoV-2 , Tomography, X-Ray Computed
11.
Sensors (Basel) ; 21(21)2021 Nov 02.
Article in English | MEDLINE | ID: covidwho-1488707

ABSTRACT

In healthcare, a multitude of data is collected from medical sensors and devices, such as X-ray machines, magnetic resonance imaging, computed tomography (CT), and so on, that can be analyzed by artificial intelligence methods for early diagnosis of diseases. Recently, the outbreak of the COVID-19 disease caused many deaths. Computer vision researchers support medical doctors by employing deep learning techniques on medical images to diagnose COVID-19 patients. Various methods were proposed for COVID-19 case classification. A new automated technique is proposed using parallel fusion and optimization of deep learning models. The proposed technique starts with a contrast enhancement using a combination of top-hat and Wiener filters. Two pre-trained deep learning models (AlexNet and VGG16) are employed and fine-tuned according to target classes (COVID-19 and healthy). Features are extracted and fused using a parallel fusion approach-parallel positive correlation. Optimal features are selected using the entropy-controlled firefly optimization method. The selected features are classified using machine learning classifiers such as multiclass support vector machine (MC-SVM). Experiments were carried out using the Radiopaedia database and achieved an accuracy of 98%. Moreover, a detailed analysis is conducted and shows the improved performance of the proposed scheme.


Subject(s)
COVID-19 , Deep Learning , Animals , Artificial Intelligence , Entropy , Fireflies , Humans , SARS-CoV-2 , Tomography, X-Ray Computed
12.
Sensors (Basel) ; 21(21)2021 Oct 27.
Article in English | MEDLINE | ID: covidwho-1488701

ABSTRACT

COVID-19 frequently provokes pneumonia, which can be diagnosed using imaging exams. Chest X-ray (CXR) is often useful because it is cheap, fast, widespread, and uses less radiation. Here, we demonstrate the impact of lung segmentation in COVID-19 identification using CXR images and evaluate which contents of the image influenced the most. Semantic segmentation was performed using a U-Net CNN architecture, and the classification using three CNN architectures (VGG, ResNet, and Inception). Explainable Artificial Intelligence techniques were employed to estimate the impact of segmentation. A three-classes database was composed: lung opacity (pneumonia), COVID-19, and normal. We assessed the impact of creating a CXR image database from different sources, and the COVID-19 generalization from one source to another. The segmentation achieved a Jaccard distance of 0.034 and a Dice coefficient of 0.982. The classification using segmented images achieved an F1-Score of 0.88 for the multi-class setup, and 0.83 for COVID-19 identification. In the cross-dataset scenario, we obtained an F1-Score of 0.74 and an area under the ROC curve of 0.9 for COVID-19 identification using segmented images. Experiments support the conclusion that even after segmentation, there is a strong bias introduced by underlying factors from different sources.


Subject(s)
COVID-19 , Deep Learning , Artificial Intelligence , Humans , Lung/diagnostic imaging , SARS-CoV-2 , X-Rays
13.
Ann Ig ; 33(6): 644-655, 2021.
Article in English | MEDLINE | ID: covidwho-1485448

ABSTRACT

Conclusions: Despite some limits, our findings support the notion that deep learning methods can be used to simplify the diagnostic process and improve disease management. Background: In order to help physicians and radiologists in diagnosing pneumonia, deep learning and other artificial intelligence methods have been described in several researches to solve this task. The main objective of the present study is to build a stacked hierarchical model by combining several models in order to increase the procedure accuracy. Methods: Firstly, the best convolutional network in terms of accuracy were evaluated and described. Later, a stacked hierarchical model was built by using the most relevant features extracted by the selected two models. Finally, over the stacked model with the best accuracy, a hierarchically dependent second stage model for inner-classification was built in order to detect both inflammation of the pulmonary alveolar space (lobar pneumonia) and interstitial tissue involvement (interstitial pneumonia). Results: The study shows how the adopted staked model lead to a higher accuracy. Having a high accuracy on pneumonia detection and classification can be a paramount asset to treat patients in real health-care environments.


