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Cell-GraphCompass: modeling single cells with graph structure foundation model

文献类型：期刊论文

作者Fang, Chen2,3,4,5,6; Cui, Wentao5,7; Hu, Zhilong5,6,7; Liu, Wenhao3,4; Chen, Shubai7,8; Chang, Shaole6; Long, Qingqing5,7; Li, Cong3,4,7; Liu, Yana3,4; Jiang, Haiping3,4
刊名NATIONAL SCIENCE REVIEW
出版日期2025-10-01
卷号12期号:10页码:14
关键词single-cell transcriptomics foundation model pre-training graph neural network knowledge embedding
ISSN号2095-5138
DOI10.1093/nsr/nwaf255
英文摘要Cells in the human body are regulated by sophisticated networks of gene regulation, which allows them to fulfill their cellular destiny and function. Inspired by the advancements in large language models, there have been several attempts focusing on constructing foundation models with single-cell transcriptomic data to decipher gene regulatory networks. However, these models tend to impose a sequential structure on genes within each cell, which may omit intrinsic biological characteristics and lack the utilization of other available prior knowledge. In this paper, we introduce Cell-GraphCompass (CGCompass), the pioneering foundation model that employs graph pre-training to model genes and cells. We use three types of gene-related information as node features for constructing cell graphs and collect data from three perspectives depicting relationships between genes as edge features. We pre-trained the model with over 50 million human cells and then fine-tuned it to a broad spectrum of tasks, such as batch integration, cell type annotation, single-cell gene perturbation and in silico gene knockout predictions, achieving commendable performance. Overall, CGCompass provides a practical architecture for leveraging graph pre-training to incorporate prior knowledge in constructing a foundation model for single-cell analysis.
资助项目National Key Research and Development Program ; Computer Network Information Center, Chinese Academy of Sciences
WOS研究方向Science & Technology - Other Topics
语种英语
WOS记录号WOS:001584636200001
出版者OXFORD UNIV PRESS
源URL[http://119.78.100.204/handle/2XEOYT63/41644]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Meng, Zhen; Zhou, Yuanchun; Chen, Linghui; Feng, Guihai; Li, Xin
作者单位1.Oristruct Biotech Co Ltd, Hefei 230026, Peoples R China
2.Univ Chinese Acad Sci, Sch Adv Interdisciplinary Sci, Beijing 100049, Peoples R China
3.Chinese Acad Sci, Inst Zool, State Key Lab Organ Regenerat & Reconstruct, Beijing 100101, Peoples R China
4.Beijing Inst Stem Cell & Regenerat Med, Beijing 100101, Peoples R China
5.Chinese Acad Sci, Comp Network Informat Ctr, Beijing 100083, Peoples R China
6.iFLYTEK Res, Hefei 230088, Peoples R China
7.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
8.Chinese Acad Sci, Inst Comp Technol, Beijing 100190, Peoples R China
9.Chinese Acad Sci, Inst Zool, Human Organ Physiopathol Emulat Syst, Beijing 100101, Peoples R China
推荐引用方式
GB/T 7714		 Fang, Chen,Cui, Wentao,Hu, Zhilong,et al. Cell-GraphCompass: modeling single cells with graph structure foundation model[J]. NATIONAL SCIENCE REVIEW,2025,12(10):14.
APA Fang, Chen.,Cui, Wentao.,Hu, Zhilong.,Liu, Wenhao.,Chen, Shubai.,...&Li, Xin.(2025).Cell-GraphCompass: modeling single cells with graph structure foundation model.NATIONAL SCIENCE REVIEW,12(10),14.
MLA Fang, Chen,et al."Cell-GraphCompass: modeling single cells with graph structure foundation model".NATIONAL SCIENCE REVIEW 12.10(2025):14.

入库方式： OAI收割

来源：计算技术研究所

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