OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization
Updated 6 h ago · first seen 11 Sept 2026
paper_01M294GKE4HHME5ENEVJ9A3ZPY
- Published
- 11 Sept 2026
- T1 · 6 h ago
- arXiv
- 2609.10055
- T1 · 6 h ago
- Category
- cs.AI
- T1 · 6 h ago
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
Source:arXiv (Atom API + RSS)T1observed 6 h agohigh
- Arxiv announce type
- new
Source:arXiv (Atom API + RSS)T1observed 6 h agohigh
- arXiv id
- 2609.10055
Source:arXiv (Atom API + RSS)T1observed 6 h agohigh
- Categories
- cs.AI, cs.CL
Source:arXiv (Atom API + RSS)T1observed 6 h agohigh
Source:arXiv (Atom API + RSS)T1observed 6 h agohigh
- Primary category
- cs.AI
Source:arXiv (Atom API + RSS)T1observed 6 h agohigh
- Published
- 11 Sept 2026
Source:arXiv (Atom API + RSS)T1observed 6 h agohigh
Each value shows its source, tier and observation time. Conflicting claims are kept side by side and flagged — never averaged. How AI Atlas records facts →
Provenance
Attributed facts
9
Source tiers
T19
Freshest observation
6 h ago
Conflicts
None
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- Authors
- Jie Song, Zhichuan Xu, Ziyu Lu
As of
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Claim history · Abstract
Abstractabstract1
| 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. | → 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 →
New paper: OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization
arxiv
| Source | Document | Type | Tier | Last observed | Snapshots |
|---|---|---|---|---|---|
| arXiv (Atom API + RSS) | rss.arxiv.org/rss/cs.AI | feed | T1· Official | 5 h ago | 1 |
Tier 1 = official/primary, 2 = quality secondary, 3 = community, 4 = unverified. Every snapshot is archived; see all sources and the methodology.