蛋白质相互作用网络的多参数模糊关系分析

分析蛋白质相互作用网络的拓扑结构特征与生物进化之间的关系,并用于预测蛋白质的功能是后基因时代重要的研究课题.本文提出了基于模糊数学理论的蛋白质网络多种拓扑属性模糊关系数学模型,并应用频数分析算法将无序的模糊关系数据进行序列化.通过分析蛋白质网络拓扑属性模糊关系参数可以为研究生物进化与蛋白质网络结构之间的关系提供数据基础,同时也为预测未知蛋白质的功能奠定了基础.该方法为研究蛋白质网络进化和标记蛋白质的功能开拓了一个新的方向.     

应用图论分析与最优化理论来数据挖掘大规模水牛普里昂蛋白结构数据

图论、最优化理论显然在蛋白质结构的研究中大有用场. 首先, 调查/回顾了研究蛋白质结构的所有图论模型. 其后, 建立了一个图论模型: 让蛋白质的侧链来作为图的顶点, 应用图论的诸如团、 $k$-团、 社群、 枢纽、聚类等概念来建立图的边. 然后, 应用数学最优化的现代摩登数据挖掘算法/方法来分析水牛普里昂蛋白结构的大数据. 成功与令人耳目一新的数值结果将展示给朋友们.     

应用图论分析与最优化理论来数据挖掘大规模水牛普里昂蛋白结构数据（英文）

图论、最优化理论显然在蛋白质结构的研究中大有用场.首先,调查/回顾了研究蛋白质结构的所有图论模型.其后,建立了一个图论模型:让蛋白质的侧链来作为图的顶点,应用图论的诸如团、k-团、社群、枢纽、聚类等概念来建立图的边.然后,应用数学最优化的现代摩登数据挖掘算法/方法来分析水牛普里昂蛋白结构的大数据.成功与令人耳目一新的数值结果将展示给朋友们.     

改进的自组织映射(SOM)蛋白质折叠算法和计算实现

蛋白质结构预测是生物信息学中的重要研究方向．为了研究蛋白质折叠的机理,人们引入了只考虑蛋白质疏水核心和亲水外围位置导致能量差别的简化HP模型．即使是求解二维HP模型已被证明是一个NP完全问题,因此需要设计有效的近似算法来求解较大规模的HP模型．从旅行商问题(TSP)的求解看,自组织映射是构造近似算法的有效工具．本文将归一化的F-W自组织模型应用到蛋白质二维HP问题的求解中,结合为克服多重映射构造的局部线搜索算法．数值试验表明,该算法改进了现有的HP模型的SOM求解算法, 只需很少的迭代步数就能找到最低能量构象．这一改进算法可以成为进一步研究的基础．     

一种基于亲疏水性的替代矩阵

主要利用蛋白质统计信息和氨基酸与疏水级映射关系,提出一种基于亲疏水性的替代矩阵HB62,解决蛋白质疏水级序列相似性计算问题.采用CB513数据集,分别利用Blosum62和HB62计算蛋白质间的相似程度,结果显示,两种方法计算结果具有一致性,验证了HB62的正确性与有效性.HB62的设计,极大地简化了蛋白质疏水级序列相似性计算问题,有效地降低预测算法复杂度,提高预测准确率,推动蛋白质亲疏水性的相关理论的发展.     

蛋白质空间结构预测的一种优化模型及算法

用理论方法预测蛋白质结构有两个难点,第一是要有一个合理的势函数,第二是要有一个有效的寻优方法找到势函数的全局极小点,本文采用联合残基力场建立了蛋白质空间结构预测模型,然后用我们给出的一种改进模拟退火算法搜索势函数的全局极小点,对脑啡肽的空间结构进行了预测和分析。     

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.     

遗传算法结合神经网络在油气产量预测中的应用

基于遗传算法的全局搜索能力和BP算法的局部精确搜索特性,通过采用遗传算法优化神经网络的方法,将遗传算法和BP算法有机结合,做到优势互补,在提高油气产量预测精度的研究中得到了很好的应用.在对国内某中小型气田油气产量的预测中,以历史产量资料进行检验,其结果表明,提出的预测方法,预测精度明显优于BP算法,证明了这种方法的有效性和可靠性.     

混沌粒子群神经网络在上证指数预测中的应用

上证指数预测是一个非常复杂的非线性问题,为了提高对上证指数预测的准确性,本文采用基于混沌粒子群(CPSO)算法对BP神经网络算法改进的方法来进行预测.BP神经网络算法目前已经应用到预测、聚类、分类等许多领域,取得了不少的成果.但自身也有明显的缺点,比如易陷入局部极小值、收敛速度慢等.用混沌粒子群算法改进BP神经网络算法的基本思想是用混沌粒子群算法优化BP神经网络算法的权值和阈值,在粒子群算法中加入混沌元素,提高粒子群算法的全局搜索能力.对上证指数预测的结果表明改进后的预测方法,具有更好的准确性.     

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.     

Global Optimization Requires Global Information

There are many global optimization algorithms which do not use global information. We broaden previous results, showing limitations on such algorithms, even if allowed to run forever. We show that deterministic algorithms must sample a dense set to find the global optimum value and can never be guaranteed to converge only to global optimizers. Further, analogous results show that introducing a stochastic element does not overcome these limitations. An example is simulated annealing in practice. Our results show that there are functions for which the probability of success is arbitrarily small.     

