基于k字位置序列的蛋白质序列分析方法及其应用

基于蛋白质序列的κ-字位置序列,利用标准化的κ-字区间平均距离和改进的标准化的κ-字区间平均距离的方法作为蛋白质序列的数字特征,并给出了比较蛋白质序列相似性的方法.最后,运用这两种方法分析了9个物种的ND5蛋白质序列和8个物种的ND6蛋白质序列的相似性,并利用交叉验证得出基于改进的标准化的κ-字区间平均距离的方法的准确度比基于标准化的κ-字区间平均距离的方法的准确度高.     

全β类蛋白编码序列的LZ复杂度对蛋白质折叠速率的影响

蛋白质折叠速率预测问题是计算生物学和生物信息学中的核心问题之一.科研工作者相继提出了许多参数和方法来探索折叠速率的决定因素.但蛋白质编码序列复杂度信息对蛋白质折叠速率的影响未被提及.提取编码序列LZ复杂度信息,融合多特征信息,建立线性回归模型进行折叠速率预测.该方法能在不需要结构信息的情况下,直接从蛋白质的编码序列出发对全β类蛋白质进行折叠速率进行预测.在卡方检验方法的验证下,发现折叠速率的预测值与实验值有很好的相关性,相关系数能达到0.9712.这一精度明显优于其他基于序列的方法,充分说明序列LZ复杂度是一个有效特征信息,蛋白质编码序列LZ复杂度信息确实影响蛋白质折叠速率及其结构.     

DNA序列的特征数值及相似性分析

利用2维图表示DNA序列,计算与该图对应的距离矩阵,求出距离矩阵的不变量—距离矩阵主对角线以外的次对角线之和的平均值,进而得到了DNA序列的一种特征数值,利用这种新的特征数值,对DNA序列进行相似性比较,得到了与现有的资料符合很好的结果.     

基于Hurst指数的风速时间序列研究

为研究风速时间序列的长程相关性和自相似性,采用重标度极差分析和去趋势波动分析对风速时间序列进行相关性分析,计算风速时间序列的Hurst指数,并对其进行了功率谱密度分析,计算其谱指数.结果表明,两种方法计算所得Hurst指数都较为接近1,说明风速时间序列具有显著的自相似性和长程正相关性;但R/S分析及DFA所得Hurst指数有所差异,这一差异说明DFA可体现出非平稳风速时间序列的幂率特征.此外,对风速时间序列Hurst指数及谱指数的分析还表明了风速波动具有"1/f噪声"特征.为风速分形混沌特性研究及风速短时预测等提供了理论依据.     

基于Hamilton路模型的蛋白质结构预测的研究

提出一种基于Hamilton路模型的新方法研究蛋白质结构预测问题,为使结构匹配序列,把已知蛋白质的3D结构信息转化为一个加权的完全图Kn,则求这个特定空间结构所匹配的氨基酸残基序列问题转化为求Kn图的最小H路问题.用此方法研究了72个单链蛋白质结构,结果表明Kn图的最小H路对应此蛋白质的序列,图的顶点数n与最小H路总长度成正比.     

蛋白质结构的主成分分析及氧链糖基化位点的人工神经网络预测

糖基化是蛋白质翻译后修饰的重要形式之一,氧链糖基化是糖基化的一种主要类型,对蛋白质氧链糖基化位点进行预测具有重要的意义.以窗口长度为41的蛋白质序列为研究对象,采用稀疏编码,利用主成分分析法研究了氧链糖基化蛋白质序列的结构特点;在提取主成分的基础上,设计了一个含单隐层的BP神经网络(256—8—4),对蛋白质氧链糖基化位点进行预测,把蛋白质序列分为4类;并同直接用BP神经网络分类的结果相比较,实验结果证明提出的方法省时,准确,预测的准确率达80~90%.     

利用提升小波的蛋白质相互作用特征提取

利用提升小波从蛋白质序列中提取出它们相互作用的频谱特征,经支持向量机训练学习后,用于预测蛋白质间的相互作用.模拟计算结果表明,在阳性数据和阴性数据平衡的前提下,利用提升小波获取的低维蛋白质相互作用特征向量可以得到较高预测精度.进一步阐述了不同物种的蛋白质相互作用网络有着不同特征,为了得到更准确的预测结果,需要利用不同的方法提取蛋白质相互作用的特征.     

现代优化计算方法在蛋白质结构预测中的应用

现代优化计算方法在蛋白质结构预测中占有重要地位.简要地介绍了模拟退火算法,遗传算法,人工神经网络和图论算法在蛋白质结构预测中的应用.对国内外近年来应用这些算法,特别是在蛋白质构象搜索问题中,解决蛋白质结构预测的研究作了回顾,并分析、比较了这几种算法的效果和特点.     

基于小波变换和改进萤火虫算法优化极限学习机的短期负荷预测

提出了一种基于小波变换和改进萤火虫优化极限学习机的短期负荷预测方法.通过小波分解和重构,对原始负荷序列进行降噪;在模型训练阶段利用改进的萤火虫算法优化极限学习机参数,获得各序列的最优模型;针对各子序列分别预测叠加得到最终预测值.通过在两种时间尺度的数据序列上进行数值计算,与传统的ARMA、BP神经网络、支持向量机及LSSVM等多种经典预测模型相比,模型预测效果更优.     

