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1.
Syst Rev ; 12(1): 94, 2023 06 05.
Article in English | MEDLINE | ID: covidwho-20238036

ABSTRACT

BACKGROUND: The COVID-19 pandemic has led to an unprecedented amount of scientific publications, growing at a pace never seen before. Multiple living systematic reviews have been developed to assist professionals with up-to-date and trustworthy health information, but it is increasingly challenging for systematic reviewers to keep up with the evidence in electronic databases. We aimed to investigate deep learning-based machine learning algorithms to classify COVID-19-related publications to help scale up the epidemiological curation process. METHODS: In this retrospective study, five different pre-trained deep learning-based language models were fine-tuned on a dataset of 6365 publications manually classified into two classes, three subclasses, and 22 sub-subclasses relevant for epidemiological triage purposes. In a k-fold cross-validation setting, each standalone model was assessed on a classification task and compared against an ensemble, which takes the standalone model predictions as input and uses different strategies to infer the optimal article class. A ranking task was also considered, in which the model outputs a ranked list of sub-subclasses associated with the article. RESULTS: The ensemble model significantly outperformed the standalone classifiers, achieving a F1-score of 89.2 at the class level of the classification task. The difference between the standalone and ensemble models increases at the sub-subclass level, where the ensemble reaches a micro F1-score of 70% against 67% for the best-performing standalone model. For the ranking task, the ensemble obtained the highest recall@3, with a performance of 89%. Using an unanimity voting rule, the ensemble can provide predictions with higher confidence on a subset of the data, achieving detection of original papers with a F1-score up to 97% on a subset of 80% of the collection instead of 93% on the whole dataset. CONCLUSION: This study shows the potential of using deep learning language models to perform triage of COVID-19 references efficiently and support epidemiological curation and review. The ensemble consistently and significantly outperforms any standalone model. Fine-tuning the voting strategy thresholds is an interesting alternative to annotate a subset with higher predictive confidence.


Subject(s)
COVID-19 , Deep Learning , Humans , Pandemics , Retrospective Studies , Language
2.
Nat Commun ; 14(1): 3478, 2023 06 13.
Article in English | MEDLINE | ID: covidwho-20236521

ABSTRACT

The relentless evolution of SARS-CoV-2 poses a significant threat to public health, as it adapts to immune pressure from vaccines and natural infections. Gaining insights into potential antigenic changes is critical but challenging due to the vast sequence space. Here, we introduce the Machine Learning-guided Antigenic Evolution Prediction (MLAEP), which combines structure modeling, multi-task learning, and genetic algorithms to predict the viral fitness landscape and explore antigenic evolution via in silico directed evolution. By analyzing existing SARS-CoV-2 variants, MLAEP accurately infers variant order along antigenic evolutionary trajectories, correlating with corresponding sampling time. Our approach identified novel mutations in immunocompromised COVID-19 patients and emerging variants like XBB1.5. Additionally, MLAEP predictions were validated through in vitro neutralizing antibody binding assays, demonstrating that the predicted variants exhibited enhanced immune evasion. By profiling existing variants and predicting potential antigenic changes, MLAEP aids in vaccine development and enhances preparedness against future SARS-CoV-2 variants.


Subject(s)
COVID-19 , Deep Learning , Humans , SARS-CoV-2/genetics , Antibodies, Neutralizing
3.
Sci Rep ; 13(1): 9171, 2023 06 06.
Article in English | MEDLINE | ID: covidwho-20235416

