A Guideline-Augmented Multi-Agent Framework for Schema-as-Code Biomedical Named Entity Recognition

Large language models (LLMs) have advanced information extraction (IE) by enabling zero-shot and few-shot named entity recognition (NER), yet their generative outputs still show persistent and systematic errors. Despite progress through instruction fine-tuning, zero-shot NER still lags far behind supervised systems. These recurring errors mirror inconsistencies observed in early-stage human annotation processes that resolve disagreements through pilot annotation. Motivated by this analogy, we introduce DiZiNER (Disagreement-guided Instruction Refinement via Pilot Annotation Simulation for Zero-shot Named Entity Recognition), a framework that simulates the pilot annotation process, employing LLMs to act as both annotators and supervisors. Multiple heterogeneous LLMs annotate shared texts, and a supervisor model analyzes inter-model disagreements to refine task instructions. Across 18 benchmarks, DiZiNER achieves zero-shot SOTA results on 14 datasets, improving prior bests by +8.0 F1 and reducing the zero-shot to supervised gap by over +11 points. It also consistently outperforms its supervisor, GPT-5 mini, indicating that improvements stem from disagreement-guided instruction refinement rather than model capacity. Pairwise agreement between models shows a strong correlation with NER performance, further supporting this finding.

Biomedical relation extraction (BioRE) extracts structured knowledge from biomedical literature for applications such as knowledge base construction and hypothesis generation. Traditional symbolic systems such as SemRep provide high precision but limited recall, while large language models (LLMs) offer stronger contextual reasoning but remain prone to false-positive predictions. We developed ANCHOR-RE, a framework that integrates ontology-guided reasoning, external knowledge grounding, and data-driven verification rules into LLM inference. We evaluated it on three BioRE benchmarks (SemRepGS, DDI, and ChemProt) using both proprietary and open-weight LLMs. To assess generalizability beyond benchmark datasets while reducing potential evaluation bias from LLM pretraining contamination, we conducted a temporal evaluation using 100 biomedical articles published in 2026. With the proprietary backbone, ANCHOR-RE outperformed direct LLM prompting, improving micro-F1 from 0.654 to 0.676 on SemRepGS, from 0.769 to 0.872 on DDI, and from 0.939 to 0.941 on ChemProt. On DDI and ChemProt, it also outperformed previously reported inference-only methods and approached fine-tuned or instruction-tuned systems without parameter updates. Similar performance gains observed with open-weight LLMs indicate that the benefits were not limited to the proprietary backbone. On the post-cutoff set, manual assessment of 500 randomly sampled predictions yielded a precision of 69%, maintaining consistent precision on previously unseen biomedical literature. Neuro-symbolic reasoning can improve the reliability of LLM-based BioRE without fine-tuning. Results across multiple benchmarks, model families, and post-cutoff literature support ANCHOR-RE as a practical training-free approach to biomedical literature mining.

Recent advancements of zero-shot Named Entity Recognition (NER) establish strong baselines by formulating sequence labeling into question answering where Large Language Models (LLMs) can be naturally adopted. However, existing LLM-based zero-shot NER methods suffer from the limitations of prompt and demonstration engineering. To address these issues with minimal human interventions, we introduce DE-NER, a dialogue elicitation framework which elicits the chatting ability of LLMs to fully extract the knowledge encoded in LLMs. Our experiments demonstrate that the proposed method outperform the competitive baselines in zero-shot settings across multiple benchmarks, with an average improvement of 3.75% F1 points. Codes are released in https://github.com/kkkenshi/DE-NER.