Quadratic Binary Programming Models in Computational Biology

In this paper we formulate four problems in computational molecular biology as 0-1 quadratic programs. These problems are all NP-hard and the current solution methods used in practice consist of heuristics or approximation algorithms tailored to each problem. Using test problems from scientific databases, we address the question, “Can a general-purpose solver obtain good answers in reasonable time?” In addition, we use the latest heuristics as incumbent solutions to address the question, “Can a general-purpose solver confirm optimality or find an improved solution in reasonable time?” Our computational experiments compare four different reformulation methods: three forms of linearization and one form of quadratic convexification

Improved Balas and Mazzola Linearization for Quadratic 0-1 Programs with Application in a New Cutting Plane Algorithm

Balas and Mazzola linearization (BML) is widely used in devising cutting plane algorithms for quadratic 0-1 programs. In this article, we improve BML by first strengthening the primal formulation of BML and then considering the dual formulation. Additionally, a new cutting plane algorithm is proposed

Linearizable special cases of the QAP

We consider special cases of the quadratic assignment problem (QAP) that are linearizable in the sense of Bookhold. We provide combinatorial characterizations of the linearizable instances of the weighted feedback arc set QAP, and of the linearizable instances of the traveling salesman QAP. As a by-product, this yields a new well-solvable special case of the weighted feedback arc set problem

An outer approximation based branch and cut algorithm for convex 0-1 MINLP problems

A branch and cut algorithm is developed for solving 0-1 MINLP problems. The algorithm integrates Branch and Bound, Outer Approximation and Gomory Cutting Planes. Only the initial Mixed Integer Linear Programming (MILP) master problem is considered. At integer solutions Nonlinear Programming (NLP) problems are solved, using a primal-dual interior point algorithm. The objective and constraints are linearized at the optimum solution of those NLP problems and the linearizations are added to all the unsolved nodes of the enumerations tree. Also, Gomory cutting planes, which are valid throughout the tree, are generated at selected nodes. These cuts help the algorithm to locate integer solutions quickly and consequently improve the linear approximation of the objective and constraints, held at the unsolved nodes of the tree. Numerical results show that the addition of Gomory cuts can reduce the number of nodes in the enumeration tree

Quadratic assignment problem : linearizations and polynomial time solvable cases

Cataloged from PDF version of article.The Quadratic Assignment Problem (QAP) is one of the hardest combinatorial optimization problems known. Exact solution attempts proposed for instances of size larger than 15 have been generally unsuccessful even though successful implementations have been reported on some test problems from the QAPLIB up to size 36. In this dissertation, we analyze the binary structure of the QAP and present new IP formulations. We focus on “flow-based” formulations, strengthen the formulations with valid inequalities, and report computational experience with a branch-and-cut algorithm. Next, we present new classes of instances of the QAP that can be completely or partially reduced to the Linear Assignment Problem and give procedures to check whether or not an instance is an element of one of these classes. We also identify classes of instances of the Koopmans-Beckmann form of the QAP that are solvable in polynomial time. Lastly, we present a strong lower bound based on Bender’s decomposition.Erdoğan, GüneşPh.D

Of keyboards and beyond - optimization in human-computer interaction

In this thesis, we present optimization frameworks in the area of Human-Computer Interaction. At first, we discuss keyboard layout problems with a special focus on a project we participated in, which aimed at designing the new French keyboard standard. The special nature of this national-scale project and its optimization ingredients are discussed in detail; we specifically highlight our algorithmic contribution to this project. Exploiting the special structure of this design problem, we propose an optimization framework that was efficiently computes keyboard layouts and provides very good optimality guarantees in form of tight lower bounds. The optimized layout that we showed to be nearly optimal was the basis of the new French keyboard standard recently published in the National Assembly in Paris. Moreover, we propose a relaxation for the quadratic assignment problem (a generalization of keyboard layouts) that is based on semidefinite programming. In a branch-and-bound framework, this relaxation achieves competitive results compared to commonly used linear programming relaxations for this problem. Finally, we introduce a modeling language for mixed integer programs that especially focuses on the challenges and features that appear in participatory optimization problems similar to the French keyboard design process.Diese Arbeit behandelt Ansätze zu Optimierungsproblemen im Bereich Human-Computer Interaction. Zuerst diskutieren wir Tastaturbelegungsprobleme mit einem besonderen Fokus auf einem Projekt, an dem wir teilgenommen haben: die Erstellung eines neuen Standards für die französische Tastatur. Wir gehen auf die besondere Struktur dieses Problems und unseren algorithmischen Beitrag ein: ein Algorithmus, der mit Optimierungsmethoden die Struktur dieses speziellen Problems ausnutzt. Mithilfe dieses Algorithmus konnten wir effizient Tastaturbelegungen berechnen und die Qualität dieser Belegungen effektiv (in Form von unteren Schranken) nachweisen. Das finale optimierte Layout, welches mit unserer Methode bewiesenermaßen nahezu optimal ist, diente als Grundlage für den kürzlich in der französischen Nationalversammlung veröffentlichten neuen französischen Tastaturstandard. Darüberhinaus beschreiben wir eine Relaxierung für das quadratische Zuweisungsproblem (eine Verallgemeinerung des Tastaturbelegungsproblems), die auf semidefinieter Programmierung basiert. Wir zeigen, dass unser Algorithmus im Vergleich zu üblich genutzten linearen Relaxierung gut abschneidet. Abschließend definieren und diskutieren wir eine Modellierungssprache für gemischt integrale Programme. Diese Sprache ist speziell auf die besonderen Herausforderungen abgestimmt, die bei interaktiven Optimierungsproblemen auftreten, welche einen ähnlichen Charakter haben wie der Prozess des Designs der französischen Tastatur