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Drug2Vec: Knowledge-aware Feature-driven Method for Drug Representation Learning

  • Ying Shen
  • , Kaiqi Yuan
  • , Yaliang Li
  • , Buzhou Tang
  • , Min Yang
  • , Nan Du
  • , Kai Lei*
  • *Corresponding author for this work
  • Peking University
  • Tencent America
  • School of Computer Science and Technology, Harbin Institute of Technology
  • Shenzhen Institute of Advanced Technology

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Proper representations of drugs have broad applications in healthcare analytics, such as drug-drug interaction (DDI) prediction and drug-drug similarity (DDS) computation. However, drug application involves accurate drug representation and rich annotated data, requiring tremendous expert time and effort. Thereby, drug feature sparseness creates a substantial barrier for drug representation learning, making it difficult to accurately identify new drug properties prior to public release. To alleviate these deficiencies, we propose a knowledge-aware feature-driven method (Drug2Vec) for exploring the interaction between two drugs. The method of Drug2Vec captures the medical information, taxonomy information and semantic information of drugs. The results of experiments demonstrate that compared with existing methods, Drug2Vec can effectively learn the drug representation and discover accurate drug-drug interaction.

Original languageEnglish
Title of host publicationProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
EditorsHarald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages757-800
Number of pages44
ISBN (Electronic)9781538654880
DOIs
StatePublished - 21 Jan 2019
Externally publishedYes
Event2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 - Madrid, Spain
Duration: 3 Dec 20186 Dec 2018

Publication series

NameProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

Conference

Conference2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
Country/TerritorySpain
CityMadrid
Period3/12/186/12/18

Keywords

  • drug representation learning
  • drug-drug interaction
  • feature processing

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