cs.AISep 16, 2026

Hyperbolic Graph Representation Learning for Differential Diagnosis on Biomedical Knowledge Graphs

Authors: Pietro MiottoLucia MelliniTommaso MarziCesare AlippiElena CasiraghiAlberto PaccanaroGiorgio ValentiniMauricio Soto-Gomez

Abstract

Biomedical knowledge graphs combine ontology-derived hierarchies with transversal associations among heterogeneous entities such as phenotypes, diseases, genes, proteins, and patients. This hybrid structure raises the question of whether hyperbolic embeddings, which naturally capture tree-like organization, remain useful beyond purely hierarchical graphs. We present a preliminary study of hyperbolic graph representation learning for Mendelian-disease differential diagnosis on a patient-integrated biomedical graph. Experiments on isolated ontology subgraphs show that hyperbolic models achieve strong performance in substantially lower dimensions than Euclidean baselines. We then evaluate the models on a link-prediction task that ranks candidate diseases for each patient. Results suggest that hyperbolic embeddings can exploit biomedical hierarchical structure while supporting diagnostic reasoning over heterogeneous patient-level graphs.

Explore similar work

CardsList
  1. A Unified Framework of Hyperbolic Graph Representation Learning Methods

    Apr 30, 2026Sofía Pérez Casulo, Marcelo Fiori, Bernardo Marenco +1Hyperbolic LearningHypergraphs

  2. Hyperbolic Graph Embedders for Link Prediction and Topology Reconstruction

    Aug 7, 2026Robert Jankowski, Maksim Kitsak, Dorota Celińska-KopczyńskaHypergraphsComplex Networks

  3. HSG: Hyperbolic Scene Graph

    Apr 19, 2026Liyang Wang, Zeyu Zhang, Hao TangHyperbolic Learning3D Scene Graphs