CellTypeAgent: Trustworthy cell type annotation with Large Language Models

Jiawen Chen; Jianghao Zhang; Huaxiu Yao; Yun Li

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arXiv · 2505.08844

CellTypeAgent: Trustworthy cell type annotation with Large Language Models

Jiawen Chen·Jianghao Zhang·Huaxiu Yao·Yun Li

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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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Jiawen Chen, Jianghao Zhang, Huaxiu Yao, Yun Li. 2025-05-13. CellTypeAgent: Trustworthy cell type annotation with Large Language Models. https://arxiv.org/abs/2505.08844

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