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通过解释由自我监督的图形转换器学到的细胞状态和利基相关性来推断单个细胞水平的空间相互作用
bioRxiv : the preprint server for biology
|November 19, 2025
概括
我们开发了一种新的图形变压器模型GITIII,用于使用空间转录学分析细胞与细胞相互作用 (CCI). 该工具增强了对细胞如何在组织中交流的理解,改善了生物洞察力.
科学领域:
- 计算生物学 计算生物学
- 基因组学就是基因组学.
- 系统生物学 系统生物学
背景情况:
- 细胞与细胞相互作用 (CCI) 对组织发育和功能至关重要.
- 空间转录学能够对CCI进行单细胞分辨率分析,但在数据解释和空间编码方面面临挑战.
研究的目的:
- 引入GITIII,一个自我监督的图形变压器模型,用于从空间转录组学数据推断和解释细胞-细胞相互作用.
- 为了解决当前CCI分析方法的局限性,包括有限的联体受体对和可解释性.
主要方法:
- 开发了GITIII,一个轻量级,可解释,自我监督的图形变压器模型.
- 概念化细胞作为单词和他们的邻里作为上下文推断CCI.
- 分析了细胞及其微环境 (利基) 之间的基因表达相关性.
主要成果:
- GITIII有效地识别和统计解释了跨不同数据集的空间CCI模式.
- 证明能够理解发送细胞对受体细胞基因表达的影响的能力.
- 启用了空间CCI模式的可视化,CCI信息的细胞聚类和网络构建.
结论:
- GITIII提供了一个强大的和可解释的框架,用于使用空间转录学分析细胞与细胞相互作用.
- 该模型成功地在脑和瘤微环境中发现了CCI,从而推进了生物学理解.
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