检索结果-内蒙古大学图书馆

Some applications of nonlinear science methods and support vector machine methods to protein problems

Mini-Reviews in Organic Chemistry 2015年第6期12卷 493-505页

作者： Hana, Guo Sheng Yu, Zu-Guo Zhao, Zhi-Qin Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University XiangtanHunan411105 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 BrisbaneQ4001 Australia

Protein folding, prediction of protein structure and functions are most important problems in bioinformatics. The protein fold process mainly reflects in the kinetic order of folding. Predicting the structural classes of low-homology protein is a difficult problem in the prediction of protein structure. In order to understanding the mechanism of programmed cell death, it is very necessary to obtain the information about subcellular locations and functions of apoptosis proteins. Predicting protein subnuclear localizations is a challenging problem which is harder than predicting protein subcellular locations. Predicting membrane protein types is related to the structure and function of proteins. In this review, we introduce some applications of nonlinear science methods and support vector machine methods to the above protein problems. The nonlinear science methods including the horizontal visibility network, kernel method, recurrence quantification analysis, global descriptor, Lempel-Ziv complexity, and Hilbert-Huang transform are used to extract features in these approaches. © 2015 Bentham science Publishers.

关键词： Support vector machines

来源：评论

学校读者我要写书评

暂无评论

3D simulation of Flow with Free Surface Based on Adaptive Octree Mesh System

引用

Transactions of Tianjin University 2015年第1期21卷 32-40页

作者：李绍武庄茜黄筱云王东 State Key Laboratory of Hydraulic Engineering Simulation and Safety Tianjin University Key Laboratory of Water-Sediment Science and Water Disaster Prevention of Hunan Province Changsha University of Science and Technology School of Civil Engineering Tianjin Chengjian University

The technique of adaptive tree mesh is an effective way to reduce computational cost through automatic adjustment of cell size according to necessity. In the present study, the 2D numerical N-S solver based on the adaptive quadtree mesh system was extended to a 3D one, in which a spatially adaptive oetree mesh system and multiple particle level set method were adopted for the convenience to deal with the air-water-structure multiple-medium coexisting domain. The stretching process of a dumbbell was simulated and the results indicate that the meshes are well adaptable to the free surface. The collapsing process of water column impinging a circle cylinder was simulated and from the results, it can be seen that the processes of fluid splitting and merging are properly simulated. The interaction of second-order Stokes waves with a square cylinder was simulated and the obtained drag force is consistent with the result by the Morison＇s wave force formula with the coefficient values of the stable drag component and the inertial force component bein~ set as 2.54.

关键词： adaptive octree mesh 3D numerical flume spatially adaptive multiple particle level set

来源：评论

学校读者我要写书评

暂无评论

Whole genome/proteome based phylogeny reconstruction for prokaryotes using higher order Markov model and chaos game representation

引用

Molecular phylogenetics and evolution 2016年 96卷 102-111页

作者： Wei-Feng Yang Zu-Guo Yu Vo Anh Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan 411105 PR China Department of Mathematics and Physics Hunan Institute of Engineering Hunan 411104 PR China. Electronic address: yangweifeng09@***. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia. Electronic address: yuzuguo@***. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia. Electronic address: v.anh@qut.edu.au.

UNLABELLED:Traditional methods for sequence comparison and phylogeny reconstruction rely on pair wise and multiple sequence alignments. But alignment could not be directly applied to whole genome/proteome comparison and phylogenomic studies due to their high computational complexity. Hence alignment-free methods became popular in recent years. Here we propose a fast alignment-free method for whole genome/proteome comparison and phylogeny reconstruction using higher order Markov model and chaos game representation. In the present method, we use the transition matrices of higher order Markov models to characterize amino acid or DNA sequences for their comparison. The order of the Markov model is uniquely identified by maximizing the average Shannon entropy of conditional probability distributions. Using one-dimensional chaos game representation and linked list, this method can reduce large memory and time consumption which is due to the large-scale conditional probability distributions. To illustrate the effectiveness of our method, we employ it for fast phylogeny reconstruction based on genome/proteome sequences of two species data sets used in previous published papers. Our results demonstrate that the present method is useful and efficient. AVAILABILITY AND IMPLEMENTATION:The source codes for our algorithm to get the distance matrix and genome/proteome sequences can be downloaded from ftp://121.199.20.25/. The software Phylip and EvolView we used to construct phylogenetic trees can be referred from their websites.

