Deep learning for predicting COVID-19 malignant progression.
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ABSTRACT:
SUBMITTER: Fang C
PROVIDER: S-EPMC8112895 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundMany COVID-19 patients rapidly progress to respiratory failure with a broad range of severities. Identification of high-risk cases is critical for early intervention.ObjectiveThe aim of this study is to develop deep learning models that can rapidly identify high-risk COVID-19 patients based on computed tomography (CT) images and clinical data.MethodsWe analyzed 297 COVID-19 patients from five hospitals in Daegu, South Korea. A mixed artificial convolutional neural network (ACNN) model, combining an artificial neural network for clinical data and a convolutional neural network for 3D CT imaging data, was developed to classify these cases as either high risk of severe progression (ie, event) or low risk (ie, event-free).ResultsUsing the mixed ACNN model, we were able to obtain high classification performance using novel coronavirus pneumonia lesion images (ie, 93.9% accuracy, 80.8% sensitivity, 96.9% specificity, and 0.916 area under the curve [AUC] score) and lung segmentation images (ie, 94.3% accuracy, 74.7% sensitivity, 95.9% specificity, and 0.928 AUC score) for event versus event-free groups.ConclusionsOur study successfully differentiated high-risk cases among COVID-19 patients using imaging and clinical features. The developed model can be used as a predictive tool for interventions in aggressive therapies.
| S-EPMC7850779 | biostudies-literature
Project description:The COVID-19 pandemic has had a significant impact on public life and health worldwide, putting the world's healthcare systems at risk. The first step in stopping this outbreak is to detect the infection in its early stages, which will relieve the risk, control the outbreak's spread, and restore full functionality to the world's healthcare systems. Currently, PCR is the most prevalent diagnosis tool for COVID-19. However, chest X-ray images may play an essential role in detecting this disease, as they are successful for many other viral pneumonia diseases. Unfortunately, there are common features between COVID-19 and other viral pneumonia, and hence manual differentiation between them seems to be a critical problem and needs the aid of artificial intelligence. This research employs deep- and transfer-learning techniques to develop accurate, general, and robust models for detecting COVID-19. The developed models utilize either convolutional neural networks or transfer-learning models or hybridize them with powerful machine-learning techniques to exploit their full potential. For experimentation, we applied the proposed models to two data sets: the COVID-19 Radiography Database from Kaggle and a local data set from Asir Hospital, Abha, Saudi Arabia. The proposed models achieved promising results in detecting COVID-19 cases and discriminating them from normal and other viral pneumonia with excellent accuracy. The hybrid models extracted features from the flatten layer or the first hidden layer of the neural network and then fed these features into a classification algorithm. This approach enhanced the results further to full accuracy for binary COVID-19 classification and 97.8% for multiclass classification.
| S-EPMC8357494 | biostudies-literature
Project description:The COVID-19 pandemic is causing a major outbreak in more than 150 countries around the world, having a severe impact on the health and life of many people globally. One of the crucial step in fighting COVID-19 is the ability to detect the infected patients early enough, and put them under special care. Detecting this disease from radiography and radiology images is perhaps one of the fastest ways to diagnose the patients. Some of the early studies showed specific abnormalities in the chest radiograms of patients infected with COVID-19. Inspired by earlier works, we study the application of deep learning models to detect COVID-19 patients from their chest radiography images. We first prepare a dataset of 5000 Chest X-rays from the publicly available datasets. Images exhibiting COVID-19 disease presence were identified by board-certified radiologist. Transfer learning on a subset of 2000 radiograms was used to train four popular convolutional neural networks, including ResNet18, ResNet50, SqueezeNet, and DenseNet-121, to identify COVID-19 disease in the analyzed chest X-ray images. We evaluated these models on the remaining 3000 images, and most of these networks achieved a sensitivity rate of 98% ( ± 3%), while having a specificity rate of around 90%. Besides sensitivity and specificity rates, we also present the receiver operating characteristic (ROC) curve, precision-recall curve, average prediction, and confusion matrix of each model. We also used a technique to generate heatmaps of lung regions potentially infected by COVID-19 and show that the generated heatmaps contain most of the infected areas annotated by our board certified radiologist. While the achieved performance is very encouraging, further analysis is required on a larger set of COVID-19 images, to have a more reliable estimation of accuracy rates. The dataset, model implementations (in PyTorch), and evaluations, are all made publicly available for research community at https://github.com/shervinmin/DeepCovid.git.
