Local protein threading by Mixed Integer Programming

During the last decade, significant progress has been made in solving the Protein Threading Problem (PTP). However, all previous approaches to PTP only perform global sequence-structure alignment. This obvious limitation is in clear contrast with the “world of sequences”, where local sequence-sequence alignments are widely used to find functionally important regions in families of proteins. This paper presents a novel approach to PTP which allows to align a part of a protein structure onto a protein sequence in order to detect local similarities. We show experimentally that such local sequence-structure alignments improve the quality of the prediction. Our approach is based on Mixed Integer Programming (MIP) which has been shown to be very successful in this domain. We describe five MIP models for local sequence-structure alignments, compare and analyze their performances by using ILOG CPLEX 10 solver on a benchmark of proteins.     

Reducing the number of variables in Integer and Linear Programming Problems

Computational difficulties in solving the Integer Programming Problems (IPP) are caused to a considerable degree by the number of variables. If the number of variables is small, then even NP-complete problems usually can be solved with a reasonable expenditure of effort.A procedure is developed for the analysis of large scale IPP with the aim of reducing the number of variables prior to starting the solution method. The procedure is based on comparing pairs of columns of the constraint matrix of the IPP. If a pair of columns thus compared meets certain conditions, then the IPP has an optimal solution, in which a variable corresponding to one of the columns in the pair is equal to zero. Corresponding theorems for Knapsack and Multidimensional Knapsack problems and for general IPP are presented. The procedure is extended to Linear and Mixed Integer Programming Problems. The presented results of computational experiments illustrate the efficiency of the developed procedure.     

A geometric way to build strong mixed-integer programming formulations

We give an explicit geometric way to build mixed-integer programming (MIP) formulations for unions of polyhedra. The construction is simply described in terms of spanning hyperplanes in an $r$-dimensional linear space. The resulting MIP formulation is ideal, and uses exactly $r$ integer variables and $2\times \left(\#\text{of spanning hyperplanes}\right)$ general inequality constraints. We use this result to derive novel logarithmic-sized ideal MIP formulations for discontinuous piecewise linear functions and structures appearing in robotics and power systems problems.     

整数规划的布谷鸟算法

布谷鸟搜索算法是一种新型的智能优化算法．本文采用截断取整的方法将基本布谷鸟搜索算法用于求解整数规划问题．通过对标准测试函数进行仿真实验并与粒子群算法进行比较,结果表明本文所提算法比粒子群算法拥有更好的性能和更强的全局寻优能力,可以作为一种实用方法用于求解整数规划问题．     

Integrating SQP and Branch-and-Bound for Mixed Integer Nonlinear Programming

This paper considers the solution of Mixed Integer Nonlinear Programming (MINLP) problems. Classical methods for the solution of MINLP problems decompose the problem by separating the nonlinear part from the integer part. This approach is largely due to the existence of packaged software for solving Nonlinear Programming (NLP) and Mixed Integer Linear Programming problems.In contrast, an integrated approach to solving MINLP problems is considered here. This new algorithm is based on branch-and-bound, but does not require the NLP problem at each node to be solved to optimality. Instead, branching is allowed after each iteration of the NLP solver. In this way, the nonlinear part of the MINLP problem is solved whilst searching the tree. The nonlinear solver that is considered in this paper is a Sequential Quadratic Programming solver.A numerical comparison of the new method with nonlinear branch-and-bound is presented and a factor of up to 3 improvement over branch-and-bound is observed.     

混合整数二次规划问题的全局最优性条件

本文给出了混合整数二次规划问题的全局最优性条件,包括全局最优充分性条件和全局最优必要性条件.我们还给出了一个数值实例用以说明如何利用本文所给出的全局最优性条件来判定一个给定点是否是全局最优解.     

Using a Mixed Integer Quadratic Programming Solver for the Unconstrained Quadratic 0-1 Problem

In this paper, we consider problem (P) of minimizing a quadratic function q(x)=x ^t Qx+c ^t x of binary variables. Our main idea is to use the recent Mixed Integer Quadratic Programming (MIQP) solvers. But, for this, we have to first convexify the objective function q(x). A classical trick is to raise up the diagonal entries of Q by a vector u until (Q+diag(u)) is positive semidefinite. Then, using the fact that x _i ²=x _i, we can obtain an equivalent convex objective function, which can then be handled by an MIQP solver. Hence, computing a suitable vector u constitutes a preprocessing phase in this exact solution method. We devise two different preprocessing methods. The first one is straightforward and consists in computing the smallest eigenvalue of Q. In the second method, vector u is obtained once a classical SDP relaxation of (P) is solved. We carry out computational tests using the generator of (Pardalos and Rodgers, 1990) and we compare our two solution methods to several other exact solution methods. Furthermore, we report computational results for the max-cut problem.     