关键词： Alignment-free whole proteome comparison Chaos game representation Higher order Markov model Phylogenetic tree Shannon entropy

来源：评论

学校读者我要写书评

暂无评论

Maximum-norm error analysis of a difference scheme for the space fractional CNLS

引用

Applied Mathematics and computation 2015年 257卷 241-251页

作者： Dongling Wang Aiguo Xiao Wei Yang Department of Mathematics and Center for Nonlinear Studies Northwest University Xi’an Shaanxi 710127 PR China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 PR China

The difference method for the space fractional coupled nonlinear Schrödinger equations (CNLS) is studied. The fractional centered difference is used to approximate the space fractional Laplacian. This scheme conserves the discrete mass and energy. Due to the nonlocal nature of fractional Laplacian, in the classic Sobolev space, it is hard to obtain the error estimation in l ∞ . To overcome this difficulty, the fractional Sobolev space H α / 2 and a fractional norm equivalence in H α / 2 are introduced. Then the convergence of order O ( h 2 + τ 2 ) in l ∞ is proved by fractional Sobolev inequality, where h is the mesh size and τ is the time step. Numerical examples are given to illustrate the theoretical results at last.

关键词： Fractional Schrödinger equations Fractional centered difference Convergence analysis

来源：评论

学校读者我要写书评

暂无评论

First-order optimality condition of basis pursuit denoise problem

引用

Applied Mathematics and Mechanics(English Edition) 2014年第10期35卷 1345-1352页

作者：朱玮舒适成礼智 School of Mathematics and Computational Science Xiangtan University Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Department of Mathematics and Computational Science College of ScienceNational University of Defense Technology

A new first-order optimality condition for the basis pursuit denoise （BPDN） problem is derived. This condition provides a new approach to choose the penalty param- eters adaptively for a fixed point iteration algorithm. Meanwhile, the result is extended to matrix completion which is a new field on the heel of the compressed sensing. The numerical experiments of sparse vector recovery and low-rank matrix completion show validity of the theoretic results.

关键词： basis pursuit denoise （BPDN） fixed point iteration first-order optimality,matrix completion

来源：评论

学校读者我要写书评

暂无评论

Whole-proteome based phylogenetic tree construction with inter-amino-acid distances and the conditional geometric distribution profiles

引用

Molecular phylogenetics and evolution 2015年 89卷 37-45页

作者： Xian-Hua Xie Zu-Guo Yu Guo-Sheng Han Wei-Feng Yang Vo Anh Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan 411105 PR China School of Mathematics and Computer Science Gannan Normal University Jiangxi 341000 PR China. Electronic address: xxianhua@***. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia. Electronic address: yuzuguo@***. Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan 411105 PR China. Electronic address: korea10282003@***. Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan 411105 PR China. Electronic address: yangweifeng09@***. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia. Electronic address: v.anh@qut.edu.au.

There has been a growing interest in alignment-free methods for whole genome comparison and phylogenomic studies. In this study, we propose an alignment-free method for phylogenetic tree construction using whole-proteome sequences. Based on the inter-amino-acid distances, we first convert the whole-proteome sequences into inter-amino-acid distance vectors, which are called observed inter-amino-acid distance profiles. Then, we propose to use conditional geometric distribution profiles (the distributions of sequences where the amino acids are placed randomly and independently) as the reference distribution profiles. Last the relative deviation between the observed and reference distribution profiles is used to define a simple metric that reflects the phylogenetic relationships between whole-proteome sequences of different organisms. We name our method inter-amino-acid distances and conditional geometric distribution profiles (IAGDP). We evaluate our method on two data sets: the benchmark dataset including 29 genomes used in previous published papers, and another one including 67 mammal genomes. Our results demonstrate that the new method is useful and efficient.