| S-EPMC7372265 | biostudies-literature
Project description:Background: Mathematical models are powerful tools to study COVID-19. However, one fundamental challenge in current modeling approaches is the lack of accurate and comprehensive data. Complex epidemiological systems such as COVID-19 are especially challenging to the commonly used mechanistic model when our understanding of this pandemic rapidly refreshes. Objective: We aim to develop a data-driven workflow to extract, process, and develop deep learning (DL) methods to model the COVID-19 epidemic. We provide an alternative modeling approach to complement the current mechanistic modeling paradigm. Method: We extensively searched, extracted, and annotated relevant datasets from over 60 official press releases in Hubei, China, in 2020. Multivariate long short-term memory (LSTM) models were developed with different architectures to track and predict multivariate COVID-19 time series for 1, 2, and 3 days ahead. As a comparison, univariate LSTMs were also developed to track new cases, total cases, and new deaths. Results: A comprehensive dataset with 10 variables was retrieved and processed for 125 days in Hubei. Multivariate LSTM had reasonably good predictability on new deaths, hospitalization of both severe and critical patients, total discharges, and total monitored in hospital. Multivariate LSTM showed better results for new and total cases, and new deaths for 1-day-ahead prediction than univariate counterparts, but not for 2-day and 3-day-ahead predictions. Besides, more complex LSTM architecture seemed not to increase overall predictability in this study. Conclusion: This study demonstrates the feasibility of DL models to complement current mechanistic approaches when the exact epidemiological mechanisms are still under investigation.
| S-EPMC8287417 | biostudies-literature
Project description:We aimed to predict keratoconus progression and the need for corneal crosslinking (CXL) using deep learning (DL). Two hundred and seventy-four corneal tomography images taken by Pentacam HR® (Oculus, Wetzlar, Germany) of 158 keratoconus patients were examined. All patients were examined two times or more, and divided into two groups; the progression group and the non-progression group. An axial map of the frontal corneal plane, a pachymetry map, and a combination of these two maps at the initial examination were assessed according to the patients' age. Training with a convolutional neural network on these learning data objects was conducted. Ninety eyes showed progression and 184 eyes showed no progression. The axial map, the pachymetry map, and their combination combined with patients' age showed mean AUC values of 0.783, 0.784, and 0.814 (95% confidence interval (0.721-0.845) (0.722-0.846), and (0.755-0.872), respectively), with sensitivities of 87.8%, 77.8%, and 77.8% ((79.2-93.7), (67.8-85.9), and (67.8-85.9)) and specificities of 59.8%, 65.8%, and 69.6% ((52.3-66.9), (58.4-72.6), and (62.4-76.1)), respectively. Using the proposed DL neural network model, keratoconus progression can be predicted on corneal tomography maps combined with patients' age.
| S-EPMC7923054 | biostudies-literature
Project description:The rapid spread of novel coronavirus pneumonia (COVID-19) has led to a dramatically increased mortality rate worldwide. Despite many efforts, the rapid development of an effective vaccine for this novel virus will take considerable time and relies on the identification of drug-target (DT) interactions utilizing commercially available medication to identify potential inhibitors. Motivated by this, we propose a new framework, called DeepH-DTA, for predicting DT binding affinities for heterogeneous drugs. We propose a heterogeneous graph attention (HGAT) model to learn topological information of compound molecules and bidirectional ConvLSTM layers for modeling spatio-sequential information in simplified molecular-input line-entry system (SMILES) sequences of drug data. For protein sequences, we propose a squeezed-excited dense convolutional network for learning hidden representations within amino acid sequences; while utilizing advanced embedding techniques for encoding both kinds of input sequences. The performance of DeepH-DTA is evaluated through extensive experiments against cutting-edge approaches utilising two public datasets (Davis, and KIBA) which comprise eclectic samples of the kinase protein family and the pertinent inhibitors. DeepH-DTA attains the highest Concordance Index (CI) of 0.924 and 0.927 and also achieved a mean square error (MSE) of 0.195 and 0.111 on the Davis and KIBA datasets respectively. Moreover, a study using FDA-approved drugs from the Drug Bank database is performed using DeepH-DTA to predict the affinity scores of drugs against SARS-CoV-2 amino acid sequences, and the results show that that the model can predict some of the SARS-Cov-2 inhibitors that have been recently approved in many clinical studies.
| S-EPMC8545313 | biostudies-literature
Project description:Target prediction and virtual screening are two powerful tools of computer-aided drug design. Target identification is of great significance for hit discovery, lead optimization, drug repurposing and elucidation of the mechanism. Virtual screening can improve the hit rate of drug screening to shorten the cycle of drug discovery and development. Therefore, target prediction and virtual screening are of great importance for developing highly effective drugs against COVID-19. Here we present D3AI-CoV, a platform for target prediction and virtual screening for the discovery of anti-COVID-19 drugs. The platform is composed of three newly developed deep learning-based models i.e., MultiDTI, MPNNs-CNN and MPNNs-CNN-R models. To compare the predictive performance of D3AI-CoV with other methods, an external test set, named Test-78, was prepared, which consists of 39 newly published independent active compounds and 39 inactive compounds from DrugBank. For target prediction, the areas under the receiver operating characteristic curves (AUCs) of MultiDTI and MPNNs-CNN models are 0.93 and 0.91, respectively, whereas the AUCs of the other reported approaches range from 0.51 to 0.74. For virtual screening, the hit rate of D3AI-CoV is also better than other methods. D3AI-CoV is available for free as a web application at http://www.d3pharma.com/D3Targets-2019-nCoV/D3AI-CoV/index.php, which can serve as a rapid online tool for predicting potential targets for active compounds and for identifying active molecules against a specific target protein for COVID-19 treatment.
