AUTHOR=Xiong Jiankang , Gong Fuzhou , Wan Lin , Ma Liang TITLE=NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data JOURNAL=Frontiers in Genetics VOLUME=11 YEAR=2020 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00786 DOI=10.3389/fgene.2020.00786 ISSN=1664-8021 ABSTRACT=

The dramatic increase in amount and size of single-cell RNA sequencing data calls for more efficient and scalable dimensional reduction and visualization tools. Here, we design a GPU-accelerated method, NeuralEE, which aggregates the advantages of elastic embedding and neural network. We show that NeuralEE is both scalable and generalizable in dimensional reduction and visualization of large-scale scRNA-seq data. In addition, the GPU-based implementation of NeuralEE makes it applicable to limited computational resources while maintains high performance, as it takes only half an hour to visualize 1.3 million mice brain cells, and NeuralEE has generalizability for integrating newly generated data.