A mathematical view of biological complexity

This essay is a trial on giving some mathematical ideas about the concept of biological complexity, trying to explore four different attributes considered to be essential to characterize a complex system in a biological context: decomposition, heterogeneous assembly, self-organization, and adequacy. It is a theoretical and speculative approach, opening some possibilities to further numerical and experimental work, illustrated by references to several researches that applied the concepts presented here.     

Merit Functions for Complementarity and Related Problems: A Survey

Merit functions have become important tools for solving various mathematical problems arising from engineering sciences and economic systems. In this paper, we are surveying basic principles and properties of merit functions and some of their applications. As a particular case we will consider the nonlinear complementarity problem (NCP) and present a collection of different merit functions. We will also introduce and study a class of smooth merit functions for the NCP.     

A Hybrid Smoothing Method for Mixed Nonlinear Complementarity Problems

In this paper, we describe a new, integral-based smoothing method for solving the mixed nonlinear complementarity problem (MNCP). This approach is based on recasting MNCP as finding the zero of a nonsmooth system and then generating iterates via two types of smooth approximations to this system. Under weak regularity conditions, we establish that the sequence of iterates converges to a solution if the limit point of this sequence is regular. In addition, we show that the rate is Q-linear, Q-superlinear, or Q-quadratic depending on the level of inexactness in the subproblem calculations and we make use of the inexact Newton theory of Dembo, Eisenstat, and Steihaug. Lastly, we demonstrate the viability of the proposed method by presenting the results of numerical tests on a variety of complementarity problems.     

一个解决线性互补问题的新型神经网络

本文构造了一个新型的解决线性互补问题的神经网络,不同于那些运用罚函数和拉格朗日函数的神经网络,它的结构简单,易于计算,我们证明了该神经网络的全局收敛性和稳定性,并给出数值实验检验其有效性。     

求解非线性互补问题的一个下降算法(英文)

在[1]中,Solodov将非线性互补问题等价地转化成一个带非负约束的优化问题.基于这种转化形式,我们给出了一种求解非线性互补问题的下降算法.在映射为强单调时,证明了算法的全局收敛性.     

混合互补问题的逐次逼近算法

针对混合互补问题 ,提出了与其等价的非光滑方程的逐次逼近算法 ,并在一定条件下证明了该算法的全局收敛性 .数值例子表明这一算法是有效的     

求解非线性互补问题的内点正算法

针对非线性互补问题,提出了与其等价的非光滑方程的内点正算法,并在一定条件下证明了该算法的收敛性定理。数值结果表明,该算法是十分有效的。     

A Comparison of Large Scale Mixed Complementarity Problem Solvers

This paper provides a means for comparing various computercodes for solving large scale mixed complementarity problems. Wediscuss inadequacies in how solvers are currently compared, andpresent a testing environment that addresses these inadequacies. Thistesting environment consists of a library of test problems, along withGAMS and MATLAB interfaces that allow these problems to be easilyaccessed. The environment is intended for use as a tool byother researchers to better understand both their algorithms and theirimplementations, and to direct research toward problem classes thatare currently the most challenging. As an initial benchmark, eightdifferent algorithm implementations for large scale mixedcomplementarity problems are briefly described and tested with defaultparameter settings using the new testing environment.     

A New Homotopy Method for Nonlinear Complementarity Problems

In this paper, we present a new homotopy method for the nonlinear complementarity problems. Without the regularity or non-singulary assumptions for▽F(x), we prove that our homotopy equations have a bounded solution curve. The numerical tests confirm the efficiency of our proposed method.     

互补约束优化问题的乘子序列部分罚函数算法

利用互补问题的Lagrange函数,
将互补约束优化问题(MPCC)转化为含参数的约束优化问题.
给出Lagrange乘子的简单修正公式,
并给出求解互补约束优化问题的部分罚函数法. 无须假设二阶必要条件成立,
只要算法产生的迭代点列的极限点满足互补约束优化问题的线性独立约束规范(MPCC-LICQ),
且极限点是MPCC的可行点, 则算法收敛到原问题的M-稳定点. 另外,
在上水平严格互补(ULSC)成立的条件下, 算法收敛到原问题的B-稳定点.     

