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OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization

arXiv · AI, language, vision and robotics · article · Sep 9, 2026 · UTC

Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective hierarchy-guided refinement. We also construct PhenoNormBench, a unified benchmark comprising 13,390 samples from seven Human Phenotype Ontology dat

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Evidence & attribution

arXiv · AI, language, vision and robotics · 2026-09-09T11:30:25.000Z

First collected: 2026-09-20T19:32:24.350Z. This is not the publication date.