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arXiv · 2509.09725

BIBERT-Pipe on Biomedical Nested Named Entity Linking at BioASQ 2025

Chunyu Li·Xindi Zheng·Siqi Liu
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Abstract

Entity linking (EL) for biomedical text is typically benchmarked on English-only corpora with flat mentions, leaving the more realistic scenario of nested and multilingual mentions largely unexplored. We present our system for the BioNNE 2025 Multilingual Biomedical Nested Named Entity Linking shared task (English & Russian), closing this gap with a lightweight pipeline that keeps the original EL model intact and modifies only three task-aligned components: Two-stage retrieval-ranking. We leverage the same base encoder model in both stages: the retrieval stage uses the original pre-trained model, while the ranking stage applies domain-specific fine-tuning. Boundary cues. In the ranking stage, we wrap each mention with learnable [Ms] / [Me] tags, providing the encoder with an explicit, language-agnostic span before robustness to overlap and nesting. Dataset augmentation. We also automatically expand the ranking training corpus with three complementary data sources, enhancing coverage without extra manual annotation. On the BioNNE 2025 leaderboard, our two stage system, bilingual bert (BIBERT-Pipe), ranks third in the multilingual track, demonstrating the effectiveness and competitiveness of these minimal yet principled modifications. Code are publicly available at https://github.com/Kaggle-Competitions-Code/BioNNE-L.

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Chunyu Li, Xindi Zheng, Siqi Liu. 2025-09-10. BIBERT-Pipe on Biomedical Nested Named Entity Linking at BioASQ 2025. https://arxiv.org/abs/2509.09725

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