Subject(s)
Deep Learning , Public Health , Artificial Intelligence , Humans , SARS-CoV-2 , X-Rays
14.
Comput Math Methods Med ; 2021: 6919483, 2021.
Article in English | MEDLINE | ID: covidwho-1484105

ABSTRACT

In March 2020, the World Health Organization announced the COVID-19 pandemic, its dangers, and its rapid spread throughout the world. In March 2021, the second wave of the pandemic began with a new strain of COVID-19, which was more dangerous for some countries, including India, recording 400,000 new cases daily and more than 4,000 deaths per day. This pandemic has overloaded the medical sector, especially radiology. Deep-learning techniques have been used to reduce the burden on hospitals and assist physicians for accurate diagnoses. In our study, two models of deep learning, ResNet-50 and AlexNet, were introduced to diagnose X-ray datasets collected from many sources. Each network diagnosed a multiclass (four classes) and a two-class dataset. The images were processed to remove noise, and a data augmentation technique was applied to the minority classes to create a balance between the classes. The features extracted by convolutional neural network (CNN) models were combined with traditional Gray-level Cooccurrence Matrix (GLCM) and Local Binary Pattern (LBP) algorithms in a 1-D vector of each image, which produced more representative features for each disease. Network parameters were tuned for optimum performance. The ResNet-50 network reached accuracy, sensitivity, specificity, and Area Under the Curve (AUC) of 95%, 94.5%, 98%, and 97.10%, respectively, with the multiclasses (COVID-19, viral pneumonia, lung opacity, and normal), while it reached accuracy, sensitivity, specificity, and AUC of 99%, 98%, 98%, and 97.51%, respectively, with the binary classes (COVID-19 and normal).


Subject(s)
COVID-19/diagnostic imaging , Deep Learning , SARS-CoV-2 , Tomography, X-Ray Computed/methods , Algorithms , Computational Biology , Databases, Factual/statistics & numerical data , Diagnosis, Computer-Assisted/methods , Diagnosis, Computer-Assisted/statistics & numerical data , Early Diagnosis , Humans , Lung/diagnostic imaging , Neural Networks, Computer , Pandemics , Pneumonia, Viral/diagnostic imaging , Tomography, X-Ray Computed/statistics & numerical data
15.
Infect Dis Poverty ; 10(1): 128, 2021 Oct 24.
Article in English | MEDLINE | ID: covidwho-1482013

ABSTRACT

BACKGROUND: Coronaviruses can be isolated from bats, civets, pangolins, birds and other wild animals. As an animal-origin pathogen, coronavirus can cross species barrier and cause pandemic in humans. In this study, a deep learning model for early prediction of pandemic risk was proposed based on the sequences of viral genomes. METHODS: A total of 3257 genomes were downloaded from the Coronavirus Genome Resource Library. We present a deep learning model of cross-species coronavirus infection that combines a bidirectional gated recurrent unit network with a one-dimensional convolution. The genome sequence of animal-origin coronavirus was directly input to extract features and predict pandemic risk. The best performances were explored with the use of pre-trained DNA vector and attention mechanism. The area under the receiver operating characteristic curve (AUROC) and the area under precision-recall curve (AUPR) were used to evaluate the predictive models. RESULTS: The six specific models achieved good performances for the corresponding virus groups (1 for AUROC and 1 for AUPR). The general model with pre-training vector and attention mechanism provided excellent predictions for all virus groups (1 for AUROC and 1 for AUPR) while those without pre-training vector or attention mechanism had obviously reduction of performance (about 5-25%). Re-training experiments showed that the general model has good capabilities of transfer learning (average for six groups: 0.968 for AUROC and 0.942 for AUPR) and should give reasonable prediction for potential pathogen of next pandemic. The artificial negative data with the replacement of the coding region of the spike protein were also predicted correctly (100% accuracy). With the application of the Python programming language, an easy-to-use tool was created to implements our predictor. CONCLUSIONS: Robust deep learning model with pre-training vector and attention mechanism mastered the features from the whole genomes of animal-origin coronaviruses and could predict the risk of cross-species infection for early warning of next pandemic.