ABSTRACT

Throughout the pandemic era, COVID-19 was one of the remarkable unexpected situations over the past few years, but with the decentralization and globalization of efforts and knowledge, a successful vaccine-based control strategy was efficiently designed and applied worldwide. On the other hand, excused confusion and hesitation have widely impacted public health. This paper aims to reduce COVID-19 vaccine hesitancy taking into consideration the patient's medical history. The dataset used in this study is the Vaccine Adverse Event Reporting System (VAERS) dataset which was created as a corporation between the Food and Drug Administration (FDA) and Centers for Disease Control and Prevention (CDC) to gather reported side effects that may be caused by PFIEZER, JANSSEN, and MODERNA vaccines. In this paper, a Deep Learning (DL) model has been developed to identify the relationship between a certain type of COVID-19 vaccine (i.e. PFIEZER, JANSSEN, and MODERNA) and the adverse reactions that may occur in vaccinated patients. The adverse reactions under study are the recovery condition, possibility to be hospitalized, and death status. In the first phase of the proposed model, the dataset has been pre-proceesed, while in the second phase, the Pigeon swarm optimization algorithm is used to optimally select the most promising features that affect the performance of the proposed model. The patient's status after vaccination dataset is grouped into three target classes (Death, Hospitalized, and Recovered). In the third phase, Recurrent Neural Network (RNN) is implemented for both each vaccine type and each target class. The results show that the proposed model gives the highest accuracy scores which are 96.031% for the Death target class in the case of PFIEZER vaccination. While in JANSSEN vaccination, the Hospitalized target class has shown the highest performance with an accuracy of 94.7%. Finally, the model has the best performance for the Recovered target class in MODERNA vaccination with an accuracy of 97.794%. Based on the accuracy and the Wilcoxon Signed Rank test, we can conclude that the proposed model is promising for identifying the relationship between the side effects of COVID-19 vaccines and the patient's status after vaccination. The study displayed that certain side effects were increased in patients according to the type of COVID-19 vaccines. Side effects related to CNS and hemopoietic systems demonstrated high values in all studied COVID-19 vaccines. In the frame of precision medicine, these findings can support the medical staff to select the best COVID-19 vaccine based on the medical history of the patient.


Subject(s)
COVID-19 , Deep Learning , Drug-Related Side Effects and Adverse Reactions , Vaccines , United States , Humans , COVID-19 Vaccines/adverse effects , COVID-19/prevention & control , Public Health , Vaccination/adverse effects
4.
Sci Data ; 10(1): 348, 2023 06 02.
Article in English | MEDLINE | ID: covidwho-20243476

ABSTRACT

The outbreak of the SARS-CoV-2 pandemic has put healthcare systems worldwide to their limits, resulting in increased waiting time for diagnosis and required medical assistance. With chest radiographs (CXR) being one of the most common COVID-19 diagnosis methods, many artificial intelligence tools for image-based COVID-19 detection have been developed, often trained on a small number of images from COVID-19-positive patients. Thus, the need for high-quality and well-annotated CXR image databases increased. This paper introduces POLCOVID dataset, containing chest X-ray (CXR) images of patients with COVID-19 or other-type pneumonia, and healthy individuals gathered from 15 Polish hospitals. The original radiographs are accompanied by the preprocessed images limited to the lung area and the corresponding lung masks obtained with the segmentation model. Moreover, the manually created lung masks are provided for a part of POLCOVID dataset and the other four publicly available CXR image collections. POLCOVID dataset can help in pneumonia or COVID-19 diagnosis, while the set of matched images and lung masks may serve for the development of lung segmentation solutions.


Subject(s)
COVID-19 , Deep Learning , Radiography, Thoracic , X-Rays , Humans , Algorithms , Artificial Intelligence , COVID-19/diagnostic imaging , COVID-19 Testing , Pneumonia , Poland , Radiography, Thoracic/methods , SARS-CoV-2
5.
Immunity ; 56(7): 1681-1698.e13, 2023 Jul 11.
Article in English | MEDLINE | ID: covidwho-20243335

