Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement

Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Andrew Wen, Andrew Harold Limper, Hongfang D Liu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

The Human Phenotype Ontology (HPO) was developed to be a semantically computable vocabulary that captures the phenotypic abnormalities found in human diseases discovered through biomedical research. Usage of this ontology facilitates the translation between genotype and phenotype. Many studies have been conducted to accelerate the implementation of precision medicine into clinical practice by utilizing the informative contents provided in the HPO. No work, however, has been done in constructing a distributed representation for nodes in HPO to provide a deep insight of phenotypic similarities by analyzing its graph structure. Node2vec is a model for generating node embeddings based on large networks. In this study, we constructed node embeddings for the HPO leveraging node2vec to assist phenotypic similarity measurement. A downstream application on link prediction driven by HPO embedding achieved 0.81 ROAUC and 0.75 F-measure. A use case study was conducted on idiopathic pulmonary fibrosis (IPF) and we demonstrated the potential possibility of using HPO embeddings in assisting phenotypic similarity measurement.

Original languageEnglish (US)
Title of host publicationProceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages29-33
Number of pages5
ISBN (Electronic)9781538667774
DOIs
StatePublished - Jul 16 2018
Event6th IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018 - New York, United States
Duration: Jun 4 2018Jun 7 2018

Other

Other6th IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018
CountryUnited States
CityNew York
Period6/4/186/7/18

Fingerprint

Phenotype
Idiopathic Pulmonary Fibrosis
Precision Medicine
Vocabulary
Node
Ontology
Biomedical Research
Genotype

Keywords

  • Human Phenotype Ontology
  • Node embeddings
  • Phenotypic similarity

ASJC Scopus subject areas

  • Information Systems and Management
  • Health Informatics

Cite this

Shen, F., Liu, S., Wang, Y., Wang, L., Wen, A., Limper, A. H., & Liu, H. D. (2018). Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. In Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018 (pp. 29-33). [8411677] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ICHI-W.2018.00011

Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. / Shen, Feichen; Liu, Sijia; Wang, Yanshan; Wang, Liwei; Wen, Andrew; Limper, Andrew Harold; Liu, Hongfang D.

Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc., 2018. p. 29-33 8411677.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Shen, F, Liu, S, Wang, Y, Wang, L, Wen, A, Limper, AH & Liu, HD 2018, Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. in Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018., 8411677, Institute of Electrical and Electronics Engineers Inc., pp. 29-33, 6th IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018, New York, United States, 6/4/18. https://doi.org/10.1109/ICHI-W.2018.00011
Shen F, Liu S, Wang Y, Wang L, Wen A, Limper AH et al. Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. In Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc. 2018. p. 29-33. 8411677 https://doi.org/10.1109/ICHI-W.2018.00011
Shen, Feichen ; Liu, Sijia ; Wang, Yanshan ; Wang, Liwei ; Wen, Andrew ; Limper, Andrew Harold ; Liu, Hongfang D. / Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc., 2018. pp. 29-33
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