用漂流岛评估细胞嵌入指标的局限性

IF 33.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Nature biotechnology Pub Date : 2025-06-11 DOI:10.1038/s41587-025-02702-z

Hanchen Wang, Jure Leskovec, Aviv Regev

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引用次数: 0

摘要

生物学研究依赖于单细胞剖面的嵌入，但评估这些嵌入的质量是具有挑战性的。在这里，我们通过训练一个三层感知器Islander来证明当前的评估指标是不完整的。Islander在多种细胞图谱上优于所有领先的嵌入方法，但它扭曲了生物结构，限制了它在生物发现中的应用。然后，我们提出了一个新的度量，scGraph，来帮助标记这种扭曲。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

Limitations of cell embedding metrics assessed using drifting islands

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Limitations of cell embedding metrics assessed using drifting islands

Biological studies rely on embeddings of single-cell profiles but assessing the quality of these embeddings is challenging. Here we show that current evaluation metrics are incomplete by training a three-layer perceptron, Islander. Islander outperforms all leading embedding methods on a diverse set of cell atlases but it distorts biological structures, limiting its use for biological discovery. We then present a new metric, scGraph, to help flag such distortions.

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来源期刊

Nature biotechnology 工程技术-生物工程与应用微生物

CiteScore

63.00

自引率

1.70%

发文量

382

审稿时长

3 months

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