# ANCHOR-RE: An Agentic Neuro-Symbolic Framework for Grounded Biomedical Relation Extraction

arXiv: https://arxiv.org/abs/2608.03154 · HTML: https://mlsanity.com/paper/2608.03154/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 16 of its 39 references that are in the map.
- First posted on arXiv 4 Aug 2026.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 16 of 16)

- [A Survey on Hallucination in Large Language Models: Principles, Taxonomy, Challenges, and Open Questions](https://mlsanity.com/paper/2311.05232/) (2023)
- [NLP Evaluation in trouble: On the Need to Measure LLM Data Contamination for each Benchmark](https://mlsanity.com/paper/2310.18018/) (2023)
- [BiomedRAG: A Retrieval Augmented Large Language Model for Biomedicine](https://mlsanity.com/paper/2405.00465/) (2024)
- [Drug Repurposing for COVID-19 via Knowledge Graph Completion](https://mlsanity.com/paper/2010.09600/) (2020)
- [PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge](https://mlsanity.com/paper/2401.11048/) (2024)
- [Revisiting Large Language Models as Zero-shot Relation Extractors](https://mlsanity.com/paper/2310.05028/) (2023)
- [SemEval-2024 Task 2: Safe Biomedical Natural Language Inference for Clinical Trials](https://mlsanity.com/paper/2404.04963/) (2024)
- [Unleashing the Power of Large Language Models in Zero-shot Relation Extraction via Self-Prompting](https://mlsanity.com/paper/2410.01154/) (2024)
- [PubMed knowledge graph 2.0: Connecting papers, patents, and clinical trials in biomedical science](https://mlsanity.com/paper/2410.07969/) (2024)
- [PEIRCE: Unifying Material and Formal Reasoning via LLM-Driven Neuro-Symbolic Refinement](https://mlsanity.com/paper/2504.04110/) (2025)
- [Recall, Retrieve and Reason: Towards Better In-Context Relation Extraction](https://mlsanity.com/paper/2404.17809/) (2024)
- [ReOnto: A Neuro-Symbolic Approach for Biomedical Relation Extraction](https://mlsanity.com/paper/2309.01370/) (2023)
- [RELATE: Relation Extraction in Biomedical Abstracts with LLMs and Ontology Constraints](https://mlsanity.com/paper/2509.19057/) (2025)
- [A Benchmark for End-to-End Zero-Shot Biomedical Relation Extraction with LLMs: Experiments with OpenAI Models](https://mlsanity.com/paper/2504.04083/) (2025)
- [Knowledge-augmented Pre-trained Language Models for Biomedical Relation Extraction](https://mlsanity.com/paper/2505.00814/) (2025)
- [Zero-Shot Document-Level Biomedical Relation Extraction via Scenario-based Prompt Design in Two-Stage with LLM](https://mlsanity.com/paper/2505.01077/) (2025)

## Abstract (arXiv)

Biomedical relation extraction (BioRE) supports knowledge graph construction and hypothesis generation. In real-world settings, most candidate entity pairs are unrelated. Symbolic systems such as SemRep offer high precision and interpretability but limited recall, whereas large language models (LLMs) can produce false-positive relations. We developed ANCHOR-RE, an agentic framework that combines retrieved demonstrations, ontology-guided semantic constraints, external biomedical knowledge, and error-driven verification to improve BioRE reliability without task-specific fine-tuning. We evaluated ANCHOR-RE on SemRepGS, DDI, and ChemProt using proprietary and open-weight LLMs. To assess generalizability while reducing potential pretraining contamination, we also conducted a post-cutoff temporal precision evaluation using 100 biomedical articles published in 2026. With the proprietary backbone, ANCHOR-RE improved micro-F1 over direct prompting from 0.654 to 0.676 on SemRepGS, from 0.769 to 0.881 on DDI, and from 0.937 to 0.941 on ChemProt, outperforming previously reported inference-only methods on DDI and ChemProt. Gains were also observed with the open-weight backbone. Additional experiments demonstrated cross-family model compatibility and sensitivity to external knowledge quality. Manual assessment of 500 randomly sampled positive predictions from the post-cutoff set yielded 69% precision. These results show that contextual evidence and error-driven verification can improve BioRE reliability across benchmarks, model families, and newly published literature, supporting ANCHOR-RE as a practical training-free approach to biomedical literature mining.