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Enhancing Single-Cell RNA-seq Data Completeness with a Graph Learning Framework.
IEEE/ACM Trans Comput Biol Bioinform
November 2024
Single cell RNA sequencing (scRNA-seq) is a powerful tool to capture gene expression snapshots in individual cells. However, a low amount of RNA in the individual cells results in dropout events, which introduce huge zero counts in the single cell expression matrix. We have developed VAImpute, a variational graph autoencoder based imputation technique that learns the inherent distribution of a large network/graph constructed from the scRNA-seq data leveraging copula correlation ( Ccor) among cells/genes.
View Article and Find Full Text PDFFSCME: A Feature Selection Method Combining Copula Correlation and Maximal Information Coefficient by Entropy Weights.
IEEE J Biomed Health Inform
September 2024
Article Synopsis
- Feature selection is essential in data mining but often faces issues of redundancy and errors due to complex mutual information methods, prompting the development of new approaches.
- The proposed FSCME method combines Copula correlation and the maximum information coefficient using entropy weights to improve relevance between features and labels while managing redundancy.
- Experimental results show that FSCME outperforms six other feature selection methods by providing a more effective feature subset, enhancing classification performance in clustering tasks.
Dynamic changes of Bacterial Microbiomes in Oropharynx during Infection and Recovery of COVID-19 Omicron Variant.
PLoS Pathog
April 2024
Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
Oropharyngeal microbiomes play a significant role in the susceptibility and severity of COVID-19, yet the role of these microbiomes play for the development of COVID-19 Omicron variant have not been reported. A total of 791 pharyngeal swab samples were prospectively included in this study, including 297 confirmed cases of Omicron variant (CCO), 222 confirmed case of Omicron who recovered (CCOR), 73 confirmed cases of original strain (CCOS) and 199 healthy controls (HC). All samples completed MiSeq sequencing.
View Article and Find Full Text PDFA copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data.
PLoS Comput Biol
March 2022
Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India.
Annotation of cells in single-cell clustering requires a homogeneous grouping of cell populations. There are various issues in single cell sequencing that effect homogeneous grouping (clustering) of cells, such as small amount of starting RNA, limited per-cell sequenced reads, cell-to-cell variability due to cell-cycle, cellular morphology, and variable reagent concentrations. Moreover, single cell data is susceptible to technical noise, which affects the quality of genes (or features) selected/extracted prior to clustering.
View Article and Find Full Text PDFIntroducing CCOR: Contact Lens Curriculum for Ophthalmology Residents.
Eye Contact Lens
November 2021
Massachusetts Eye & Ear, Harvard Medical School, Boston, MA.
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