ABSTRACT

CD4+ T cell responses are exquisitely antigen specific and directed toward peptide epitopes displayed by human leukocyte antigen class II (HLA-II) on antigen-presenting cells. Underrepresentation of diverse alleles in ligand databases and an incomplete understanding of factors affecting antigen presentation in vivo have limited progress in defining principles of peptide immunogenicity. Here, we employed monoallelic immunopeptidomics to identify 358,024 HLA-II binders, with a particular focus on HLA-DQ and HLA-DP. We uncovered peptide-binding patterns across a spectrum of binding affinities and enrichment of structural antigen features. These aspects underpinned the development of context-aware predictor of T cell antigens (CAPTAn), a deep learning model that predicts peptide antigens based on their affinity to HLA-II and full sequence of their source proteins. CAPTAn was instrumental in discovering prevalent T cell epitopes from bacteria in the human microbiome and a pan-variant epitope from SARS-CoV-2. Together CAPTAn and associated datasets present a resource for antigen discovery and the unraveling genetic associations of HLA alleles with immunopathologies.


Subject(s)
COVID-19 , Deep Learning , Humans , Captan , SARS-CoV-2 , HLA Antigens , Epitopes, T-Lymphocyte , Peptides
6.
Anal Chem ; 95(25): 9397-9403, 2023 06 27.
Article in English | MEDLINE | ID: covidwho-20243247

ABSTRACT

Peak-detection algorithms currently used to process untargeted metabolomics data were designed to maximize sensitivity at the sacrifice of selectively. Peak lists returned by conventional software tools therefore contain a high density of artifacts that do not represent real chemical analytes, which, in turn, hinder downstream analyses. Although some innovative approaches to remove artifacts have recently been introduced, they involve extensive user intervention due to the diversity of peak shapes present within and across metabolomics data sets. To address this bottleneck in metabolomics data processing, we developed a semisupervised deep learning-based approach, PeakDetective, for classification of detected peaks as artifacts or true peaks. Our approach utilizes two techniques for artifact removal. First, an unsupervised autoencoder is used to extract a low-dimensional, latent representation of each peak. Second, a classifier is trained with active learning to discriminate between artifacts and true peaks. Through active learning, the classifier is trained with less than 100 user-labeled peaks in a matter of minutes. Given the speed of its training, PeakDetective can be rapidly tailored to specific LC/MS methods and sample types to maximize performance on each type of data set. In addition to curation, the trained models can also be utilized for peak detection to immediately detect peaks with both high sensitivity and selectivity. We validated PeakDetective on five diverse LC/MS data sets, where PeakDetective showed greater accuracy compared to current approaches. When applied to a SARS-CoV-2 data set, PeakDetective enabled more statistically significant metabolites to be detected. PeakDetective is open source and available as a Python package at https://github.com/pattilab/PeakDetective.


Subject(s)
COVID-19 , Deep Learning , Humans , SARS-CoV-2 , Software , Metabolomics/methods
7.
Comput Math Methods Med ; 2023: 7091301, 2023.
Article in English | MEDLINE | ID: covidwho-20243039

ABSTRACT

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


Subject(s)
COVID-19 , Deep Learning , Child , Humans , Diagnostic Imaging/methods , Neural Networks, Computer , Image Processing, Computer-Assisted/methods
8.
Sensors (Basel) ; 23(11)2023 Jun 03.
Article in English | MEDLINE | ID: covidwho-20242759

ABSTRACT

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


Subject(s)
COVID-19 , Coleoptera , Deep Learning , Perciformes , Pneumonia , Female , Male , Animals , COVID-19/diagnostic imaging , Fishes , Tomography, X-Ray Computed , Lung/diagnostic imaging
9.
Gigascience ; 122022 12 28.
Article in English | MEDLINE | ID: covidwho-20242676

