scPerb: Predict single-cell perturbation via style transfer-based variational autoencoder
Year: 2024
Type: article
Abstract: INTRODUCTION: Traditional methods for obtaining cellular responses after perturbation are usually labor-intensive and costly, especially when working with multiple different experimental conditions. Therefore, accurate prediction of cellular responses to perturbations is of great importance in computational biology. Existing methodologies, such as graph-based approaches, vector arithmetic, and neural networks, either mix perturbation-related variances with cell-type-specific patterns or implicitly distinguish them within black-box models. OBJECTIVES: This study aims to introduce and demonstrate a novel framework, scPerb, which explicitly extracts perturbation-related variances and transfers them from unperturbed to perturbed cells to accurately predict the effect of perturbation in single-cell level. METHODS: scPerb utilizes a style transfer strategy by incorporating a style encoder into the architecture of a variational autoencoder. The style encoder captures the differences in latent representations between unperturbed and perturbed cells, enabling accurate prediction of post-perturbation gene expression data. RESULTS: values of 0.98, 0.98, and 0.96 on three benchmarking datasets. CONCLUSION: scPerb offers a significant advancement in predicting cellular responses by effectively separating and transferring perturbation-related variances. This framework not only enhances prediction accuracy but also provides a robust tool for computational biology, addressing the limitations of current methodologies.
Source: Journal of Advanced Research
Authors: Zijia Tang, Minghao Zhou, Kai Zhang, Qianqian Song
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,000
OpenAlex ID: W4403931101