Better Generalizing to Unseen Concepts: An Evaluation Framework and An LLM-Based Auto-Labeled Pipeline for Biomedical Concept Recognition

Shanshan Liu; Noriki Nishida; Fei Cheng; Narumi Tokunaga; Rumana Ferdous Munne; Yuki Yamagata; Kouji Kozaki; Takehito Utsuro; Yuji Matsumoto

arXiv · 2601.16711

Better Generalizing to Unseen Concepts: An Evaluation Framework and An LLM-Based Auto-Labeled Pipeline for Biomedical Concept Recognition

Shanshan Liu·Noriki Nishida·Fei Cheng·Narumi Tokunaga·Rumana Ferdous Munne·Yuki Yamagata·Kouji Kozaki·Takehito Utsuro·Yuji Matsumoto

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Abstract

Generalization to unseen concepts is a central challenge due to the scarcity of human annotations in Mention-agnostic Biomedical Concept Recognition (MA-BCR). This work makes two key contributions to systematically address this issue. First, we propose an evaluation framework built on hierarchical concept indices and novel metrics to measure generalization. Second, we explore LLM-based Auto-Labeled Data (ALD) as a scalable resource, creating a task-specific pipeline for its generation. Our research unequivocally shows that while LLM-generated ALD cannot fully substitute for manual annotations, it is a valuable resource for improving generalization, successfully providing models with the broader coverage and structural knowledge needed to approach recognizing unseen concepts. Code and datasets are available at https://github.com/bio-ie-tool/hi-ald.

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Shanshan Liu, Noriki Nishida, Fei Cheng, Narumi Tokunaga, Rumana Ferdous Munne, Yuki Yamagata, Kouji Kozaki, Takehito Utsuro, Yuji Matsumoto. 2026-01-23. Better Generalizing to Unseen Concepts: An Evaluation Framework and An LLM-Based Auto-Labeled Pipeline for Biomedical Concept Recognition. https://arxiv.org/abs/2601.16711

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