# CellTypeAgent: Trustworthy cell type annotation with Large Language Models

arXiv: https://arxiv.org/abs/2505.08844 · HTML: https://mlsanity.com/paper/2505.08844/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 5 of its 18 references that are in the map.
- First posted on arXiv 13 May 2025.

## Builds on (most cited first, 5 of 5)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [A Survey on Hallucination in Large Language Models: Principles, Taxonomy, Challenges, and Open Questions](https://mlsanity.com/paper/2311.05232/) (2023)
- [Privacy Issues in Large Language Models: A Survey](https://mlsanity.com/paper/2312.06717/) (2023)
- [Evaluating the Potential of Leading Large Language Models in Reasoning Biology Questions](https://mlsanity.com/paper/2311.07582/) (2023)

## Built on by (most cited first, 1 of 1)

- [From EduVisBench to EduVisAgent: A Benchmark and Multi-Agent Framework for Reasoning-Driven Pedagogical Visualization](https://mlsanity.com/paper/2505.16832/) (2025)

## Abstract (arXiv)

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.