A Herd of Language Models Makes a Better Zero-shot Annotator for Clinical Named Entity Recognition

Clinical named entity recognition (NER) remains difficult to scale due to the high cost of manual annotation. Although large language models (LLMs) enable zero-shot annotation, their performance on clinical NER is still limited. To this end, we improve the annotation quality by aggregating annotations from a herd of diverse LLMs, including general-purpose, medically adapted, and NER-specialized models. A key challenge in this multi-LLM setting is effectively leveraging entities extracted by only a minority of models: although they account for a substantial portion of true positives, they are heavily intermixed with noise. To address this, we introduce MARY, a labelmodeling method for Multi-LLM Annotation using Representation learning to capture contextual similaritY. During aggregation, MARY selectively incorporates minority-extracted entities whose contexts are similar to those of majority-extracted entities, yielding more reliable and comprehensive annotations. Experimental results show that MARY improves the average F1 score by 8.6% over vanilla zero-shot baselines while reducing annotation costs 1 .