ABSTRACT

BACKGROUND: Literature about SARS-CoV-2 widely discusses the effects of variations that have spread in the past 3 years. Such information is dispersed in the texts of several research articles, hindering the possibility of practically integrating it with related datasets (e.g., millions of SARS-CoV-2 sequences available to the community). We aim to fill this gap, by mining literature abstracts to extract-for each variant/mutation-its related effects (in epidemiological, immunological, clinical, or viral kinetics terms) with labeled higher/lower levels in relation to the nonmutated virus. RESULTS: The proposed framework comprises (i) the provisioning of abstracts from a COVID-19-related big data corpus (CORD-19) and (ii) the identification of mutation/variant effects in abstracts using a GPT2-based prediction model. The above techniques enable the prediction of mutations/variants with their effects and levels in 2 distinct scenarios: (i) the batch annotation of the most relevant CORD-19 abstracts and (ii) the on-demand annotation of any user-selected CORD-19 abstract through the CoVEffect web application (http://gmql.eu/coveffect), which assists expert users with semiautomated data labeling. On the interface, users can inspect the predictions and correct them; user inputs can then extend the training dataset used by the prediction model. Our prototype model was trained through a carefully designed process, using a minimal and highly diversified pool of samples. CONCLUSIONS: The CoVEffect interface serves for the assisted annotation of abstracts, allowing the download of curated datasets for further use in data integration or analysis pipelines. The overall framework can be adapted to resolve similar unstructured-to-structured text translation tasks, which are typical of biomedical domains.


Subject(s)
COVID-19 , Deep Learning , Humans , SARS-CoV-2/genetics , COVID-19/genetics , Mutation , Kinetics
10.
Int J Mol Sci ; 24(9)2023 Apr 24.
Article in English | MEDLINE | ID: covidwho-2320161

ABSTRACT

The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric regulation, the emerging structural biology technologies and AI approaches remains largely unexplored, calling for the development of AI-augmented integrative structural biology. In this review, we focus on the latest remarkable progress in deep high-throughput mining and comprehensive mapping of allosteric protein landscapes and allosteric regulatory mechanisms as well as on the new developments in AI methods for prediction and characterization of allosteric binding sites on the proteome level. We also discuss new AI-augmented structural biology approaches that expand our knowledge of the universe of protein dynamics and allostery. We conclude with an outlook and highlight the importance of developing an open science infrastructure for machine learning studies of allosteric regulation and validation of computational approaches using integrative studies of allosteric mechanisms. The development of community-accessible tools that uniquely leverage the existing experimental and simulation knowledgebase to enable interrogation of the allosteric functions can provide a much-needed boost to further innovation and integration of experimental and computational technologies empowered by booming AI field.


Subject(s)
Artificial Intelligence , Deep Learning , Allosteric Site , Big Data , Proteins/chemistry
11.
PLoS One ; 18(5): e0285121, 2023.
Article in English | MEDLINE | ID: covidwho-2319931

ABSTRACT

BACKGROUND: Recently, artificial intelligence (AI)-based applications for chest imaging have emerged as potential tools to assist clinicians in the diagnosis and management of patients with coronavirus disease 2019 (COVID-19). OBJECTIVES: To develop a deep learning-based clinical decision support system for automatic diagnosis of COVID-19 on chest CT scans. Secondarily, to develop a complementary segmentation tool to assess the extent of lung involvement and measure disease severity. METHODS: The Imaging COVID-19 AI initiative was formed to conduct a retrospective multicentre cohort study including 20 institutions from seven different European countries. Patients with suspected or known COVID-19 who underwent a chest CT were included. The dataset was split on the institution-level to allow external evaluation. Data annotation was performed by 34 radiologists/radiology residents and included quality control measures. A multi-class classification model was created using a custom 3D convolutional neural network. For the segmentation task, a UNET-like architecture with a backbone Residual Network (ResNet-34) was selected. RESULTS: A total of 2,802 CT scans were included (2,667 unique patients, mean [standard deviation] age = 64.6 [16.2] years, male/female ratio 1.3:1). The distribution of classes (COVID-19/Other type of pulmonary infection/No imaging signs of infection) was 1,490 (53.2%), 402 (14.3%), and 910 (32.5%), respectively. On the external test dataset, the diagnostic multiclassification model yielded high micro-average and macro-average AUC values (0.93 and 0.91, respectively). The model provided the likelihood of COVID-19 vs other cases with a sensitivity of 87% and a specificity of 94%. The segmentation performance was moderate with Dice similarity coefficient (DSC) of 0.59. An imaging analysis pipeline was developed that returned a quantitative report to the user. CONCLUSION: We developed a deep learning-based clinical decision support system that could become an efficient concurrent reading tool to assist clinicians, utilising a newly created European dataset including more than 2,800 CT scans.