整数规划的渐进强对偶方法

虽然整数规划中经典的Lagrange对偶方法是一个有效的方法，但是由于对偶缝隙的原因它经常不能求出原问题的最优解。该文提出一个用于有界整数规划的指数对偶公式。此公式具有渐进强对偶的特性并且可以保证找到原问题的最优解。它的另一个特性是当参数选择的合适时不需要进行实际的对偶搜索。     

Sequence Independent Lifting for Mixed Integer Programs with Variable Upper Bounds

We investigate the convex hull of the set defined by a single inequality with continuous and binary variables with variable upper bound constraints. We extend the traditional flow cover inequality, and show that it is valid for a restriction of the set in which some variables are fixed. We also give conditions under which this inequality is facet-defining and, when it is not, we show how it can be lifted to obtain valid inequalities for the entire set using sequence independent lifting. In general, computing the lifting function is NP-hard, but under an additional restriction on the cover we obtain a closed form. Finally, we show how these results imply and extend known results about the single node fixed charge flow polyhedron. This material is based upon work supported by the National Science Foundation under Grant No. 0084826. Received: April 2004     

A hierarchy of relaxations for linear generalized disjunctive programming

Generalized disjunctive programming (GDP), originally developed by Raman and Grossmann (1994), is an extension of the well-known disjunctive programming paradigm developed by Balas in the mid 70s in his seminal technical report (Balas, 1974). This mathematical representation of discrete-continuous optimization problems, which represents an alternative to the mixed-integer program (MIP), led to the development of customized algorithms that successfully exploited the underlying logical structure of the problem. The underlying theory of these methods, however, borrowed only in a limited way from the theories of disjunctive programming, and the unique insights from Balas’ work have not been fully exploited.In this paper, we establish new connections between the fields of disjunctive programming and generalized disjunctive programming for the linear case. We then propose a novel hierarchy of relaxations to the original linear GDP model that subsumes known relaxations for this model, and show that a subset of these relaxations are tighter than the latter. We discuss the usefulness of these relaxations within the context of MIP and illustrate these results on the classic strip-packing problem.     

A Note on Reducing the Number of Variables in Integer Programming Problems

A necessary and sufficient condition for identification of dominatedcolumns, which correspond to one type of redundant integer variables,in the matrix of a general Integer Programming problem, isderived. The given condition extends our recent work on eliminatingdominated integer variables in Knapsack problems, and revises arecently published procedure for reducing the number of variables ingeneral Integer Programming problems given in the literature. Areport on computational experiments for one class of large scaleKnapsack problems, illustrating the function of this approach, isincluded.     

Cover and Pack Inequalities for (Mixed) Integer Programming

We review strong inequalities for fundamental knapsack relaxations of (mixed) integer programs. These relaxations are the 0-1 knapsack set, the mixed 0-1 knapsack set, the integer knapsack set, and the mixed integer knapsack set. Our aim is to give a unified presentation of the inequalities based on covers and packs and highlight the connections among them. The focus of the paper is on recent research on the use of superadditive functions for the analysis of knapsack polyhedra. We also present some new results on integer knapsacks. In particular, we give an integer version of the cover inequalities and describe a necessary and sufficient facet condition for them. This condition generalizes the well-known facet condition of minimality of covers for 0-1 knapsacks. The author is supported, in part, by NSF Grants 0070127 and 0218265.     

Exact Penalty Function and Asymptotic Strong Nonlinear Duality in Integer Programming

In this paper,a logarithmic-exponential penalty function with two parameters for integer program-ming is discussed.We obtain the exact penalty properties and then establish the asymptotic strong nonlinearduality in the corresponding logarithmic-exponential dual formulation by using the obtained exact penaltyproperties.The discussion is based on the logarithmic-exponential nonlinear dual formulation proposed in [6].     

Decomposition and Dynamic Cut Generation in Integer Linear Programming

Decomposition algorithms such as Lagrangian relaxation and Dantzig-Wolfe decomposition are well-known methods that can be used to generate bounds for mixed-integer linear programming problems. Traditionally, these methods have been viewed as distinct from polyhedral methods, in which bounds are obtained by dynamically generating valid inequalities to strengthen an initial linear programming relaxation. Recently, a number of authors have proposed methods for integrating dynamic cut generation with various decomposition methods to yield further improvement in computed bounds. In this paper, we describe a framework within which most of these methods can be viewed from a common theoretical perspective. We then discuss how the framework can be extended to obtain a decomposition-based separation technique we call decompose and cut. As a by-product, we describe how these methods can take advantage of the fact that solutions with known structure, such as those to a given relaxation, can frequently be separated much more easily than arbitrary real vectors.     