| S-EPMC9310271 | biostudies-literature
Project description:The SARS-CoV-2 virus has caused tremendous healthcare burden worldwide. Our focus was to develop a practical and easy-to-deploy system to predict the severe manifestation of disease in patients with COVID-19 with an aim to assist clinicians in triage and treatment decisions. Our proposed predictive algorithm is a trained artificial intelligence-based network using 8,427 COVID-19 patient records from four healthcare systems. The model provides a severity risk score along with likelihoods of various clinical outcomes, namely ventilator use and mortality. The trained model using patient age and nine laboratory markers has the prediction accuracy with an area under the curve (AUC) of 0.78, 95% CI: 0.77-0.82, and the negative predictive value NPV of 0.86, 95% CI: 0.84-0.88 for the need to use a ventilator and has an accuracy with AUC of 0.85, 95% CI: 0.84-0.86, and the NPV of 0.94, 95% CI: 0.92-0.96 for predicting in-hospital 30-day mortality.
| S-EPMC8626152 | biostudies-literature
Project description:The worldwide coronavirus (COVID-19) pandemic made dramatic and rapid progress in the year 2020 and requires urgent global effort to accelerate the development of a vaccine to stop the daily infections and deaths. Several types of vaccine have been designed to teach the immune system how to fight off certain kinds of pathogens. mRNA vaccines are the most important candidate vaccines because of their capacity for rapid development, high potency, safe administration and potential for low-cost manufacture. mRNA vaccine acts by training the body to recognize and response to the proteins produced by disease-causing organisms such as viruses or bacteria. This type of vaccine is the fastest candidate to treat COVID-19 but it currently facing several limitations. In particular, it is a challenge to design stable mRNA molecules because of the inefficient in vivo delivery of mRNA, its tendency for spontaneous degradation and low protein expression levels. This work designed and implemented a sequence deep model based on bidirectional GRU and LSTM models applied on the Stanford COVID-19 mRNA vaccine dataset to predict the mRNA sequences responsible for degradation by predicting five reactivity values for every position in the sequence. Four of these values determine the likelihood of degradation with/without magnesium at high pH (pH 10) and high temperature (50 degrees Celsius) and the fifth reactivity value is used to determine the likely secondary structure of the RNA sample. The model relies on two types of features, namely numerical and categorical features, where the categorical features are extracted from the mRNA sequences, structure and predicted loop. These features are represented and encoded by numbers, and then, the features are extracted using embedding layer learning. There are five numerical features depending on the likelihood for each pair of nucleotides in the RNA. The model gives promising results because it predicts the five reactivity values with a validation mean columnwise root mean square error (MCRMSE) of 0.125 using LSTM model with augmentation and the codon encoding method. Codon encoding outperforms Base encoding in MCRMSE validation error using the LSTM model meanwhile Base encoding outperforms codon encoding due to less over-fitting and the difference between the training and validation loss error is 0.008.
| S-EPMC8237341 | biostudies-literature
Project description:ObjectivesOne of the major challenges in treating patients with coronavirus disease 2019 (COVID-19) is predicting the severity of disease. We aimed to develop a new score for predicting progression from mild/moderate to severe COVID-19.MethodsA total of 239 hospitalized patients with COVID-19 from two medical centers in China between February 6 and April 6, 2020 were retrospectively included. The prognostic abilities of variables, including clinical data and laboratory findings from the electronic medical records of each hospital, were analysed using the Cox proportional hazards model and Kaplan-Meier methods. A prognostic score was developed to predict progression from mild/moderate to severe COVID-19.ResultsAmong the 239 patients, 216 (90.38%) patients had mild/moderate disease, and 23 (9.62%) progressed to severe disease. After adjusting for multiple confounding factors, pulmonary disease, age > 75, IgM, CD16+/CD56+ NK cells and aspartate aminotransferase were independent predictors of progression to severe COVID-19. Based on these five factors, a new predictive score (the 'PAINT score') was established and showed a high predictive value (C-index = 0.91, 0.902 ± 0.021, p < 0.001). The PAINT score was validated using a nomogram, bootstrap analysis, calibration curves, decision curves and clinical impact curves, all of which confirmed its high predictive value.ConclusionsThe PAINT score for progression from mild/moderate to severe COVID-19 may be helpful in identifying patients at high risk of progression.
| S-EPMC9134988 | biostudies-literature