Online t-SNE for single-cell RNA-seq

Abstract: Due to the sequential sample arrival, changing experiment conditions, and evolution of knowledge, the demand to continually visualize evolving structures of sequential and diverse single-cell RNA-sequencing (scRNA-seq) data becomes indispensable. However, as one of the state-of-the-art visualization and analysis methods for scRNA-seq, t-distributed stochastic neighbor embedding (t-SNE) merely visualizes static scRNA-seq data offline and fails to meet the demand well. To address these challenges, we introduce online t-SNE to seamlessly integrate sequential scRNA-seq data. Online t-SNE achieves this by leveraging the embedding space of old samples, exploring the embedding space of new samples, and aligning the two embedding spaces on the fly. Consequently, online t-SNE dramatically enables the continual discovery of new structures and high-quality visualization of new scRNA-seq data without retraining from scratch. We showcase the formidable visualization capabilities of online t-SNE across diverse sequential scRNA-seq datasets.