关键词： Alignment-free whole-proteome comparison Conditional geometric distribution profile Inter-amino-acid distances Phylogenetic tree

来源：评论

学校读者我要写书评

暂无评论

Exponentially Accurate Rayleigh–Ritz Method for Fractional Variational Problems

引用

Journal of computational and Nonlinear Dynamics 2015年第5期10卷 051009页

作者： Mao, Zhi Xiao, Aiguo Wang, Dongling Yu, Zuguo Shi, Long Hunan Key Laboratory for Computationand Simulation in Science and Engineering Xiangtan UniversityXiangtan Hunan 411105 China School of Mathematics Northwest UniversityXi’an Shaanxi 710127 China

A high accurate Rayleigh–Ritz method is developed for solving fractional variational problems (FVPs). The Jacobi poly-fractonomials proposed by Zayernouri and Karniadakis (2013, “Fractional Sturm–Liouville Eigen-Problems: Theory and Numerical Approximation,” J. Comput. Phys.,252(1), pp. 495–517.) are chosen as basis functions to approximate the true solutions, and the Rayleigh–Ritz technique is used to reduce FVPs to a system of algebraic equations. This method leads to exponential decay of the errors, which is superior to the existing methods in the literature. The fractional variational errors are discussed. Numerical examples are given to illustrate the exponential convergence of the method.

关键词： Errors Integration methods Algorithms Rayleigh-Ritz methods

来源：评论

学校读者我要写书评

暂无评论

Proximity point algorithm for low-rank matrix recovery from sparse noise corrupted data

引用

Applied Mathematics and Mechanics(English Edition) 2014年第2期35卷 259-268页

The method of recovering a low-rank matrix with an unknown fraction whose entries are arbitrarily corrupted is known as the robust principal component analysis （RPCA）. This RPCA problem, under some conditions, can be exactly solved via convex optimization by minimizing a combination of the nuclear norm and the 11 norm. In this paper, an algorithm based on the Douglas-Rachford splitting method is proposed for solving the RPCA problem. First, the convex optimization problem is solved by canceling the constraint of the variables, and ~hen the proximity operators of the objective function are computed alternately. The new algorithm can exactly recover the low-rank and sparse components simultaneously, and it is proved to be convergent. Numerical simulations demonstrate the practical utility of the proposed algorithm.

关键词： low-rank matrix recovery sparse noise Douglas-Rachford splitting method,proximity operator

来源：评论

学校读者我要写书评

暂无评论

A linearly implicit conservative difference scheme for the space fractional coupled nonlinear Schrödinger equations

引用

Journal of computational Physics 2014年 272卷 644-655页

作者： Wang, Dongling Xiao, Aiguo Yang, Wei Department of Mathematics Northwest University Xi'an 710069 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and oInformation Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China

In this paper, a linearly implicit conservative difference scheme for the coupled nonlinear Schrödinger equations with space fractional derivative is proposed. This scheme conserves the mass and energy in the discrete level and only needs to solve a linear system at each step. The existence and uniqueness of the difference solution are proved. The stability and convergence of the scheme are discussed, and it is shown to be convergent of order O(τ2 + h2) in the discrete l2 norm with the time step τ and mesh size h. When the fractional order is two, all those results are in accord with the difference scheme proposed for the classical non-fractional coupled nonlinear Schrödinger equations. Some numerical examples are also reported. © 2014 Elsevier Inc.

关键词： Linear systems

来源：评论

学校读者我要写书评

暂无评论

An Efficient Proximity Point Algorithm for Total-Variation-Based Image Restoration

引用

Advances in Applied Mathematics and Mechanics 2014年第2期6卷 145-164页

作者： Wei Zhu Shi Shu Lizhi Cheng School of Mathematics and Computational Science Xiangtan UniversityXiangtan 411105HunanChina Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan UniversityXiangtan 411105HunanChina Department of Mathematics and Computational Science College of ScienceNational University of Defense TechnologyChangsha 410073HunanChina

In this paper,we propose a fast proximity point algorithm and apply it to total variation(TV)based image *** novel method is derived from the idea of establishing a general proximity point operator framework based on which new first-order schemes for total variation(TV)based image restoration have been *** current algorithms for TV-based image restoration,such as Chambolle’s projection algorithm,the split Bregman algorithm,the Berm´udez-Moreno algorithm,the Jia-Zhao denoising algorithm,and the fixed point algorithm,can be viewed as special cases of the new first-order ***,the convergence of the new algorithm has been analyzed at ***,we make comparisons with the split Bregman algorithm which is one of the best algorithms for solving TV-based image restoration at *** experiments illustrate the efficiency of the proposed algorithms.

关键词： Proximity point operator image restoration total variation first-order schemes.

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：