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

Abstract

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 datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at https://github.com/zhelishisongjie/OntologyAligner.

Authors 11

Jie Song, Zhichuan Xu, Ziyu Lu, Meng Xiao, Cheng Bi, Yuxin Zhang, Xin Zheng, Xiaoran Li, Qiongfang Cao, Hao Yang, Bairong Shen

Specification

Official page: arxiv.org/abs/2609.10055
Source:arXiv (Atom API + RSS)T1observed 7 h agohigh
Arxiv announce type: new
Source:arXiv (Atom API + RSS)T1observed 7 h agohigh
arXiv id: 2609.10055
Source:arXiv (Atom API + RSS)T1observed 7 h agohigh
Categories: cs.AI, cs.CL
Source:arXiv (Atom API + RSS)T1observed 7 h agohigh
PDF: arxiv.org/pdf/2609.10055
Source:arXiv (Atom API + RSS)T1observed 7 h agohigh
Primary category: cs.AI
Source:arXiv (Atom API + RSS)T1observed 7 h agohigh
Published: 11 Sept 2026
Source:arXiv (Atom API + RSS)T1observed 7 h agohigh

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9

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T19

Freshest observation

7 h ago

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None

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Authors: Jie Song, Zhichuan Xu, Ziyu Lu

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Claim history

9 claims · 9 properties

Official pageofficial_url1

Claim history for Official page
Value	Valid from → to	Status	Source	Confidence	Extractor
https://arxiv.org/abs/2609.10055	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Abstractabstract1

Claim history for Abstract
Value	Valid from → to	Status	Source	Confidence	Extractor
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 datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at https://github.com/zhelishisongjie/OntologyAligner.	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Arxiv announce typearxiv_announce_type1

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new	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

arXiv idarxiv_id1

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2609.10055	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Authorsauthors1

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Value	Valid from → to	Status	Source	Confidence	Extractor
Jie Song, Zhichuan Xu, Ziyu Lu, Meng Xiao, Cheng Bi, Yuxin Zhang, Xin Zheng, Xiaoran Li, Qiongfang Cao, Hao Yang, Bairong Shen	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Categoriescategories1

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cs.AI, cs.CL	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

PDFpdf_url1

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https://arxiv.org/pdf/2609.10055	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Primary categoryprimary_category1

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cs.AI	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Publishedpublished_at1

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11 Sept 2026	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Claims are temporal and append-only: a new observation closes the previous claim (valid_to) instead of overwriting it. Conflicting claims from different sources are kept side by side and flagged — never averaged. Methodology →

11 Sept 2026
New paperPaperOntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization
New paper: OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization
arxiv
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Source documents
Source	Document	Type	Tier	Last observed	Snapshots
arXiv (Atom API + RSS)	rss.arxiv.org/rss/cs.AI	feed	T1· Official	6 h ago	1

Tier 1 = official/primary, 2 = quality secondary, 3 = community, 4 = unverified. Every snapshot is archived; see all sources and the methodology.