Subject(s)
COVID-19 , Deep Learning , Humans , Female , Male , Middle Aged , COVID-19/diagnostic imaging , Artificial Intelligence , Lung/diagnostic imaging , COVID-19 Testing , Cohort Studies , SARS-CoV-2 , Tomography, X-Ray Computed/methods
12.
Artif Intell Med ; 142: 102571, 2023 08.
Article in English | MEDLINE | ID: covidwho-2317551

ABSTRACT

Evolutionary algorithms have been successfully employed to find the best structure for many learning algorithms including neural networks. Due to their flexibility and promising results, Convolutional Neural Networks (CNNs) have found their application in many image processing applications. The structure of CNNs greatly affects the performance of these algorithms both in terms of accuracy and computational cost, thus, finding the best architecture for these networks is a crucial task before they are employed. In this paper, we develop a genetic programming approach for the optimization of CNN structure in diagnosing COVID-19 cases via X-ray images. A graph representation for CNN architecture is proposed and evolutionary operators including crossover and mutation are specifically designed for the proposed representation. The proposed architecture of CNNs is defined by two sets of parameters, one is the skeleton which determines the arrangement of the convolutional and pooling operators and their connections and one is the numerical parameters of the operators which determine the properties of these operators like filter size and kernel size. The proposed algorithm in this paper optimizes the skeleton and the numerical parameters of the CNN architectures in a co-evolutionary scheme. The proposed algorithm is used to identify covid-19 cases via X-ray images.


Subject(s)
COVID-19 , Deep Learning , Humans , X-Rays , COVID-19/diagnostic imaging , Algorithms , Neural Networks, Computer
13.
Eur Radiol ; 33(6): 4280-4291, 2023 Jun.
Article in English | MEDLINE | ID: covidwho-2317195

ABSTRACT

OBJECTIVES: Differentiation between COVID-19 and community-acquired pneumonia (CAP) in computed tomography (CT) is a task that can be performed by human radiologists and artificial intelligence (AI). The present study aims to (1) develop an AI algorithm for differentiating COVID-19 from CAP and (2) evaluate its performance. (3) Evaluate the benefit of using the AI result as assistance for radiological diagnosis and the impact on relevant parameters such as accuracy of the diagnosis, diagnostic time, and confidence. METHODS: We included n = 1591 multicenter, multivendor chest CT scans and divided them into AI training and validation datasets to develop an AI algorithm (n = 991 CT scans; n = 462 COVID-19, and n = 529 CAP) from three centers in China. An independent Chinese and German test dataset of n = 600 CT scans from six centers (COVID-19 / CAP; n = 300 each) was used to test the performance of eight blinded radiologists and the AI algorithm. A subtest dataset (180 CT scans; n = 90 each) was used to evaluate the radiologists' performance without and with AI assistance to quantify changes in diagnostic accuracy, reporting time, and diagnostic confidence. RESULTS: The diagnostic accuracy of the AI algorithm in the Chinese-German test dataset was 76.5%. Without AI assistance, the eight radiologists' diagnostic accuracy was 79.1% and increased with AI assistance to 81.5%, going along with significantly shorter decision times and higher confidence scores. CONCLUSION: This large multicenter study demonstrates that AI assistance in CT-based differentiation of COVID-19 and CAP increases radiological performance with higher accuracy and specificity, faster diagnostic time, and improved diagnostic confidence. KEY POINTS: • AI can help radiologists to get higher diagnostic accuracy, make faster decisions, and improve diagnostic confidence. • The China-German multicenter study demonstrates the advantages of a human-machine interaction using AI in clinical radiology for diagnostic differentiation between COVID-19 and CAP in CT scans.


