Background: The outbreak of the novel coronavirus disease 2019 (COVID-19) has been raging around the world for more than 1 year. Analysis of previous COVID-19 data is useful to explore its epidemic patterns. Utilizing data mining and machine learning methods for COVID-19 forecasting might provide a better insight into the trends of COVID-19 cases. This study aims to model the COVID-19 cases and perform forecasting of three important indicators of COVID-19 in the United States of America (USA), which are the adjusted percentage of daily admitted hospitalized COVID-19 cases (hospital admission), the number of daily confirmed COVID-19 cases (confirmed cases), and the number of daily death cases caused by COVID-19 (death cases).Materials and Methods: The actual COVID-19 data from March 1, 2020 to August 5, 2021 were obtained from Carnegie Mellon University Delphi Research Group. A novel forecasting algorithm was proposed to model and predict the three indicators. This algorithm is a hybrid of an unsupervised time series anomaly detection technique called matrix profile and an attention-based long short-term memory (LSTM) model. Several classic statistical models and the baseline recurrent neural network (RNN) models were used as the baseline models. All models were evaluated using a repeated holdout training and test strategy.Results: The proposed matrix profile-assisted attention-based LSTM model performed the best among all the compared models, which has the root mean square error (RMSE) = 1.23, 31612.81, 467.17, mean absolute error (MAE) = 0.95, 26259.55, 364.02, and mean absolute percentage error (MAPE) = 0.25, 1.06, 0.55, for hospital admission, confirmed cases, and death cases, respectively.Conclusion: The proposed model is more powerful in forecasting COVID-19 cases. It can potentially aid policymakers in making prevention plans and guide health care managers to allocate health care resources reasonably.
Cell type identification using single-cell RNA sequencing (scRNA-seq) data is critical for understanding disease mechanisms and drug discovery. Cell clustering analysis has been widely studied in health research for rare tumor cell detection. In this study, we propose a Gaussian mixture model-based variational graph autoencoder on scRNA-seq data (scGMM-VGAE) that integrates a statistical clustering model to a deep learning algorithm to significantly improve the cell clustering performance. This model feeds a cell-cell graph adjacency matrix and a gene feature matrix into a graph variational autoencoder (VGAE) to generate latent data. These data are then used for cell clustering by the Gaussian mixture model (GMM) module. To optimize the algorithm, a designed loss function is derived by combining parameter estimates from the GMM and VGAE. We test the proposed method on four publicly available and three simulated datasets which contain many biological and technical zeros. The scGMM-VGAE outperforms four selected baseline methods on three evaluation metrics in cell clustering. By successfully incorporating GMM into deep learning VGAE on scRNA-seq data, the proposed method shows higher accuracy in cell clustering on scRNA-seq data. This improvement has a significant impact on detecting rare cell types in health research. All source codes used in this study can be found at https://github.com/ericlin1230/scGMM-VGAE.
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