检索结果-内蒙古大学图书馆

Identification of pre-microRNAs by characterizing their sequence order evolution information and secondary structure graphs

引用

BMC bioinformatics 2018年第SUPPL 19期19卷 521页

作者： Yuanlin Ma Zuguo Yu Guosheng Han Jinyan Li Vo Anh Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan 411105 China. Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan 411105 China. yuzuguo@***. School of Electrical Engineering and Computer Science Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia. yuzuguo@***. Advanced Analytics Institute Faculty of Engineering & IT University of Technology Sydney P.O Box 123 Broadway NSW 2007 Australia. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia.

BACKGROUND:Distinction between pre-microRNAs (precursor microRNAs) and length-similar pseudo pre-microRNAs can reveal more about the regulatory mechanism of RNA biological processes. Machine learning techniques have been widely applied to deal with this challenging problem. However, most of them mainly focus on secondary structure information of pre-microRNAs, while ignoring sequence-order information and sequence evolution information. RESULTS:We use new features for the machine learning algorithms to improve the classification performance by characterizing both sequence order evolution information and secondary structure graphs. We developed three steps to extract these features of pre-microRNAs. We first extract features from PSI-BLAST profiles and Hilbert-Huang transforms, which contain rich sequence evolution information and sequence-order information respectively. We then obtain properties of small molecular networks of pre-microRNAs, which contain refined secondary structure information. These structural features are carefully generated so that they can depict both global and local characteristics of pre-microRNAs. In total, our feature space covers 591 features. The maximum relevance and minimum redundancy (mRMR) feature selection method is adopted before support vector machine (SVM) is applied as our classifier. The constructed classification model is named MicroRNA -NHPred. The performance of MicroRNA -NHPred is high and stable, which is better than that of those state-of-the-art methods, achieving an accuracy of up to 94.83% on same benchmark datasets. CONCLUSIONS:The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the sequences and secondary structures, which are capable of characterizing the sequence evolution information and sequence-order information, and global and local information of pre-microRNAs secondary structures. MicroRNA -NHPred is a valuable method for pre-microRNAs iden

关键词： Hibert-Huang transform Network PSI-BLAST profiles Pre-microRNA SVM mRMR

来源：评论

学校读者我要写书评

暂无评论

Uniform convergence of multigrid finite element method for time-dependent riesz tempered fractional problem

arXiv

引用

arXiv 2017年

作者： Chen, Minghua Bu, Weiping Qi, Wenya Wang, Yantao School of Mathematics and Statistics Gansu Key Laboratory of Applied Mathematics and Complex Systems Lanzhou University Lanzhou730000 China School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan411105 China South University of Science and Technology of China Shenzhen518055 China

In this article a theoretical framework for the Galerkin finite element approximation to the time-dependent Riesz tempered fractional problem is provided without the fractional regularity assumption. Because the time-dependent problems should become easier to solve as the time step τ → 0, which correspond to the mass matrix dominant [R. E. Bank and T. Dupont, Math. Comp., 153 (1981), pp. 35-51]. Based on the introduced and analysis of the fractional τ-norm, the uniform convergence estimates of the V-cycle multigrid method with the time-dependent fractional problem is strictly proved, which means that the convergence rate of the V-cycle MGM is independent of the mesh size h and the time step τ. The numerical experiments are performed to verify the convergence with only O(NlogN) complexity by the fast Fourier transform method, where N is the number of the grid points. To the best of our knowledge, this is the first proof for the convergence rate of the V-cycle multigrid finite element method with τ → 0. Copyright © 2.17, The Authors. All rights reserved.

关键词： Fast Fourier transforms

来源：评论

学校读者我要写书评

暂无评论

Multifractal temporally weighted detrended cross-correlation analysis to quantify power-law cross-correlation and its application to stock markets

引用

Chaos 2017年第6期27卷 063111-063111页

作者： Wei, Yun-Lan Yu, Zu-Guo Zou, Hai-Long Anh, Vo Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia

A new method-multifractal temporally weighted detrended cross-correlation analysis (MF-TWXDFA)-is proposed to investigate multifractal cross-correlations in this paper. This new method is based on multifractal temporally weighted detrended fluctuation analysis and multifractal cross-correlation analysis (MFCCA). An innovation of the method is applying geographically weighted regression to estimate local trends in the nonstationary time series. We also take into consideration the sign of the fluctuations in computing the corresponding detrended cross-covariance function. To test the performance of the MF-TWXDFA algorithm, we apply it and the MFCCA method on simulated and actual series. Numerical tests on artificially simulated series demonstrate that our method can accurately detect long-range cross-correlations for two simultaneously recorded series. To further show the utility of MF-TWXDFA, we apply it on time series from stock markets and find that power-law cross-correlation between stock returns is significantly multifractal. A new coefficient, MF-TWXDFA cross-correlation coefficient, is also defined to quantify the levels of cross-correlation between two time series. © 2.17 Author(s).

