VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder / 基因组蛋白质组与生物信息学报·英文版

Single-cell RNA sequencing (scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities at the single cell level. It is an important step for studying cell sub-populations and lineages, with an effective low-dimensional representation and visualization of the original scRNA-Seq data. At the single cell level, the transcriptional fluctuations are much larger than the average of a cell population, and the low amount of RNA transcripts will increase the rate of technical dropout events. Therefore, scRNA-seq data are much noisier than traditional bulk RNA-seq data. In this study, we proposed the deep variational autoencoder for scRNA-seq data (VASC), a deep multi-layer generative model, for the unsupervised dimension reduction and visualization of scRNA-seq data. VASC can explicitly model the dropout events and find the nonlinear hierarchical feature representations of the original data. Tested on over 20 datasets, VASC shows superior performances in most cases and exhibits broader dataset compatibility compared to four state-of-the-art dimension reduction and visualization methods. In addition, VASC provides better representations for very rare cell populations in the 2D visualization. As a case study, VASC successfully re-establishes the cell dynamics in pre-implantation embryos and identifies several candidate marker genes associated with early embryo development. Moreover, VASC also performs well on a 10× Genomics dataset with more cells and higher dropout rate.

Research on manufacturing text classification based on improved genetic algorithm

ABSTRACT According to the features of texts, a text classification model is proposed. Base on this model, an optimized objective function is designed by utilizing the occurrence frequency of each feature in each category. According to the relation matrix oftext resource and features, an improved genetic algorithm is adopted for solution with integral matrix crossover, transposition and recombination of entire population. At last the sample date of manufacturing text information from professional resources database system is taken as an example to illustrate the proposed model and solution for feature dimension reduction and text classification. The crossover and mutation probabilities of algorithm are compared vertically and horizontally to determine a group of better parameters. The experiment results show that the proposed method is fast and effective.