# Tools Are Not Islands: Set-Level Tool Retrieval for LLM Agents via Query-Conditioned Hyperedge Prediction

arXiv: https://arxiv.org/abs/2607.25718 · HTML: https://mlsanity.com/paper/2607.25718/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Placed in Tool learning and function calling, one of 16 directions in LLM agents and tool use.
- Builds on 19 of its 22 references that are in the map.
- First posted on arXiv 28 Jul 2026.

## Placed in

- LLM agents and tool use / [Tool learning and function calling](https://mlsanity.com/agents/tool-learning-and-function-calling/)

## Builds on (most cited first, 19 of 19)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [Dense Passage Retrieval for Open-Domain Question Answering](https://mlsanity.com/paper/2004.04906/) (2020)
- [Lost in the Middle: How Language Models Use Long Contexts](https://mlsanity.com/paper/2307.03172/) (2023)
- [ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world APIs](https://mlsanity.com/paper/2307.16789/) (2023)
- [Gorilla: Large Language Model Connected with Massive APIs](https://mlsanity.com/paper/2305.15334/) (2023)
- [Unsupervised Dense Information Retrieval with Contrastive Learning](https://mlsanity.com/paper/2112.09118/) (2021)
- [HuggingGPT: Solving AI Tasks with ChatGPT and its Friends in Hugging Face](https://mlsanity.com/paper/2303.17580/) (2023)
- [Contrastive Learning with Hard Negative Samples](https://mlsanity.com/paper/2010.04592/) (2020)
- [Transformer Memory as a Differentiable Search Index](https://mlsanity.com/paper/2202.06991/) (2022)
- [Planning, Creation, Usage: Benchmarking LLMs for Comprehensive Tool Utilization in Real-World Complex Scenarios](https://mlsanity.com/paper/2401.17167/) (2024)
- [ToolGen: Unified Tool Retrieval and Calling via Generation](https://mlsanity.com/paper/2410.03439/) (2024)
- [SkillRouter: Skill Routing for LLM Agents at Scale](https://mlsanity.com/paper/2603.22455/) (2026)
- [ToolRerank: Adaptive and Hierarchy-Aware Reranking for Tool Retrieval](https://mlsanity.com/paper/2403.06551/) (2024)
- [Latent Space Modelling of Hypergraph Data](https://mlsanity.com/paper/1909.00472/) (2019)
- [A General Latent Embedding Approach for Modeling Non-uniform High-dimensional Sparse Hypergraphs with Multiplicity](https://mlsanity.com/paper/2410.12108/) (2024)

## Built on by (most cited first, 3 of 3)

- [What Does a Skill Actually Do? Estimands and Evaluation Validity for Tool and Skill Use in LLM Agents: A Critical Review](https://mlsanity.com/paper/2609.33153/) (2026)
- [Self-Evolving Agents via Likelihood-Guided Tool-Space Optimization](https://mlsanity.com/paper/2609.34151/) (2026)
- [What Can Component-Replacement Evidence Establish? A Critical Scoping Review of Local Decisions in LLM Agents](https://mlsanity.com/paper/2609.39989/) (2026)

## Abstract (arXiv)

Large language model (LLM) agents increasingly rely on invoking external tools to complete real-world tasks. Tool retrieval, which selects a small task-relevant subset from a library of thousands of tools before the agent acts, has therefore become a critical component of LLM agent pipelines. However, existing retrievers either score each tool in isolation or assemble the tool set sequentially, so the joint utility of a candidate set is never evaluated as a whole. In this paper, we propose HYSET, short for HYperedge-based SEt-level Tool retrieval. Our contributions are threefold: (i) we formulate tool retrieval as query-conditioned hyperedge prediction on a tool co-invocation hypergraph, under which the tool set itself becomes the unit of scoring and most existing retrieval paradigms reduce to restricted instances; (ii) we capture size-dependent tool compatibility through cardinality-specific interactions; and (iii) we design HYSET as a pre-selection module requiring no modification to the downstream agent. Experiments on ToolBench demonstrate that HYSET consistently outperforms state-of-the-art baselines in both tool retrieval performance and end-to-end task success. Beyond the in-domain setting, HYSET further supports zero-shot/few-shot transfer, generalizing to held-out tools/categories and unseen domains with minimal supervision.