Subject(s)
Coronavirus Infections , Coronavirus , Pandemics , Animals , Coronavirus/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Deep Learning , Humans , Models, Statistical , Risk Assessment/methods
16.
Int J Environ Res Public Health ; 18(21)2021 10 21.
Article in English | MEDLINE | ID: covidwho-1480751

ABSTRACT

In the recent pandemic, accurate and rapid testing of patients remained a critical task in the diagnosis and control of COVID-19 disease spread in the healthcare industry. Because of the sudden increase in cases, most countries have faced scarcity and a low rate of testing. Chest X-rays have been shown in the literature to be a potential source of testing for COVID-19 patients, but manually checking X-ray reports is time-consuming and error-prone. Considering these limitations and the advancements in data science, we proposed a Vision Transformer-based deep learning pipeline for COVID-19 detection from chest X-ray-based imaging. Due to the lack of large data sets, we collected data from three open-source data sets of chest X-ray images and aggregated them to form a 30 K image data set, which is the largest publicly available collection of chest X-ray images in this domain to our knowledge. Our proposed transformer model effectively differentiates COVID-19 from normal chest X-rays with an accuracy of 98% along with an AUC score of 99% in the binary classification task. It distinguishes COVID-19, normal, and pneumonia patient's X-rays with an accuracy of 92% and AUC score of 98% in the Multi-class classification task. For evaluation on our data set, we fine-tuned some of the widely used models in literature, namely, EfficientNetB0, InceptionV3, Resnet50, MobileNetV3, Xception, and DenseNet-121, as baselines. Our proposed transformer model outperformed them in terms of all metrics. In addition, a Grad-CAM based visualization is created which makes our approach interpretable by radiologists and can be used to monitor the progression of the disease in the affected lungs, assisting healthcare.


Subject(s)
COVID-19 , Deep Learning , COVID-19 Testing , Delivery of Health Care , Humans , SARS-CoV-2
17.
J Phys Chem B ; 125(44): 12166-12176, 2021 11 11.
Article in English | MEDLINE | ID: covidwho-1475246

ABSTRACT

The prerequisite of therapeutic drug design and discovery is to identify novel molecules and developing lead candidates with desired biophysical and biochemical properties. Deep generative models have demonstrated their ability to find such molecules by exploring a huge chemical space efficiently. An effective way to generate new molecules with desired target properties is by constraining the critical fucntional groups or the core scaffolds in the generation process. To this end, we developed a domain aware generative framework called 3D-Scaffold that takes 3D coordinates of the desired scaffold as an input and generates 3D coordinates of novel therapeutic candidates as an output while always preserving the desired scaffolds in generated structures. We demonstrated that our framework generates predominantly valid, unique, novel, and experimentally synthesizable molecules that have drug-like properties similar to the molecules in the training set. Using domain specific data sets, we generate covalent and noncovalent antiviral inhibitors targeting viral proteins. To measure the success of our framework in generating therapeutic candidates, generated structures were subjected to high throughput virtual screening via docking simulations, which shows favorable interaction against SARS-CoV-2 main protease (Mpro) and nonstructural protein endoribonuclease (NSP15) targets. Most importantly, our deep learning model performs well with relatively small 3D structural training data and quickly learns to generalize to new scaffolds, highlighting its potential application to other domains for generating target specific candidates.


Subject(s)
COVID-19 , Deep Learning , Pharmaceutical Preparations , Antiviral Agents/pharmacology , Drug Design , Humans , Molecular Docking Simulation , SARS-CoV-2
18.
Sensors (Basel) ; 21(20)2021 Oct 15.
Article in English | MEDLINE | ID: covidwho-1470953