Subject(s)
COVID-19 , Community-Acquired Infections , Deep Learning , Pneumonia , Humans , Artificial Intelligence , SARS-CoV-2 , Tomography, X-Ray Computed/methods , COVID-19 Testing
14.
J Med Internet Res ; 25: e44804, 2023 05 09.
Article in English | MEDLINE | ID: covidwho-2315173

ABSTRACT

BACKGROUND: To date, performance comparisons between men and machines have been carried out in many health domains. Yet machine learning (ML) models and human performance comparisons in audio-based respiratory diagnosis remain largely unexplored. OBJECTIVE: The primary objective of this study was to compare human clinicians and an ML model in predicting COVID-19 from respiratory sound recordings. METHODS: In this study, we compared human clinicians and an ML model in predicting COVID-19 from respiratory sound recordings. Prediction performance on 24 audio samples (12 tested positive) made by 36 clinicians with experience in treating COVID-19 or other respiratory illnesses was compared with predictions made by an ML model trained on 1162 samples. Each sample consisted of voice, cough, and breathing sound recordings from 1 subject, and the length of each sample was around 20 seconds. We also investigated whether combining the predictions of the model and human experts could further enhance the performance in terms of both accuracy and confidence. RESULTS: The ML model outperformed the clinicians, yielding a sensitivity of 0.75 and a specificity of 0.83, whereas the best performance achieved by the clinicians was 0.67 in terms of sensitivity and 0.75 in terms of specificity. Integrating the clinicians' and the model's predictions, however, could enhance performance further, achieving a sensitivity of 0.83 and a specificity of 0.92. CONCLUSIONS: Our findings suggest that the clinicians and the ML model could make better clinical decisions via a cooperative approach and achieve higher confidence in audio-based respiratory diagnosis.


Subject(s)
COVID-19 , Respiratory Sounds , Respiratory Tract Diseases , Humans , Male , COVID-19/diagnosis , Machine Learning , Physicians , Respiratory Tract Diseases/diagnosis , Deep Learning
15.
Gigascience ; 122022 12 28.
Article in English | MEDLINE | ID: covidwho-2313424

ABSTRACT

BACKGROUND: Since the beginning of the coronavirus disease 2019 pandemic, there has been an explosion of sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, making it the most widely sequenced virus in the history. Several databases and tools have been created to keep track of genome sequences and variants of the virus; most notably, the GISAID platform hosts millions of complete genome sequences, and it is continuously expanding every day. A challenging task is the development of fast and accurate tools that are able to distinguish between the different SARS-CoV-2 variants and assign them to a clade. RESULTS: In this article, we leverage the frequency chaos game representation (FCGR) and convolutional neural networks (CNNs) to develop an original method that learns how to classify genome sequences that we implement into CouGaR-g, a tool for the clade assignment problem on SARS-CoV-2 sequences. On a testing subset of the GISAID, CouGaR-g achieved an $96.29\%$ overall accuracy, while a similar tool, Covidex, obtained a $77,12\%$ overall accuracy. As far as we know, our method is the first using deep learning and FCGR for intraspecies classification. Furthermore, by using some feature importance methods, CouGaR-g allows to identify k-mers that match SARS-CoV-2 marker variants. CONCLUSIONS: By combining FCGR and CNNs, we develop a method that achieves a better accuracy than Covidex (which is based on random forest) for clade assignment of SARS-CoV-2 genome sequences, also thanks to our training on a much larger dataset, with comparable running times. Our method implemented in CouGaR-g is able to detect k-mers that capture relevant biological information that distinguishes the clades, known as marker variants. AVAILABILITY: The trained models can be tested online providing a FASTA file (with 1 or multiple sequences) at https://huggingface.co/spaces/BIASLab/sars-cov-2-classification-fcgr. CouGaR-g is also available at https://github.com/AlgoLab/CouGaR-g under the GPL.


