CellTypeAgent: Trustworthy cell type annotation with Large Language Models

• URL: http://arxiv.org/abs/2505.08844v1
• Date: Tue, 13 May 2025 14:34:11 GMT
• Title: CellTypeAgent: Trustworthy cell type annotation with Large Language Models
• Authors: Jiawen Chen, Jianghao Zhang, Huaxiu Yao, Yun Li,
• Abstract summary: We present a trustworthy large language model (LLM)-agent, CellTypeAgent, which integrates LLMs with verification from relevant databases.<n>We evaluated CellTypeAgent across nine real datasets involving 303 cell types from 36 tissues.
• Score: 21.976870680376358
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Cell type annotation is a critical yet laborious step in single-cell RNA sequencing analysis. We present a trustworthy large language model (LLM)-agent, CellTypeAgent, which integrates LLMs with verification from relevant databases. CellTypeAgent achieves higher accuracy than existing methods while mitigating hallucinations. We evaluated CellTypeAgent across nine real datasets involving 303 cell types from 36 tissues. This combined approach holds promise for more efficient and reliable cell type annotation.

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