CASTER: Predicting drug interactions with chemical substructure representation

Kexin Huang, Cao Xiao, Trong Nghia Hoang, Lucas M. Glass, Jimeng Sun

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


Adverse drug-drug interactions (DDIs) remain a leading cause of morbidity and mortality. Identifying potential DDIs during the drug design process is critical for patients and society. Although several computational models have been proposed for DDI prediction, there are still limitations: (1) specialized design of drug representation for DDI predictions is lacking; (2) predictions are based on limited labelled data and do not generalize well to unseen drugs or DDIs; and (3) models are characterized by a large number of parameters, thus are hard to interpret. In this work, we develop a ChemicAl SubstrucTurE Representation (CASTER) framework that predicts DDIs given chemical structures of drugs. CASTER aims to mitigate these limitations via (1) a sequential pattern mining module rooted in the DDI mechanism to efficiently characterize functional sub-structures of drugs; (2) an auto-encoding module that leverages both labelled and unlabelled chemical structure data to improve predictive accuracy and generalizability; and (3) a dictionary learning module that explains the prediction via a small set of coefficients which measure the relevance of each input sub-structures to the DDI outcome. We evaluated CASTER on two real-world DDI datasets and showed that it performed better than state-of-the-art baselines and provided interpretable predictions.

Original languageEnglish (US)
Title of host publicationAAAI 2020 - 34th AAAI Conference on Artificial Intelligence
PublisherAmerican Association for Artificial Intelligence (AAAI) Press
Number of pages8
ISBN (Electronic)9781577358350
StatePublished - 2020
Externally publishedYes
Event34th AAAI Conference on Artificial Intelligence, AAAI 2020 - New York, United States
Duration: Feb 7 2020Feb 12 2020

Publication series

NameAAAI 2020 - 34th AAAI Conference on Artificial Intelligence


Conference34th AAAI Conference on Artificial Intelligence, AAAI 2020
Country/TerritoryUnited States
CityNew York

ASJC Scopus subject areas

  • Artificial Intelligence


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