ABSTRACT

The COVID-19 pandemic has affected almost every country causing devastating economic and social disruption and stretching healthcare systems to the limit. Furthermore, while being the current gold standard, existing test methods including NAAT (Nucleic Acid Amplification Tests), clinical analysis of chest CT (Computer Tomography) scan images, and blood test results, require in-person visits to a hospital which is not an adequate way to control such a highly contagious pandemic. Therefore, top priority must be given, among other things, to enlisting recent and adequate technologies to reduce the adverse impact of this pandemic. Modern smartphones possess a rich variety of embedded MEMS (Micro-Electro-Mechanical-Systems) sensors capable of recording movements, temperature, audio, and video of their carriers. This study leverages the smartphone sensors for the preliminary diagnosis of COVID-19. Deep learning, an important breakthrough in the domain of artificial intelligence in the past decade, has huge potential for extracting apt and appropriate features in healthcare. Motivated from these facts, this paper presents a new framework that leverages advanced machine learning and data analytics techniques for the early detection of coronavirus disease using smartphone embedded sensors. The proposal provides a simple to use and quickly deployable screening tool that can be easily configured with a smartphone. Experimental results indicate that the model can detect positive cases with an overall accuracy of 79% using only the data from the smartphone sensors. This means that the patient can either be isolated or treated immediately to prevent further spread, thereby saving more lives. The proposed approach does not involve any medical tests and is a cost-effective solution that provides robust results.


Subject(s)
COVID-19 , Deep Learning , Artificial Intelligence , Humans , Pandemics , SARS-CoV-2 , Smartphone
19.
Int J Environ Res Public Health ; 18(20)2021 10 14.
Article in English | MEDLINE | ID: covidwho-1470838

ABSTRACT

The use of mobile fitness apps has been on the rise for the last decade and especially during the worldwide SARS-CoV-2 pandemic, which led to the closure of gyms and to reduced outdoor mobility. Fitness apps constitute a promising means for promoting more active lifestyles, although their attrition rates are remarkable and adherence to their training plans remains a challenge for developers. The aim of this project was to design an automatic classification of users into adherent and non-adherent, based on their training behavior in the first three months of app usage, for which purpose we proposed an ensemble of regression models to predict their behaviour (adherence) in the fourth month. The study was conducted using data from a total of 246 Mammoth Hunters Fitness app users. Firstly, pre-processing and clustering steps were taken in order to prepare the data and to categorize users into similar groups, taking into account the first 90 days of workout sessions. Then, an ensemble approach for regression models was used to predict user training behaviour during the fourth month, which were trained with users belonging to the same cluster. This was used to reach a conclusion regarding their adherence status, via an approach that combined affinity propagation (AP) clustering algorithm, followed by the long short-term memory (LSTM), rendering the best results (87% accuracy and 85% F1_score). This study illustrates the suggested the capacity of the system to anticipate future adherence or non-adherence, potentially opening the door to fitness app creators to pursue advanced measures aimed at reducing app attrition.


Subject(s)
COVID-19 , Deep Learning , Mobile Applications , Exercise , Humans , SARS-CoV-2
20.
Sensors (Basel) ; 21(18)2021 Sep 08.
Article in English | MEDLINE | ID: covidwho-1468446

ABSTRACT

Edge intelligence (EI) has received a lot of interest because it can reduce latency, increase efficiency, and preserve privacy. More significantly, as the Internet of Things (IoT) has proliferated, billions of portable and embedded devices have been interconnected, producing zillions of gigabytes on edge networks. Thus, there is an immediate need to push AI (artificial intelligence) breakthroughs within edge networks to achieve the full promise of edge data analytics. EI solutions have supported digital technology workloads and applications from the infrastructure level to edge networks; however, there are still many challenges with the heterogeneity of computational capabilities and the spread of information sources. We propose a novel event-driven deep-learning framework, called EDL-EI (event-driven deep learning for edge intelligence), via the design of a novel event model by defining events using correlation analysis with multiple sensors in real-world settings and incorporating multi-sensor fusion techniques, a transformation method for sensor streams into images, and lightweight 2-dimensional convolutional neural network (CNN) models. To demonstrate the feasibility of the EDL-EI framework, we presented an IoT-based prototype system that we developed with multiple sensors and edge devices. To verify the proposed framework, we have a case study of air-quality scenarios based on the benchmark data provided by the USA Environmental Protection Agency for the most polluted cities in South Korea and China. We have obtained outstanding predictive accuracy (97.65% and 97.19%) from two deep-learning models on the cities' air-quality patterns. Furthermore, the air-quality changes from 2019 to 2020 have been analyzed to check the effects of the COVID-19 pandemic lockdown.


Subject(s)
COVID-19 , Deep Learning , Artificial Intelligence , Communicable Disease Control , Humans , Intelligence , Pandemics , SARS-CoV-2 , United States
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