Predicting anticancer hyperfoods with graph convolutional networks.

Human Genomics
Guadalupe GonzalezKirill Veselkov

Abstract

Recent efforts in the field of nutritional science have allowed the discovery of disease-beating molecules within foods based on the commonality of bioactive food molecules to FDA-approved drugs. The pioneering work in this field used an unsupervised network propagation algorithm to learn the systemic-wide effect on the human interactome of 1962 FDA-approved drugs and a supervised algorithm to predict anticancer therapeutics using the learned representations. Then, a set of bioactive molecules within foods was fed into the model, which predicted molecules with cancer-beating potential.The employed methodology consisted of disjoint unsupervised feature generation and classification tasks, which can result in sub-optimal learned drug representations with respect to the classification task. Additionally, due to the disjoint nature of the tasks, the employed approach proved cumbersome to optimize, requiring testing of thousands of hyperparameter combinations and significant computational resources.To overcome the technical limitations highlighted above, we represent each drug as a graph (human interactome) with its targets as binary node features on the graph and formulate the problem as a graph classification task. To solve this t...Continue Reading

References

Jan 1, 1992·Biomedicine & Pharmacotherapy = Biomédecine & Pharmacothérapie·A V SchallyD Gonzalez-Barcena
Jun 1, 1997·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·A JungwirthA V Schally
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Jan 10, 2003·Nucleic Acids Research·Christian von MeringBerend Snel
Nov 5, 2003·Reproductive Biology and Endocrinology : RB&E·Carsten Gründker, Günter Emons
Nov 19, 2003·The Journal of Steroid Biochemistry and Molecular Biology·Jürgen Geisler
Jun 10, 2004·British Journal of Cancer·S BamfordR Wooster
Oct 22, 2004·Nutrition Journal·Michael S Donaldson
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Dec 18, 2007·Nucleic Acids Research·Michael KuhnPeer Bork
Jul 16, 2009·Anti-cancer Agents in Medicinal Chemistry·Kwabina Aidoo-GyamfiSabbir Ahmed
Dec 6, 2012·Annals of Oncology : Official Journal of the European Society for Medical Oncology·Q J WuY B Xiang
Oct 31, 2014·Nucleic Acids Research·Garth R BrownTerence D Murphy
Nov 11, 2014·Nature·David Tilman, Michael Clark
Feb 11, 2015·PLoS Computational Biology·Kasper JensenIrene Kouskoumvekaki
May 23, 2015·Molecular Cell·Nevan J KroganTrey Ideker
Jul 1, 2015·Nature Methods·Pau CreixellUNKNOWN Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consortium
Aug 16, 2015·Cancer Letters·Savio G Barreto, Rachel E Neale
Feb 27, 2016·Journal of Cancer·Mohamed Ben-EltrikiEmma S Tomlinson Guns
Jun 2, 2016·The British Journal of Nutrition·Ruoxu DouShuji Ogino
Oct 30, 2016·Nucleic Acids Research·Oleg UrsuTudor I Oprea
Dec 3, 2016·Nucleic Acids Research·UNKNOWN The UniProt Consortium
Dec 22, 2016·Critical Reviews in Food Science and Nutrition·Abdur RaufMohammad S Mubarak
Jan 17, 2017·Reviews in Endocrine & Metabolic Disorders·Immacolata Cristina NettorePaolo Emidio Macchia
Mar 23, 2017·Critical Reviews in Oncology/hematology·Michael J DuffyJohn Crown
Jun 14, 2017·Nature Reviews. Genetics·Lenore CowenRoded Sharan
Jun 27, 2017·NPJ Systems Biology and Applications·Jörg MencheAlbert-László Barabási
Oct 17, 2017·Frontiers in Physiology·Tingting ZhengGianni Panagiotou
Oct 27, 2017·Critical Reviews in Oncology/hematology·Vidya MukundAfroz Alam
Nov 11, 2017·Nucleic Acids Research·David S WishartMichael Wilson
Dec 7, 2017·International Journal of Cancer. Journal International Du Cancer·Lukas SchwingshacklSabrina Schlesinger
Dec 7, 2017·BioFactors·Yi-Rong LiChi-Chien Lin
Dec 9, 2017·Database : the Journal of Biological Databases and Curation·Yueqiong NiGianni Panagiotou
Jan 19, 2018·International Journal of Molecular Sciences·Rong-Jane ChenHung-Chi Cheng
Feb 7, 2018·Journal of Laboratory Physicians·Ashish MahendraShivangi Gupta
Jun 29, 2018·Bioinformatics·Marinka ZitnikJure Leskovec
Jul 8, 2018·The Journal of Steroid Biochemistry and Molecular Biology·Gemma Ferrer-MayorgaAlberto Muñoz
Jan 9, 2019·CA: a Cancer Journal for Clinicians·Rebecca L SiegelAhmedin Jemal
Jul 5, 2019·Scientific Reports·Kirill VeselkovIvan Laponogov

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Software Mentioned

GraphSAGE
PyTorch
RWR
GSEA
GCN
ChebNet
STITCH
Gene Set Enrichment Analysis ( GSEA )
Torch Geometric Library

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