DBP: Adaptive and Interpretable Factor Analysis for Single-cell RNA-seq Data with Deep Beta Processes

Factor analysis is a method that condenses multiple variables into a few latent factors. It can be used to extract the underlying sources of biological variation in high-dimensional data and distill them into interpretable gene programs. However, existing factorization methods lack adaptability in selecting the optimal number of factors and interpretability in capturing biological variation. To address these concerns, we propose Deep Beta Process (DBP), a deep probabilistic framework for adaptive and interpretable factor analysis of single-cell transcriptomic data. DBP achieves adaptive selection of factors through a stick-breaking Beta process and performs batch correction using an adversarial learning strategy. We validate the flexible factor extraction and robust batch correction capabilities of DBP on simulated datasets. We also demonstrate its superior performance in dimensionality reduction and biological interpretability while explaining biological variation from both cell and gene perspectives using factor and loading matrices. The application of DBP to a gastric adenocarcinoma dataset reveals malignant epithelial cell heterogeneity, providing valuable insights for investigating the molecular mechanisms of disease onset and progression. DBP is available at https://github.com/labomics/DBP and https://ngdc.cncb.ac.cn/biocode/tool/BT007954.