Abstract

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 label-modeling method for **M**ulti-LLM **A**nnotation using **R**epresentation learning to capture contextual similarit**Y**. 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.