# ReCellTy: Domain-Specific Knowledge Graph Retrieval-Augmented LLMs Reasoning Workflow for Single-Cell Annotation

arXiv: https://arxiv.org/abs/2505.00017 · HTML: https://mlsanity.com/paper/2505.00017/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 12 of its 36 references that are in the map.
- First posted on arXiv 24 Apr 2025.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)
- Retrieval-augmented generation / [Medical and biomedical RAG](https://mlsanity.com/rag/medical-and-biomedical-rag/)

## Builds on (most cited first, 12 of 12)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Sparks of Artificial General Intelligence: Early experiments with GPT-4](https://mlsanity.com/paper/2303.12712/) (2023)
- [From Local to Global: A Graph RAG Approach to Query-Focused Summarization](https://mlsanity.com/paper/2404.16130/) (2024)
- [An Empirical Study of Catastrophic Forgetting in Large Language Models During Continual Fine-tuning](https://mlsanity.com/paper/2308.08747/) (2023)
- [Seven Failure Points When Engineering a Retrieval Augmented Generation System](https://mlsanity.com/paper/2401.05856/) (2024)
- [Medical Graph RAG: Towards Safe Medical Large Language Model via Graph Retrieval-Augmented Generation](https://mlsanity.com/paper/2408.04187/) (2024)
- [MedRAG: Enhancing Retrieval-augmented Generation with Knowledge Graph-Elicited Reasoning for Healthcare Copilot](https://mlsanity.com/paper/2502.04413/) (2025)
- [Fine-tuning Large Language Models for Domain-specific Machine Translation](https://mlsanity.com/paper/2402.15061/) (2024)
- [KG4Diagnosis: A Hierarchical Multi-Agent LLM Framework with Knowledge Graph Enhancement for Medical Diagnosis](https://mlsanity.com/paper/2412.16833/) (2024)
- [Learning the rules of peptide self-assembly through data mining with large language models](https://mlsanity.com/paper/2411.05421/) (2024)

## Abstract (arXiv)

With the rapid development of large language models (LLMs), their application to cell type annotation has drawn increasing attention. However, general-purpose LLMs often face limitations in this specific task due to the lack of guidance from external domain knowledge. To enable more accurate and fully automated cell type annotation, we develop a globally connected knowledge graph comprising 18850 biological information nodes, including cell types, gene markers, features, and other related entities, along with 48,944 edges connecting these nodes, which is used by LLMs to retrieve entities associated with differential genes for cell reconstruction. Additionally, a multi-task reasoning workflow is designed to optimise the annotation process. Compared to general-purpose LLMs, our method improves human evaluation scores by up to 0.21 and semantic similarity by 6.1% across multiple tissue types, while more closely aligning with the cognitive logic of manual annotation. Meanwhile, it narrows the performance gap between large and small LLMs in cell type annotation, offering a paradigm for structured knowledge integration and reasoning in bioinformatics.