Hemnet: Integration of electronic medical records with molecular interaction networks and domain knowledge for survival analysis

Edward W. Huang, Ran Zhang, Jie Liu, Sheng Wang, Baoyan Liu, Xuezhong Zhou, Chengxiang Zhai, Bingxue Li, Runshun Zhang, Hongsheng Lin

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

Abstract

The continual growth of electronic medical record (EMR) databases has paved the way for many data mining applications, including the discovery of novel disease-drug associations and the prediction of patient survival rates. However, these tasks are hindered because EMRs are usually segmented or incomplete. EMR analysis is further limited by the overabundance of medical term synonyms and morphologies, which causes existing techniques to mismatch records containing semantically similar but lexically distinct terms. Current solutions ill in missing values with techniques that tend to introduce noise rather than reduce it. In this paper, we propose to simultaneously infer missing data and solve semantic mismatching in EMRs by irst integrating EMR data with molecular interaction networks and domain knowledge to build the HEMnet, a heterogeneous medical information network. We then project this network onto a low-dimensional space, and group entities in the network according to their relative distances. Lastly, we use this entity distance information to enrich the original EMRs. We evaluate the effectiveness of this method according to its ability to separate patients with dissimilar survival functions. We show that our method can obtain signiicant (p-value < 0.01) results for each cancer subtype in a lung cancer dataset, while the baselines cannot.

Original languageEnglish (US)
Title of host publicationACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics
PublisherAssociation for Computing Machinery, Inc
Pages378-387
Number of pages10
ISBN (Electronic)9781450347228
DOIs
StatePublished - Aug 20 2017
Event8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2017 - Boston, United States
Duration: Aug 20 2017Aug 23 2017

Publication series

NameACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics

Other

Other8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2017
Country/TerritoryUnited States
CityBoston
Period8/20/178/23/17

ASJC Scopus subject areas

  • Software
  • Biomedical Engineering
  • Health Informatics
  • Computer Science Applications

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