Subject(s)
COVID-19 , Deep Learning , Puma , Animals , SARS-CoV-2/genetics , Puma/genetics , Genome, Viral
16.
BMC Bioinformatics ; 24(1): 190, 2023 May 09.
Article in English | MEDLINE | ID: covidwho-2312815

ABSTRACT

BACKGROUND: An artificial-intelligence (AI) model for predicting the prognosis or mortality of coronavirus disease 2019 (COVID-19) patients will allow efficient allocation of limited medical resources. We developed an early mortality prediction ensemble model for COVID-19 using AI models with initial chest X-ray and electronic health record (EHR) data. RESULTS: We used convolutional neural network (CNN) models (Inception-ResNet-V2 and EfficientNet) for chest X-ray analysis and multilayer perceptron (MLP), Extreme Gradient Boosting (XGBoost), and random forest (RF) models for EHR data analysis. The Gradient-weighted Class Activation Mapping and Shapley Additive Explanations (SHAP) methods were used to determine the effects of these features on COVID-19. We developed an ensemble model (Area under the receiver operating characteristic curve of 0.8698) using a soft voting method with weight differences for CNN, XGBoost, MLP, and RF models. To resolve the data imbalance, we conducted F1-score optimization by adjusting the cutoff values to optimize the model performance (F1 score of 0.77). CONCLUSIONS: Our study is meaningful in that we developed an early mortality prediction model using only the initial chest X-ray and EHR data of COVID-19 patients. Early prediction of the clinical courses of patients is helpful for not only treatment but also bed management. Our results confirmed the performance improvement of the ensemble model achieved by combining AI models. Through the SHAP method, laboratory tests that indicate the factors affecting COVID-19 mortality were discovered, highlighting the importance of these tests in managing COVID-19 patients.


Subject(s)
COVID-19 , Deep Learning , Humans , Electronic Health Records , COVID-19/diagnostic imaging , X-Rays , Artificial Intelligence
17.
Math Biosci Eng ; 20(6): 10954-10976, 2023 Apr 21.
Article in English | MEDLINE | ID: covidwho-2319238

ABSTRACT

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


Subject(s)
COVID-19 , Deep Learning , Humans , COVID-19/diagnostic imaging , Algorithms , Technology , Tomography, X-Ray Computed , Image Processing, Computer-Assisted
18.
J Med Internet Res ; 25: e43841, 2023 06 06.
Article in English | MEDLINE | ID: covidwho-2314273

ABSTRACT

BACKGROUND: Shortly after the worst of the COVID-19 pandemic, an outbreak of mpox introduced another critical public health emergency. Like the COVID-19 pandemic, the mpox outbreak was characterized by a rising prevalence of public health misinformation on social media, through which many US adults receive and engage with news. Digital misinformation continues to challenge the efforts of public health officials in providing accurate and timely information to the public. We examine the evolving topic distributions of social media narratives during the mpox outbreak to map the tension between rapidly diffusing misinformation and public health communication. OBJECTIVE: This study aims to observe topical themes occurring in a large-scale collection of tweets about mpox using deep learning. METHODS: We leveraged a data set comprised of all mpox-related tweets that were posted between May 7, 2022, and July 23, 2022. We then applied Sentence Bidirectional Encoder Representations From Transformers (S-BERT) to the content of each tweet to generate a representation of its content in high-dimensional vector space, where semantically similar tweets will be located closely together. We projected the set of tweet embeddings to a 2D map by applying principal component analysis and Uniform Manifold Approximation Projection (UMAP). Finally, we group these data points into 7 topical clusters using k-means clustering and analyze each cluster to determine its dominant topics. We analyze the prevalence of each cluster over time to evaluate longitudinal thematic changes. RESULTS: Our deep-learning pipeline revealed 7 distinct clusters of content: (1) cynicism, (2) exasperation, (3) COVID-19, (4) men who have sex with men, (5) case reports, (6) vaccination, and (7) World Health Organization (WHO). Clusters that largely communicated erroneous or irrelevant information began earlier and grew faster, reaching a wider audience than later communications by official instances and health officials. CONCLUSIONS: Within a few weeks of the first reported mpox cases, an avalanche of mostly false, misleading, irrelevant, or damaging information started to circulate on social media. Official institutions, including the WHO, acted promptly, providing case reports and accurate information within weeks, but were overshadowed by rapidly spreading social media chatter. Our results point to the need for real-time monitoring of social media content to optimize responses to public health emergencies.