关于非线性规划的同伦算法与罚函数法

本文揭示了关于非线性规划问题的同伦算法与外点罚函数法的关系，并讨论了有关同伦算法的收敛条件，给出了一些典型的检验问题的计算结果以表明利用结构的分段线性同伦算法的有效性。     

数据分割的分子动力学算法

数据分割研究的基本内容是数据的分类和聚类,是数据挖掘的核心问题之一,在实际问题中应用广泛.特别是针对有向网络数据的研究更是学科发展的前沿.但由于这类问题结构的非对称性,使得模型与算法的构建存在本质困难,因此相应的研究结果较少.本文借鉴分子动力学方法的思想,提出了一类新的网络数据半监督分类模型及算法.该算法不仅适用于关系对称的无向网络数据,而且适用于关系非对称的有向网络.最后针对期刊引用网络数据进行了数值实验,结果表明了模型及算法的可行性和有效性.     

Heuristic anytime approaches to stochastic decision processes

This paper proposes a set of methods for solving stochastic decision problems modeled as partially observable Markov decision processes (POMDPs). This approach (Real Time Heuristic Decision System, RT-HDS) is based on the use of prediction methods combined with several existing heuristic decision algorithms. The prediction process is one of tree creation. The value function for the last step uses some of the classic heuristic decision methods. To illustrate how this approach works, comparative results of different algorithms with a variety of simple and complex benchmark problems are reported. The algorithm has also been tested in a mobile robot supervision architecture.     

Integrating Interval Estimates of Global Optima and Local Search Methods for Combinatorial Optimization Problems

The problem of estimating the global optimal values of intractable combinatorial optimization problems is of interest to researchers developing and evaluating heuristics for these problems. In this paper we present a method for combining statistical optimum prediction techniques with local search methods such as simulated annealing and tabu search and illustrate the approach on a single machine scheduling problem. Computational experiments show that the approach yields useful estimates of optimal values with very reasonable computational effort.     

Global Optimization Performance Measures for Generalized Hill Climbing Algorithms

Generalized hill climbing algorithms provide a framework for modeling several local search algorithms for hard discrete optimization problems. This paper introduces and analyzes generalized hill climbing algorithm performance measures that reflect how effectively an algorithm has performed to date in visiting a global optimum and how effectively an algorithm may pes]rform in the future in visiting such a solution. These measures are also used to obtain a necessary asymptotic convergence (in probability) condition to a global optimum, which is then used to show that a common formulation of threshold accepting does not converge. These measures assume particularly simple forms when applied to specific search strategies such as Monte Carlo search and threshold accepting.     

Smooth methods of multipliers for complementarity problems

This paper describes several methods for solving nonlinear complementarity problems. A general duality framework for pairs of monotone operators is developed and then applied to the monotone complementarity problem, obtaining primal, dual, and primal-dual formulations. We derive Bregman-function-based generalized proximal algorithms for each of these formulations, generating three classes of complementarity algorithms. The primal class is well-known. The dual class is new and constitutes a general collection of methods of multipliers, or augmented Lagrangian methods, for complementarity problems. In a special case, it corresponds to a class of variational inequality algorithms proposed by Gabay. By appropriate choice of Bregman function, the augmented Lagrangian subproblem in these methods can be made continuously differentiable. The primal-dual class of methods is entirely new and combines the best theoretical features of the primal and dual methods. Some preliminary computation shows that this class of algorithms is effective at solving many of the standard complementarity test problems. Received February 21, 1997 / Revised version received December 11, 1998? Published online May 12, 1999     

Interior projection-like methods for monotone variational inequalities

We propose new interior projection type methods for solving monotone variational inequalities. The methods can be viewed as a natural extension of the extragradient and hyperplane projection algorithms, and are based on using non Euclidean projection-like maps. We prove global convergence results and establish rate of convergence estimates. The projection-like maps are given by analytical formulas for standard constraints such as box, simplex, and conic type constraints, and generate interior trajectories. We then demonstrate that within an appropriate primal-dual variational inequality framework, the proposed algorithms can be applied to general convex constraints resulting in methods which at each iteration entail only explicit formulas and do not require the solution of any convex optimization problem. As a consequence, the algorithms are easy to implement, with low computational cost, and naturally lead to decomposition schemes for problems with a separable structure. This is illustrated through examples for convex programming, convex-concave saddle point problems and semidefinite programming.The work of this author was partially supported by the United States–Israel Binational Science Foundation, BSF Grant No. 2002-2010.     

Evaluation of the multiobjective ant colony algorithm performances on biobjective quadratic assignment problems

The difficulty of resolving the multiobjective combinatorial optimization problems with traditional methods has directed researchers to investigate new approaches which perform better. In recent years some algorithms based on ant colony optimization (ACO) metaheuristic have been suggested to solve these multiobjective problems. In this study these algorithms have been reported and programmed both to solve the biobjective quadratic assignment problem (BiQAP) instances and to evaluate the performances of these algorithms. The robust parameter sets for each 12 multiobjective ant colony optimization (MOACO) algorithms have been calculated and BiQAP instances in the literature have been solved within these parameter sets. The performances of the algorithms have been evaluated by comparing the Pareto fronts obtained from these algorithms. In the evaluation step, a multi significance test is used in a non hierarchical structure, and a performance metric (P metric) essential for this test is introduced. Through this study, decision makers will be able to put in the biobjective algorithms in an order according to the priority values calculated from the algorithms’ Pareto fronts. Moreover, this is the first time that MOACO algorithms have been compared by solving BiQAPs.