关键词： CORRELATION (Statistics) STOCK price indexes REGRESSION analysis TIME series analysis COEFFICIENTS (Statistics)

来源：评论

学校读者我要写书评

暂无评论

Protein folding kinetic order prediction from amino acid sequence based on horizontal visibility network

引用

Current Bioinformatics 2016年第2期11卷 173-185页

作者： Zhao, Zhi-Qin Yu, Zu-Guo Anh, Vo Wu, Jing-Yang Han, Guo-Sheng 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 School of Science Xi’an Shiyou University 18 Second Dianzi Road Yanta District Xi’anShaanxi710065 China

Protein folding is one of the most important problems in molecular biology. The kinetic order of protein folding is one of the main aspects of the folding process. Previous methods for predicting protein folding kinetic order require to use the information on tertiary or predicted secondary structure of a protein. In this paper, based on physicochemical properties of amino acids, we propose an approach to predict the protein folding kinetic order from the primary structure of a protein using support vector machine combined with principal component analysis. The horizontal visibility network, Hilbert-Huang transform, global descriptor, and Lempel-Ziv complexity are used to extract features in our approach. To evaluate our approach, the leave-one-out cross-validation test is employed on two widely-used data sets ("IvankovData" and "ZhengData" data sets) consisting of two-state and multi-state proteins. The overall accuracies of prediction can reach 83.87% for "IvankovData" data set and 85% for "ZhengData" data set respectively. Comparisons with the existing methods show that the present approach performs better on the "IvankovData" data set. These results indicate that the present approach is effective and valuable for predicting protein folding kinetic order. Based on factor analysis, we find that the length of protein sequence, hydrophobicity and hydrophilicity of amino acids are important features in our approach. © 2.16 Bentham science Publishers

关键词： Hilbert-Huang transform

来源：评论

学校读者我要写书评

暂无评论

From standard alpha-stable Lévy motions to horizontal visibility networks: dependence of multifractal and Laplacian spectrum

引用

Journal of Statistical Mechanics: Theory and Experiment 2018年第5期2018卷

作者： Hai-Long Zou Zu-Guo Yu Vo Anh Yuan-Lin Ma Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan 411105 People's Republic of China School of Electrical Engineering and Computer Science Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia Author to whom any correspondence should be addressed. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia

In recent years, researchers have proposed several methods to transform time series (such as those of fractional Brownian motion) into complex networks. In this paper, we construct horizontal visibility networks (HVNs) based on the -stable Lévy motion. We aim to study the relations of multifractal and Laplacian spectrum of transformed networks on the parameters and of the -stable Lévy motion. First, we employ the sandbox algorithm to compute the mass exponents and multifractal spectrum to investigate the multifractality of these HVNs. Then we perform least squares fits to find possible relations of the average fractal dimension , the average information dimension and the average correlation dimension against using several methods of model selection. We also investigate possible dependence relations of eigenvalues and energy on , calculated from the Laplacian and normalized Laplacian operators of the constructed HVNs. All of these constructions and estimates will help us to evaluate the validity and usefulness of the mappings between time series and networks, especially between time series of -stable Lévy motions and HVNs.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Correlating the Structure and Optical Absorption Properties of Au76（SR）44 Cluster

Correlating the Structure and Optical Absorption Properties ...

引用

第九届计算纳米科学与新能源材料国际研讨会

作者： Zhongyun Ma P.Wang G.Zhou J.Tang H.Li Y.Pei Department of Chemistry Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of EducationXiangtan University Hunan Key Laboratory for Computation and Simulation in Science and Engineering Institute for Computational and Applied MathematicsXiangtan University School of Materials Science and Engineering Central South University

The atomic structure of recently synthesized thiolate-protected Au cluster is theoretically predicted via a simple structural rule summarized from the crystal structures of thiolate-protected Au（SR）, Au（SR） and Au（SR） clusters. We find that the Au（SR）（N = 7） and recently reported Au（SR）（N = 4）, Au（SR）（N = 3）, Au（SR）（N = 2. and Au（SR）（N = 1） belong to a family of homologous Au（SR） cluster whose Au-cores follow one-dimensional polytetrahedral growth pathway. The Au（SR） cluster is predicted to contain an anisotropic face-centered cubic（FCC） Au-core, which can be viewed as combination of two helical tetrahedra-Au4 chains and is remarkably different from the well-known spherical Au-core in ligand protected gold clusters in the size region of 1-2.nm. The intense near infrared（NIR） absorption of Au（SR） is attributed to the synergistic effect of anisotropic Au-core structure and ligand protections. A plausible cluster-to-cluster transformation mechanism is further suggested.

关键词： thiolated-protected gold nanocluster Au76SR44 face-centered cubic near infrared adsorption

来源：评论

学校读者我要写书评

暂无评论

Convergence Analysis of Legendre-Collocation Methods for Nonlinear Volterra Type Integro Equations

引用

Advances in Applied Mathematics and Mechanics 2015年第1期7卷 74-88页

作者： Yin Yang Yanping Chen Yunqing Huang Wei Yang Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan UniversityXiangtan 411105China School ofMathematical Sciences South China Normal UniversityGuangzhou 510631China

A Legendre-collocation method is proposed to solve the nonlinear Volterra integral equations of the second *** provide a rigorous error analysis for the proposed method,which indicate that the numerical errors in L2.norm and L¥-norm will decay exponentially provided that the kernel function is sufficiently *** results are presented,which confirm the theoretical prediction of the exponential rate of convergence.

关键词： Spectral method nonlinear Volterra integral equations

来源：评论

学校读者我要写书评

暂无评论

Total Reflection and Cloaking by Triangular Defects Embedded in Zero Index Metamaterials

引用

Advances in Applied Mathematics and Mechanics 2015年第2期7卷 135-144页

作者： Yunqing Huang Jichun Li Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan UniversityChina Department of Mathematical Sciences University of Nevada Las VegasLas VegasNevada 89154-4020USA

In this work,we investigate wave propagation through a zero index meta-material(ZIM)waveguide embedded with triangular dielectric *** provide a theoretical guidance on how to achieve total reﬂection and total transmission(i.e.,cloaking)by adjusting the defect sizes and/or permittivities of the *** work provides a systematical way in manipulating wave propagation through ZIM in addi-tion to the widely studied dielectric defects with cylindrical and rectangular geome-tries.

关键词： Metamaterials invisibility cloaks Maxwell’s equatons

来源：评论

学校读者我要写书评

暂无评论

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

引用

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. © 2.15 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

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://12..199.2..2./. 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

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：