Subject(s)
COVID-19 , Deep Learning , Health Communication , Monkeypox , Social Media , Adult , Humans , Male , COVID-19/epidemiology , Disease Outbreaks , Homosexuality, Male , Pandemics , Public Health , Sexual and Gender Minorities
19.
Chemosphere ; 331: 138830, 2023 Aug.
Article in English | MEDLINE | ID: covidwho-2311558

ABSTRACT

Accurate and efficient predictions of pollutants in the atmosphere provide a reliable basis for the scientific management of atmospheric pollution. This study develops a model that combines an attention mechanism, convolutional neural network (CNN), and long short-term memory (LSTM) unit to predict the O3 and PM2.5 levels in the atmosphere, as well as an air quality index (AQI). The prediction results given by the proposed model are compared with those from CNN-LSTM and LSTM models as well as random forest and support vector regression models. The proposed model achieves a correlation coefficient between the predicted and observed values of more than 0.90, outperforming the other four models. The model errors are also consistently lower when using the proposed approach. Sobol-based sensitivity analysis is applied to identify the variables that make the greatest contribution to the model prediction results. Taking the COVID-19 outbreak as the time boundary, we find some homology in the interactions among the pollutants and meteorological factors in the atmosphere during different periods. Solar irradiance is the most important factor for O3, CO is the most important factor for PM2.5, and particulate matter has the most significant effect on AQI. The key influencing factors are the same over the whole phase and before the COVID-19 outbreak, indicating that the impact of COVID-19 restrictions on AQI gradually stabilized. Removing variables that contribute the least to the prediction results without affecting the model prediction performance improves the modeling efficiency and reduces the computational costs.


Subject(s)
Air Pollutants , Air Pollution , COVID-19 , Deep Learning , Environmental Pollutants , Humans , Air Pollution/analysis , Air Pollutants/analysis , Environmental Pollutants/analysis , Environmental Monitoring/methods , Particulate Matter/analysis
20.
Comput Biol Med ; 157: 106726, 2023 05.
Article in English | MEDLINE | ID: covidwho-2309093

ABSTRACT

Deep learning-based methods have become the dominant methodology in medical image processing with the advancement of deep learning in natural image classification, detection, and segmentation. Deep learning-based approaches have proven to be quite effective in single lesion recognition and segmentation. Multiple-lesion recognition is more difficult than single-lesion recognition due to the little variation between lesions or the too wide range of lesions involved. Several studies have recently explored deep learning-based algorithms to solve the multiple-lesion recognition challenge. This paper includes an in-depth overview and analysis of deep learning-based methods for multiple-lesion recognition developed in recent years, including multiple-lesion recognition in diverse body areas and recognition of whole-body multiple diseases. We discuss the challenges that still persist in the multiple-lesion recognition tasks by critically assessing these efforts. Finally, we outline existing problems and potential future research areas, with the hope that this review will help researchers in developing future approaches that will drive additional advances.


Subject(s)
Deep Learning , Image Processing, Computer-Assisted/methods , Algorithms
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