HCOE: hyperbolic ontology embeddings map BioBERT into a Poincaré ball for hierarchy-aware clinical concept representation
This arXiv v1 paper introduces Hyperbolic Clinical Ontology Embeddings (HCOE), which map frozen BioBERT embeddings into a Poincaré ball and train with parent-side and child-side ontology-guided contrastive learning plus coarse-to-fine ontology-path aggregation. HCOE is built using ICD codes organized by CCS and ATC medication hierarchies; evaluations report it outperforms baselines on ICD/ATC clinical relation prediction, CCS-to-PheCode hierarchy transfer, and downstream MIMIC‑IV tasks including mortality and readmission prediction, medication recommendation, and rare drug prediction.