线性互补问题的宽邻域预估校正算法

对线性互补问题提出了一种新的宽邻域预估校正算法,算法是基于经典线性规划路径跟踪算法的思想,将Maziar Salahi关于线性规划预估校正算法推广到线性互补问题中,给出了算法的具体迭代步骤并讨论了算法迭代复杂性,最后证明了算法具有多项式复杂性为O(ηlog(X~0)~Ts~0/ε)。     

对称锥互补问题的一个惩罚NR函数(英文)

本文建立了一个对称锥互补问题的惩罚自然剩余函数,并且证明了单调情形下其相应势函数的水平有界性.     

非光滑非线性互补问题的牛顿法

研究了非光滑的非线性互补问题. 首先将非光滑的非线性互补问题转化为一个非光滑方程组,然后用牛顿法求解这个非光滑方程组. 在该牛顿法中,每次迭代只需一个原始函数B-微分中的一个元素. 最后证明了该牛顿法的超线性收敛性.     

非线性互补问题的水平值估计算法

本文研究非线性互补问题（NCP）的求解算法，先将NCP转化为约束全局优化问题（CGOP），然后直接移植求解问题（CGOP）的水平值估计算法^[4,5]来求解问题（NCP）．文章证明了算法对于NCP是收敛的，数值实验说明了算法的有效性．     

A Semidefinite Programming Heuristic for Quadratic Programming Problems with Complementarity Constraints

The presence of complementarity constraints brings a combinatorial flavour to an optimization problem. A quadratic programming problem with complementarity constraints can be relaxed to give a semidefinite programming problem. The solution to this relaxation can be used to generate feasible solutions to the complementarity constraints. A quadratic programming problem is solved for each of these feasible solutions and the best resulting solution provides an estimate for the optimal solution to the quadratic program with complementarity constraints. Computational testing of such an approach is described for a problem arising in portfolio optimization.Research supported in part by the National Science Foundations VIGRE Program (Grant DMS-9983646).Research partially supported by NSF Grant number CCR-9901822.     

A Finite Algorithm for Almost Linear Complementarity Problems

We present an algorithm for solving a class of nonlinear complementarity problems called the almost linear complementarity problem (ALCP), which can be used to simulate free boundary problems. The algorithm makes use of a procedure for identifying an active index subset of an ALCP by bounding its solution with an interval vector. It is shown that an acceptable solution of the given ALCP can be obtained by solving at most n systems of equations. Numerical results are reported to illustrate the efficiency of the algorithm for large-scale problems.     

求解垂直互补问题的参数牛顿法

给出了求解垂直互补问题的一种参数牛顿法,在较为温和的条件下证明了该方法的局部超线性收敛结果,并且给出了具体数值计算.     

大规模非线性互补问题的共轭梯度法

提出求解大规模非线性互补问题NCP(F)的PRP型共轭梯度法,算法自然满足充分下降条件.当F是可微P_0+R_0函数且F'(χ)在水平集上全局Lipschitz连续条件下,证明了算法的全局收敛性.数值结果表明算法的有效性.     

A Null Space Approach for Solving Nonlinear Complementarity Problems

In this work, null space techniques are employed to tackle nonlinear complementarity problems （NCPs）. NCP conditions are transform into a nonlinear programming problem, which is handled by null space algorithms, The NCP conditions are divided into two groups, Some equalities and inequalities in an NCP are treated as constraints, While other equalities and inequalities in an NCP are to be regarded as objective function. Two groups are all updated in every step. Null space approaches are extended to nonlinear complementarity problems. Two different solvers are employed for all NCP in an algorithm.     

Sensitivity of chemical reaction networks: A structural approach. 3. Regular multimolecular systems

We present a systematic mathematical analysis of the qualitative steady‐state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions, multiple reaction products, nonmonotone rate functions, and non‐closed autonomous systems. Our structural sensitivity analysis is based on the stoichiometry of the reaction network, only. It does not require numerical data on reaction rates. Instead, we impose mild and generic nondegeneracy conditions of algebraic type. From the structural data, only, we derive which steady‐state concentrations are sensitive to, and hence influenced by, changes of any particular reaction rate—and which are not. We also establish transitivity properties for influences involving rate perturbations. This allows us to derive an influence graph which globally summarizes the influence pattern of any given network. The influence graph allows the computational, but meaningful, automatic identification of functional subunits in general networks, which hierarchically influence each other. We illustrate our results for several variants of the glycolytic citric acid cycle. Biological applications include enzyme knockout experiments and metabolic control.