Diagnosis Prediction over Patient Data using Hierarchical Medical Taxonomies

Emil Riis Hansen, Tomer Sagi, Katja Hose

Research output: Contribution to journalConference articlepeer-review


A variety of hierarchical domain taxonomies exist in the medical domain for describing medical concepts such as laboratory tests, medications, and procedures. The structural information contained within domain taxonomies contains rich semantic information pertaining to the described concepts and their relationships to each other. As AI models are successfully applied in many medical areas, it is only natural to explore integrating AI models with medical domain taxonomies. However, only a few, nascent attempts have been made. In this work, we investigate how the structure of hierarchical medical taxonomies can be used to improve the performance of a diagnosis prediction task. Specifically, we suggest a method titled TreeEmb to pre-initialize the node embeddings of a patient graph derived from electronic health records using information from the taxonomy. We expect this method to improve the performance of graph convolution network models over the enriched patient graph. We evaluate our method over a patient graph created from the MIMIC-IV electronic health record dataset enriched by initializing node embeddings using hierarchical medical taxonomies. We use type-specific domain knowledge from hierarchical medical taxonomies such as the ICD-9 procedures, ATC medication, and LOINC laboratory test taxonomies. Experimental results from a multi-label diagnosis prediction task over this graph demonstrate the efficacy of our approach.

Original languageEnglish
JournalCEUR Workshop Proceedings
StatePublished - 2023
Externally publishedYes
Event2023 Workshops of the EDBT/ICDT Joint Conference, EDBT/ICDT-WS 2023 - Ioannina, Greece
Duration: 28 Mar 2023 → …

Bibliographical note

Funding Information:
This work is partially supported by the Poul Due Jensen Foundation.

Publisher Copyright:
© 2023 Copyright for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0). CEUR Workshop Proceedings (CEUR-WS.org)


  • Embedding Initialization
  • Graph Convolution Networks
  • Hierarchical Domain Knowledge
  • Inductive Artificial Intelligence
  • Multi-Label Classification
  • Patient Diagnosis Prediction

ASJC Scopus subject areas

  • Computer Science (all)


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