HCOE: Hyperbolic Clinical Ontology Embeddings from Biomedical Language Models

arXiv:2609.30763 · cs.AI, cs.LG · Submitted 2026-09-25 · Read on arXiv

cs.AI, cs.LG

Submitted: 2026-09-25

Updated: 2026-09-25

Comments: Accepted at IEEE BIBM 2026. 7 pages, 3 figures, 4 tables

License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/

Terminology

• Ontology — 57× in this paper · explained in 2 episodes
• Embeddings — 46× in this paper · explained in 2 episodes
• Contrastive Learning — 19× in this paper · explained in 5 episodes
• Aggregation — 13× in this paper · explained in 1 episode
• Representation Learning — 7× in this paper · explained in 2 episodes
• Hyperbolic Clinical Ontology Embeddings — 6× in this paper
• Ablation — 4× in this paper · explained in 1 episode
• Knowledge Graph — 3× in this paper · explained in 7 episodes
• Ablation Studies — 2× in this paper · explained in 1 episode
• Accuracy — 2× in this paper · explained in 1 episode
• Alignment — 2× in this paper · explained in 1 episode
• Anatomical Therapeutic Chemical — 2× in this paper
• Clinical Classifications Software — 2× in this paper
• Downstream Tasks — 2× in this paper · explained in 2 episodes
• International Classification of Diseases — 2× in this paper
• Knowledge graphs — 2× in this paper · explained in 2 episodes
• Transformer — 2× in this paper · explained in 2 episodes
• Adam — 1× in this paper · explained in 2 episodes
• Area Under Precision-Recall Curve — 1× in this paper
• Area Under Receiver Operating Characteristic Curve — 1× in this paper
• Foundation Model — 1× in this paper · explained in 3 episodes
• Foundation Models — 1× in this paper · explained in 7 episodes

Sources

• SafeRx-Agent: A Knowledge-Grounded Multi-Agent Framework for Safe and Explainable Medication Recommendation
• Pre-training of Graph Augmented Transformers for Medication Recommendation
• RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space

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