Success Guarantee of Dual Search in Integer Programming: p-th Power Lagrangian Method

Although the Lagrangian method is a powerful dual search approach in integer programming, it often fails to identify an optimal solution of the primal problem. The p-th power Lagrangian method developed in this paper offers a success guarantee for the dual search in generating an optimal solution of the primal integer programming problem in an equivalent setting via two key transformations. One other prominent feature of the p-th power Lagrangian method is that the dual search only involves a one-dimensional search within [0,1]. Some potential applications of the method as well as the issue of its implementation are discussed.     

Computations with disjunctive cuts for two-stage stochastic mixed 0-1 integer programs

Two-stage stochastic mixed-integer programming (SMIP) problems with recourse are generally difficult to solve. This paper presents a first computational study of a disjunctive cutting plane method for stochastic mixed 0-1 programs that uses lift-and-project cuts based on the extensive form of the two-stage SMIP problem. An extension of the method based on where the data uncertainty appears in the problem is made, and it is shown how a valid inequality derived for one scenario can be made valid for other scenarios, potentially reducing solution time. Computational results amply demonstrate the effectiveness of disjunctive cuts in solving several large-scale problem instances from the literature. The results are compared to the computational results of disjunctive cuts based on the subproblem space of the formulation and it is shown that the two methods are equivalently effective on the test instances.     

The C 3 Theorem and a D 2 Algorithm for Large Scale Stochastic Mixed-Integer Programming: Set Convexification

This paper considers the two-stage stochastic integer programming problem, with an emphasis on instances in which integer variables appear in the second stage. Drawing heavily on the theory of disjunctive programming, we characterize convexifications of the second stage problem and develop a decomposition-based algorithm for the solution of such problems. In particular, we verify that problems with fixed recourse are characterized by scenario-dependent second stage convexifications that have a great deal in common. We refer to this characterization as the C³ (Common Cut Coefficients) Theorem. Based on the C³ Theorem, we develop a decomposition algorithm which we refer to as Disjunctive Decomposition (D²). In this new class of algorithms, we work with master and subproblems that result from convexifications of two coupled disjunctive programs. We show that when the second stage consists of 0-1 MILP problems, we can obtain accurate second stage objective function estimates after finitely many steps. This result implies the convergence of the D² algorithm.This research was funded by NSF grants DMII 9978780 and CISE 9975050.     

Exact Algorithm for the Surrogate Dual of an Integer Programming Problem: Subgradient Method Approach

One of the critical issues in the effective use of surrogate relaxation for an integer programming problem is how to solve the surrogate dual within a reasonable amount of computational time. In this paper, we present an exact and efficient algorithm for solving the surrogate dual of an integer programming problem. Our algorithm follows the approach which Sarin et al. (Ref. 8) introduced in their surrogate dual multiplier search algorithms. The algorithms of Sarin et al. adopt an ad-hoc stopping rule in solving subproblems and cannot guarantee the optimality of the solutions obtained. Our work shows that this heuristic nature can actually be eliminated. Convergence proof for our algorithm is provided. Computational results show the practical applicability of our algorithm.     

On multistage Stochastic Integer Programming for incorporating logical constraints in asset and liability management under uncertainty

We present a model for optimizing a mean-risk function of the terminal wealth for a fixed income asset portfolio restructuring with uncertainty in the interest rate path and the liabilities along a given time horizon. Some logical constraints are considered to be satisfied by the assets portfolio. Uncertainty is represented by a scenario tree and is dealt with by a multistage stochastic mixed 0-1 model with complete recourse. The problem is modelled as a splitting variable representation of the Deterministic Equivalent Model for the stochastic model, where the 0-1 variables and the continuous variables appear at any stage. A Branch-and-Fix Coordination approach for the multistage 0–1 program solving is proposed. Some computational experience is reported.      

混合整数规划求解多联票据印刷过程中的生产调度问题

多联票据的印刷过程包括排版、单联印刷和多联配页与装订三个过程。该过程是柔性的流水生产线与装配混合的生产系统。本文研究了该系统中的票据印刷生产调度问题,目标是最小化所有产品的最大完成时间（Makespan）。该问题到目前为止还没有人研究,本文首先建立了该问题的混合整数规划模型,然后提出了该模型的求解方法,并给出了该问题的下界。最后的量化示例和算例试验表明本文的模型是有效的。