非等间距序列的灰色模型

在对原始数据序列的一次累加生成时 ,考虑序列的间距 ,提出了对非等间距序列建立 GM( 1,1)模型的基本理论和方法 .通过对算例进行的计算 ,表明本文提出的方法概念明确、计算方便、有较高的拟合和预测精度 .对解决各个领域中广泛存在的非等间距序列的建模拟合和预测问题提供了一种比较好的方法     

Hermitian positive semidefinite matrices whose entries are 0 or 1 in Modulus

We show that a matrix is a Hermitian positive semidefinite matrix whose nonzero entries have modulus 1 if and only if it is similar to a direct sum of all I's matrices and a 0 matrix via a unitary monomial similarity. In particular, the only such nonsingular matrix is the identity matrix and the only such irreducible matrix is similar to an all l's matrix by means of a unitary diagonal similarity. Our results extend earlier results of Jain and Snyder for the case in which the nonzero entries (actually) equal 1. Our methods of proof, which reiy on the so called principal submatrix rank property, differ from the approach used by Jain and Snyder.     

矩阵代数上的局部合同变换和局部相似变换

令F表示任意域,Mn（F）表示由F上所有n×n矩阵形成的结合代数.本文的目的是研究Mn（F）上具有如下性质的两类线性映射,其中一类线性映射在Mn（F）上每一点的取值与Mn（F）的某个合同变换在该点的取值相同,另一类线性映射在Mn（F）上每一点的取值与Mn（F）的某个相似变换在该点的取值相同,随着Mn（F）上的点不同,这些合同变换和相似变换可能也不同.利用矩阵的秩、幂等阵以及幂零阵的性质,通过矩阵计算的方法证明了第一类线性映射或者是合同变换或者是合同变换与转置变换的复合,第二类线性映射或者是相似变换或者是相似变换与转置变换的复合.由这个结果可知存在真正意义上的局部合同变换和局部相似变换,从而丰富了局部映射理论的研究。     

一类矩阵方程的反中心对称最佳逼近解

利用矩阵的正交相似变换和广义奇异值分解,讨论了矩阵方程 AXB=C具有反中心对称解的充要条件,得到了解的具体表达式.然后应用Frobenius范数正交矩阵乘积不变性,在该方程的反中心对称解解集合中导出了与给定相同类型矩阵的最佳逼近解的表达式.     

谈矩阵多项式的一个应用

本文得到下列结果：通过应用矩阵多项式，得到一个相似变换下变换矩阵的简便解法。     

A clustering algorithm for item assignment in a synchronized zone order picking system

In a synchronized zone order picking system, all the zones process the same order simultaneously. There may be some idle time when the zone pickers wait until all the pickers complete the current order. This paper develops a heuristic algorithm to balance the workload among all pickers so that the utilization of the order picking system is improved and to reduce the time needed for fulfilling each requested order. A similarity measurement, using customer orders, of any two items is first presented for measuring the co-appearance of both items in the same order. With this similarity measurement, a natural cluster model, which is a relaxation of the well-studied NP-hard homogeneous cluster model, is constructed. The heuristic algorithm is then proposed to solve the model for locating all the items into distinct zones. Finally, empirical data and simulation experiments verify that the objectives of the item cluster model are achieved.     

The $$ \ell _1 $$-Analysis in Phase Retrieval with Redundant Dictionary

This article presents new results concerning the recovery of a signal from the magnitude only measurements where the signal is not sparse in an orthonormal basis but in a redundant dictionary, which we call it phase retrieval with redundant dictionary for short. To solve this phaseless problem, we analyze the \( \ell _1 \)-analysis model. Firstly we investigate the noiseless case with presenting a null space property of the measurement matrix under which the \( \ell _1 \)-analysis model provides an exact recovery. Secondly we introduce a new property (S-DRIP) of the measurement matrix. By solving the \( \ell _1 \)-analysis model, we prove that this property can guarantee a stable recovery of real signals that are nearly sparse in overcomplete dictionaries.     

Nonlinear self-adjointness through differential substitutions

It is known (Ibragimov, 2011; Galiakberova and Ibragimov, 2013) [14,18] that the property of nonlinear self-adjointness allows to associate conservation laws of the equations under study, with their symmetries. In this paper we show that, even when the equation is nonlinearly self-adjoint with a non differential substitution, finding the explicit form of the differential substitution can provide new conservation laws associated to its symmetries. By using the general theorem on conservation laws (Ibragimov, 2007) [11] and the property of nonlinear self-adjointness we find some new conservation laws for the modified Harry-Dym equation. By using a differential substitution we construct a conservation law for the Harry-Dym equation, which has not been derived before using Ibragimov method.     

Remarks on Lipschitz properties of matrix groups actions

It is proved that a large class of matrix group actions, including joint similarity and congruence-like actions, as well as actions of the type of matrix equivalence, have local Lipschitz property. Under additional hypotheses, global Lipschitz property is proved. These results are specialized and applied to obtain local Lipschitz property of canonical bases of matrices that are selfadjoint in an indefinite inner product. Real, complex, and quaternionic matrices are considered.     

Jackknifing in generalized linear models

In a generalized linear model, the jackknife estimator of the asymptotic covariance matrix of the maximum likelihood estimator is shown to be consistent. The corresponding jackknife studentized statistic is asymptotically normal. In addition, these results remain true even if there exist unequal dispersion parameters in the model. On the other hand, the variance estimator and the studentized statistic based on the standard method (substitution and linearization) do not enjoy this robustness property against the presence of unequal dispersion parameters.This research was supported by an Operating Grant from the Natural Science and Engineering Research Council of Canada.     

Stress Integration of the Hoek-Brown Material Model Using Incremental Plasticity Theory

This paper presents the formulation of the stress integration procedure for the Hoek-Brown (HB) material model with non-associative yielding condition by using the incremental plasticity method. Main idea of this method is to reach the solution by calculating the plastic matrix according to the method of incremental plasticity (used for elastic constitutive matrix corrections), and with the use of the total strain increment. Computational procedure is implemented within the PAK program package. Results of this procedure were compared with the solutions obtained by other program that contains this material model. (© 2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)