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

文献类型：期刊论文

作者Yu, Junchi2,3,4; Xu, Tingyang2; Rong, Yu2; Huang, Junzhou2; He, Ran1,3,4
刊名PATTERN RECOGNITION
出版日期2022-06-01
卷号126页码:9
ISSN号0031-3203
关键词Molecule optimization Conditional generation Drug discovery
DOI10.1016/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.
WOS关键词GRAPH ALIGNMENT
资助项目National Natural Science Foundation of China[U20A20223] ; Youth Innovation Promotion Association CAS[Y201929]
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
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.Chinese Acad Sci, Ctr Excellence Brain Sci & Intelligence Technol, Beijing, Peoples R China
2.Tencent AI Lab, Shanghai, Peoples R China
3.Chinese Acad Sci, Inst Automat, Beijing, Peoples R China
4.Univ Chinese Acad Sci, 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.

入库方式： OAI收割

来源：自动化研究所

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