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Molecular Sparse Representation by a 3D Ellipsoid Radial Basis Function Neural Network via L1 Regularization

文献类型：期刊论文

作者Gui, Sheng1,2,3; Chen, Zhaodi3; Lu, Benzhuo1,2; Chen, Minxin3
刊名JOURNAL OF CHEMICAL INFORMATION AND MODELING
出版日期2020-12-28
卷号60期号:12页码:6054-6064
ISSN号1549-9596
DOI10.1021/acs.jcim.0c00585
英文摘要The three-dimensional structures and shapes of biomolecules provide essential information about their interactions and functions. Unfortunately, the computational cost of bio-molecular shape representation is an active challenge which increases rapidly as the number of atoms increase. Recent developments in sparse representation and deep learning have shown significant improvements in terms of time and space. A sparse representation of molecular shape is also useful in various other applications, such as molecular structure alignment, docking, and coarse-grained molecular modeling. We have developed an ellipsoid radial basis function neural network (ERBFNN) and an algorithm for sparsely representing molecular shape. To evaluate a sparse representation model of molecular shape, the Gaussian density map of the molecule is approximated using ERBFNN with a relatively small number of neurons. The deep learning models were trained by optimizing a nonlinear loss function with L1 regularization. Experimental results reveal that our algorithm can represent the original molecular shape with a relatively higher accuracy and fewer scale of ERBFNN. Our network in principle is applicable to the multiresolution sparse representation of molecular shape and coarse-grained molecular modeling. Executable files are available at https://github.com/SGUI-LSEC/SparseGaussianMolecule. The program was implemented in PyTorch and was run on Linux.
资助项目National Key Research and Development Program of China[2016YF-B0201304] ; China NSF (NSFC)[11771435] ; China NSF (NSFC)[21573274]
WOS研究方向Pharmacology & Pharmacy ; Chemistry ; Computer Science
语种英语
WOS记录号WOS:000608875100046
出版者AMER CHEMICAL SOC
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/58034]  
专题中国科学院数学与系统科学研究院
通讯作者Lu, Benzhuo; Chen, Minxin
作者单位1.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, State Key Lab Sci & Engn Comp, Beijing 100190, Peoples R China
2.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
3.Soochow Univ, Dept Math, Suzhou 215006, Peoples R China
推荐引用方式
GB/T 7714		 Gui, Sheng,Chen, Zhaodi,Lu, Benzhuo,et al. Molecular Sparse Representation by a 3D Ellipsoid Radial Basis Function Neural Network via L1 Regularization[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING,2020,60(12):6054-6064.
APA Gui, Sheng,Chen, Zhaodi,Lu, Benzhuo,&Chen, Minxin.(2020).Molecular Sparse Representation by a 3D Ellipsoid Radial Basis Function Neural Network via L1 Regularization.JOURNAL OF CHEMICAL INFORMATION AND MODELING,60(12),6054-6064.
MLA Gui, Sheng,et al."Molecular Sparse Representation by a 3D Ellipsoid Radial Basis Function Neural Network via L1 Regularization".JOURNAL OF CHEMICAL INFORMATION AND MODELING 60.12(2020):6054-6064.

入库方式： OAI收割

来源：数学与系统科学研究院

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