# GATHER: Convergence-Centric Hyper-Entity Retrieval for Zero-Shot Cell-Type Annotation

arXiv: https://arxiv.org/abs/2605.06403 · HTML: https://mlsanity.com/paper/2605.06403/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 22 references that are in the map.
- First posted on arXiv 7 May 2026.

## Builds on (most cited first, 7 of 7)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Unifying Large Language Models and Knowledge Graphs: A Roadmap](https://mlsanity.com/paper/2306.08302/) (2023)
- [A Survey on RAG Meeting LLMs: Towards Retrieval-Augmented Large Language Models](https://mlsanity.com/paper/2405.06211/) (2024)
- [Think-on-Graph: Deep and Responsible Reasoning of Large Language Model on Knowledge Graph](https://mlsanity.com/paper/2307.07697/) (2023)
- [LLMs for Knowledge Graph Construction and Reasoning: Recent Capabilities and Future Opportunities](https://mlsanity.com/paper/2305.13168/) (2023)
- [Paths-over-Graph: Knowledge Graph Empowered Large Language Model Reasoning](https://mlsanity.com/paper/2410.14211/) (2024)
- [LangCell: Language-Cell Pre-training for Cell Identity Understanding](https://mlsanity.com/paper/2405.06708/) (2024)

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

- [Towards Trustworthy and Cost-Efficient Data Integration: From Na"ive RAG to Agentic RAG](https://mlsanity.com/paper/2607.22319/) (2026)

## Abstract (arXiv)

Zero-shot single-cell cell-type annotation aims to determine a cell's type from a given set of expressed genes without any training. Existing knowledge-graph-based RAG approaches retrieve evidence by expanding from source entities and relying on iterative LLM reasoning. However, in this setting each query contains tens to hundreds of genes, where no single gene is decisive and the label emerges only from their collective co-occurrence. Such hyper-entity queries fundamentally challenge local, entity-wise exploration strategies, which reason from individual genes, leading to poor scalability and substantial LLM cost. We propose GATHER (Graph-Aware Traversal with Hyper-Entity Retrieval), a convergence-centric retriever tailored to hyper-entity queries. It performs global multi-source graph traversal and identifies topological convergence points -- nodes jointly reachable from many input genes. These convergence nodes act as high-information hyper-entities that capture entity synergy. By incorporating node- and path-importance scoring, GATHER selects informative evidence entirely without LLM involvement during retrieval. Instantiated on a self-constructed cell-centric biological knowledge graph (VCKG), GATHER outperforms strong KG-RAG baselines (ToG, ToG-2, RoG, PoG) on two datasets (Immune and Lung), achieving the highest exact-match accuracy (27.45% and 59.64%) with only a single LLM call per sample, compared to 2--61 calls for KG-RAG baselines. Our results demonstrate that convergence nodes compress multi-entity signals into compact, high-information evidence that conveys more per item than multi-hop paths, providing an efficient global alternative to local entity-wise reasoning.