Structure-aware conditional variational auto-encoder for constrained molecule optimization

doi:10.1016/j.patcog.2022.108581

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	Structure-aware conditional variational auto-encoder for constrained molecule optimization
	Yu, Junchi 1,2,3; Xu, Tingyang 1; Rong, Yu 1; Huang, Junzhou 1; He, Ran 2,3,4
刊名	PATTERN RECOGNITION
	2022-06-01
卷号	126 页码:9
关键词	Molecule optimization Conditional generation Drug discovery
ISSN号	0031-3203
DOI	10.1016/j.patcog.2022.108581
通讯作者	He, Ran(rhe@nlpr.ia.ac.cn)
英文摘要	The goal of molecule optimization is to optimize molecular properties by modifying molecule structures. Conditional generative models provide a promising way to transfer the input molecules to the ones with better property. However, molecular properties are highly sensitive to small changes in molecular struc-tures. This leads to an interesting thought that we can improve the property of molecules with lim-ited modification in structure. In this paper, we propose a structure-aware conditional Variational Auto-Encoder, namely SCVAE, which exploits the topology of molecules as structure condition and optimizes the molecular properties with constrained structural modification. SCVAE leverages graph alignment of two-level molecule structures in an unsupervised manner to bind the structure conditions between two molecules. Then, this structure condition facilitates the molecule optimization with limited struc-tural modification, namely, constrained molecule optimization, under a novel variational auto-encoder framework. Extensive experimental evaluations demonstrate that structure-aware CVAE generates new molecules with high similarity to the original ones and better molecular properties. (c) 2022 Elsevier Ltd. All rights reserved.
资助项目	National Natural Science Foundation of China[U20A20223] ; Youth Innovation Promotion Association CAS[Y201929]
WOS关键词	GRAPH ALIGNMENT
WOS研究方向	Computer Science ; Engineering
语种	英语
出版者	ELSEVIER SCI LTD
WOS记录号	WOS:000761147800004
资助机构	National Natural Science Foundation of China ; Youth Innovation Promotion Association CAS
内容类型	期刊论文
源URL	[http://ir.ia.ac.cn/handle/173211/48063]
专题	自动化研究所_智能感知与计算研究中心
通讯作者	He, Ran
作者单位	1.Tencent AI Lab, Shanghai, Peoples R China 2.Chinese Acad Sci, Inst Automat, Beijing, Peoples R China 3.Univ Chinese Acad Sci, Beijing, Peoples R China 4.Chinese Acad Sci, Ctr Excellence Brain Sci & Intelligence Technol, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Yu, Junchi,Xu, Tingyang,Rong, Yu,et al. Structure-aware conditional variational auto-encoder for constrained molecule optimization[J]. PATTERN RECOGNITION,2022,126:9.
APA	Yu, Junchi,Xu, Tingyang,Rong, Yu,Huang, Junzhou,&He, Ran.(2022).Structure-aware conditional variational auto-encoder for constrained molecule optimization.PATTERN RECOGNITION,126,9.
MLA	Yu, Junchi,et al."Structure-aware conditional variational auto-encoder for constrained molecule optimization".PATTERN RECOGNITION 126(2022):9.