# OEMA: Ontology-Enhanced Multi-Agent Collaboration Framework for Zero-Shot Clinical Named Entity Recognition

arXiv: https://arxiv.org/abs/2511.15211 · HTML: https://mlsanity.com/paper/2511.15211/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 30 references that are in the map.
- First posted on arXiv 19 Nov 2025.

## Builds on (most cited first, 15 of 15)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [PaLM: Scaling Language Modeling with Pathways](https://mlsanity.com/paper/2204.02311/) (2022)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Bidirectional LSTM-CRF Models for Sequence Tagging](https://mlsanity.com/paper/1508.01991/) (2015)
- [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://mlsanity.com/paper/1904.05342/) (2019)
- [ChatIE: Zero-Shot Information Extraction via Chatting with ChatGPT](https://mlsanity.com/paper/2302.10205/) (2023)
- [GPT-NER: Named Entity Recognition via Large Language Models](https://mlsanity.com/paper/2304.10428/) (2023)
- [Empirical Study of Zero-Shot NER with ChatGPT](https://mlsanity.com/paper/2310.10035/) (2023)
- [Self-Improving for Zero-Shot Named Entity Recognition with Large Language Models](https://mlsanity.com/paper/2311.08921/) (2023)
- [Bidirectional LSTM-CRF for Clinical Concept Extraction](https://mlsanity.com/paper/1611.08373/) (2016)
- [ReverseNER: A Self-Generated Example-Driven Framework for Zero-Shot Named Entity Recognition with Large Language Models](https://mlsanity.com/paper/2411.00533/) (2024)

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

- [Institution-Specific LLM Prompting Recovers PHI That De-identification Systems and Their Gold Standards Both Miss](https://mlsanity.com/paper/2608.17051/) (2026)

## Abstract (arXiv)

With the rapid expansion of unstructured clinical texts in electronic health records (EHRs), clinical named entity recognition (NER) has become a crucial technique for extracting medical information. However, traditional supervised models such as CRF and BioClinicalBERT suffer from high annotation costs. Although zero-shot NER based on large language models (LLMs) reduces the dependency on labeled data, challenges remain in aligning example selection with task granularity and effectively integrating prompt design with self-improvement frameworks. To address these limitations, we propose OEMA, a novel zero-shot clinical NER framework based on multi-agent collaboration. OEMA consists of three core components: (1) a self-annotator that autonomously generates candidate examples; (2) a discriminator that leverages SNOMED CT to filter token-level examples by clinical relevance; and (3) a predictor that incorporates entity-type descriptions to enhance inference accuracy. Experimental results on two benchmark datasets, MTSamples and VAERS, demonstrate that OEMA achieves state-of-the-art performance under exact-match evaluation. Moreover, under related-match criteria, OEMA performs comparably to the supervised BioClinicalBERT model while significantly outperforming the traditional CRF method. OEMA improves zero-shot clinical NER, achieving near-supervised performance under related-match criteria. Future work will focus on continual learning and open-domain adaptation to expand its applicability in clinical NLP.