scButterfly: a versatile single-cell cross-modality translation method via dual-aligned variational autoencoders

Yichuan Cao, Xiamiao Zhao, Songming Tang, Qun Jiang, Sijie Li, Siyu Li and Shengquan Chen ()
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Yichuan Cao: Nankai University
Xiamiao Zhao: Nankai University
Songming Tang: Nankai University
Qun Jiang: Tsinghua University
Sijie Li: Nankai University
Siyu Li: Nankai University
Shengquan Chen: Nankai University

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: Abstract Recent advancements for simultaneously profiling multi-omics modalities within individual cells have enabled the interrogation of cellular heterogeneity and molecular hierarchy. However, technical limitations lead to highly noisy multi-modal data and substantial costs. Although computational methods have been proposed to translate single-cell data across modalities, broad applications of the methods still remain impeded by formidable challenges. Here, we propose scButterfly, a versatile single-cell cross-modality translation method based on dual-aligned variational autoencoders and data augmentation schemes. With comprehensive experiments on multiple datasets, we provide compelling evidence of scButterfly’s superiority over baseline methods in preserving cellular heterogeneity while translating datasets of various contexts and in revealing cell type-specific biological insights. Besides, we demonstrate the extensive applications of scButterfly for integrative multi-omics analysis of single-modality data, data enhancement of poor-quality single-cell multi-omics, and automatic cell type annotation of scATAC-seq data. Moreover, scButterfly can be generalized to unpaired data training, perturbation-response analysis, and consecutive translation.

Date: 2024
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DOI: 10.1038/s41467-024-47418-x

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