Conditional Molecular Design with Deep Generative Models

Journal of Chemical Information and Modeling
Seokho Kang, Kyunghyun Cho

Abstract

Although machine learning has been successfully used to propose novel molecules that satisfy desired properties, it is still challenging to explore a large chemical space efficiently. In this paper, we present a conditional molecular design method that facilitates generating new molecules with desired properties. The proposed model, which simultaneously performs both property prediction and molecule generation, is built as a semisupervised variational autoencoder trained on a set of existing molecules with only a partial annotation. We generate new molecules with desired properties by sampling from the generative distribution estimated by the model. We demonstrate the effectiveness of the proposed model by evaluating it on drug-like molecules. The model improves the performance of property prediction by exploiting unlabeled molecules and efficiently generates novel molecules fulfilling various target conditions.

References

Mar 18, 1997·Proceedings of the National Academy of Sciences of the United States of America·I Huc, J M Lehn
Dec 10, 2002·Current Medicinal Chemistry·Gisbert Schneider
Apr 30, 2010·Journal of Chemical Information and Modeling·David Rogers, Mathew Hahn
Jan 25, 2012·Nature Chemistry·G Richard BickertonAndrew L Hopkins
Mar 10, 2012·Physical Review Letters·Matthias RuppO Anatole von Lilienfeld
May 16, 2012·Journal of Chemical Information and Modeling·Alexandre Varnek, Igor Baskin
Jun 26, 2013·Journal of Chemical Information and Modeling·Alessandro LusciPierre Baldi
Jan 31, 2015·Journal of Chemical Information and Modeling·Junshui MaVladimir Svetnik
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Jun 27, 2015·The Journal of Physical Chemistry Letters·Katja HansenAlexandre Tkatchenko
Sep 25, 2015·Nucleic Acids Research·Sunghwan KimStephen H Bryant
Oct 20, 2015·Journal of Chemical Information and Modeling·Teague Sterling, John J Irwin
Nov 18, 2015·Journal of Chemical Theory and Computation·Raghunathan RamakrishnanO Anatole von Lilienfeld
Aug 26, 2016·Journal of Computer-aided Molecular Design·Steven KearnesPatrick Riley
Jan 10, 2017·Nature Communications·Kristof T SchüttAlexandre Tkatchenko
Mar 9, 2017·Journal of Computational Chemistry·Garrett B GohAbhinav Vishnu
Jul 12, 2017·Journal of Chemical Information and Modeling·Connor W ColeyKlavs F Jensen
Nov 1, 2017·Journal of Cheminformatics·Marcus OlivecronaHongming Chen
Feb 3, 2018·ACS Central Science·Marwin H S SeglerMark P Waller
Mar 14, 2018·ACS Central Science·Rafael Gómez-BombarelliAlán Aspuru-Guzik

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Citations

Nov 20, 2018·Expert Opinion on Drug Discovery·Yinqiu XuKejiang Lin
Feb 11, 2020·Frontiers in Chemistry·Tânia F G G Cova, Alberto A C C Pais
Mar 20, 2020·Chemical Science·Ryan-Rhys Griffiths, José Miguel Hernández-Lobato
Apr 2, 2020·Expert Opinion on Drug Discovery·Igor I Baskin
Aug 14, 2019·Journal of Computer-aided Molecular Design·Arkadii LinAlexandre Varnek
Aug 28, 2020·Frontiers in Cellular and Infection Microbiology·Sneha P CouvillionThomas O Metz
Jan 5, 2021·Frontiers in Pharmacology·Daniil PolykovskiyAlex Zhavoronkov
Jan 13, 2021·Journal of Cheminformatics·Jacob O Spiegel, Jacob D Durrant
Jan 14, 2021·Biotechnology and Bioprocess Engineering : BBE·Hyunho KimHojung Nam
Mar 13, 2021·Nature Biomedical Engineering·Payel DasAleksandra Mojsilovic
May 13, 2021·Chemical Reviews·Ricardo M BorgesRyan S Renslow
Dec 3, 2019·Chemical Science·Jaechang LimWoo Youn Kim
Oct 2, 2019·ACS Central Science·Philippe SchwallerAlpha A Lee
Jul 21, 2020·Journal of Chemical Information and Modeling·Kaifu GaoGuo-Wei Wei
Feb 15, 2019·Journal of Chemical Information and Modeling·Miha SkalicGianni De Fabritiis
Dec 11, 2019·Journal of Chemical Information and Modeling·Seung Hwan HongWoo Youn Kim
Jan 7, 2020·Journal of Chemical Information and Modeling·Francesca GrisoniGisbert Schneider
Jul 6, 2019·Journal of Chemical Information and Modeling·Niclas StåhlJonas Boström
Aug 28, 2021·International Journal of Molecular Sciences·Shi-Ping PengYi Zhao
Sep 18, 2021·Journal of Medicinal Chemistry·Xiaochu TongMingyue Zheng
Oct 27, 2021·Journal of Chemical Information and Modeling·Tiago SousaMiguel Rocha
Nov 5, 2021·Briefings in Bioinformatics·Jianyuan DengFusheng Wang
Dec 8, 2021·Bioinformatics·Yang FanTao Qin

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