【论文速递】Benchmarking Recent Single-Cell Synthetic Data Generation Methods on the OneK1K

英文标题：Benchmarking Recent Single-Cell Synthetic Data Generation Methods on the OneK1K Dataset

arXiv编号：2610.31454
作者：Buse Giledereli, Basar Temiz, Amirreza Sattarzadeh Khanehbargh
来源：arXiv
原文链接：https://arxiv.org/abs/2610.31454

中文摘要：
Synthetic single-cell RNA-seq data generation offers a promising route for privacy-aware biomedical data sharing, but donor-linked datasets require careful balancing of biological utility and privacy risk. In this work, we benchmark synthetic generation methods for the CAMDA 2026 ELSA Health Privacy Challenge using the donor-split OneK1K dataset, comparing scGFT, scLDM, and Cell2Sentence across statistical fidelity, downstream biological preservation, and membership inference vulnerability. Because full-transcriptome generation is computationally demanding, we focus generative modeling on highly variable genes and evaluate alternative strategies for reconstructing non-HVG expression. Our results show that non-HVG handling is a central determinant of privacy: directly copying non-HVG values leads to severe leakage, whereas Poisson-based reconstruction substantially reduces membership inference risk. We further find that scGFT and scLDM better preserve biological structure than an independent Poisson baseline, while maintaining near-random privacy profiles under appropriate configurations. These findings highlight the importance of evaluating synthetic single-cell data beyond marginal similarity alone, emphasizing robustness, interpretability, and privacy-conscious design choices throughout preprocessing, generation, and post-processing.

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