Learning Drug-Disease-Target Embedding (DDTE) from knowledge graphs to inform drug repurposing hypotheses.

Journal of Biomedical Informatics
Changsung MoonAlexander Tropsha

Abstract

We aimed to develop and validate a new graph embedding algorithm for embedding drug-disease-target networks to generate novel drug repurposing hypotheses. Our model denotes drugs, diseases and targets as subjects, predicates and objects, respectively. Each entity is represented by a multidimensional vector and the predicate is regarded as a translation vector from a subject to an object vectors. These vectors are optimized so that when a subject-predicate-object triple represents a known drug-disease-target relationship, the summed vector between the subject and the predicate is to be close to that of the object; otherwise, the summed vector is distant from the object. The DTINet dataset was utilized to test this algorithm and discover unknown links between drugs and diseases. In cross-validation experiments, this new algorithm outperformed the original DTINet model. The MRR (Mean Reciprocal Rank) values of our models were around 0.80 while those of the original model were about 0.70. In addition, we have identified and verified several pairs of new therapeutic relations as well as adverse effect relations that were not recorded in the original DTINet dataset. This approach showed excellent performance, and the predicted drug-d...Continue Reading

References

Dec 31, 2005·Nucleic Acids Research·David S WishartJennifer Woolsey
Feb 10, 2007·Journal of Chemical Information and Modeling·Jean-François Truchon, Christopher I Bayly
Nov 8, 2008·Nucleic Acids Research·T S Keshava PrasadAkhilesh Pandey
Jul 17, 2009·Bioinformatics·Kevin Bleakley, Yoshihiro Yamanishi
Jul 22, 2009·BMC Bioinformatics·Wei ZhaoJames M Boyett
Jan 21, 2010·Molecular Systems Biology·Michael KuhnPeer Bork
Mar 1, 2012·Drug Discovery Today. Therapeutic Strategies·Tudor I OpreaLarry A Sklar
Apr 28, 2012·Molecular BioSystems·Xing ChenGui-Ying Yan
Sep 16, 2015·The International Journal of Neuropsychopharmacology·Monica Dines, Raphael Lamprecht
Nov 18, 2016·KDD : Proceedings·Aditya Grover, Jure Leskovec
Dec 3, 2016·Nucleic Acids Research·Dac-Trung NguyenRajarshi Guha
Jan 24, 2017·Future Medicinal Chemistry·William P KattRichard A Cerione
Jan 5, 2018·Journal of Chemical Information and Modeling·Stephen J CapuzziAlexander Tropsha
Jan 14, 2018·Drug Discovery Today·Nancy C BakerAlexander Tropsha
Sep 25, 2018·Nucleic Acids Research·Allan Peter DavisCarolyn J Mattingly
Oct 4, 2020·Journal of Translational Medicine·Ghazale FahimianReza H Sajedi

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