Computational Performance Evaluation of Two Integer Linear Programming Models for the Minimum Common String Partition Problem

In the minimum common string partition (MCSP) problem two related input strings are given. "Related" refers to the property that both strings consist of the same set of letters appearing the same number of times in each of the two strings. The MCSP seeks a minimum cardinality partitioning of one string into non-overlapping substrings that is also a valid partitioning for the second string. This problem has applications in bioinformatics e.g. in analyzing related DNA or protein sequences. For strings with lengths less than about 1000 letters, a previously published integer linear programming (ILP) formulation yields, when solved with a state-of-the-art solver such as CPLEX, satisfactory results. In this work, we propose a new, alternative ILP model that is compared to the former one. While a polyhedral study shows the linear programming relaxations of the two models to be equally strong, a comprehensive experimental comparison using real-world as well as artificially created benchmark instances indicates substantial computational advantages of the new formulation.Comment: arXiv admin note: text overlap with arXiv:1405.5646 This paper version replaces the one submitted on January 10, 2015, due to detected error in the calculation of the variables involved in the ILP model

Large neighborhood search for the most strings with few bad columns problem

In this work, we consider the following NP-hard combinatorial optimization problem from computational biology. Given a set of input strings of equal length, the goal is to identify a maximum cardinality subset of strings that differ maximally in a pre-defined number of positions. First of all, we introduce an integer linear programming model for this problem. Second, two variants of a rather simple greedy strategy are proposed. Finally, a large neighborhood search algorithm is presented. A comprehensive experimental comparison among the proposed techniques shows, first, that larger neighborhood search generally outperforms both greedy strategies. Second, while large neighborhood search shows to be competitive with the stand-alone application of CPLEX for small- and medium-sized problem instances, it outperforms CPLEX in the context of larger instances.Peer ReviewedPostprint (author's final draft

Solving the Minimum Label Spanning Tree Problem by Mathematical Programming Techniques

We present exact mixed integer programming approaches including branch-and-cut and branch-and-cut-and-price for the minimum label spanning tree problem as well as a variant of it having multiple labels assigned to each edge. We compare formulations based on network flows and directed connectivity cuts. Further, we show how to use odd-hole inequalities and additional inequalities to strengthen the formulation. Label variables can be added dynamically to the model in the pricing step. Primal heuristics are incorporated into the framework to speed up the overall solution process. After a polyhedral comparison of the involved formulations, comprehensive computational experiments are presented in order to compare and evaluate the underlying formulations and the particular algorithmic building blocks of the overall branch-and-cut- (and-price) framework

Signed double Roman domination on cubic graphs

The signed double Roman domination problem is a combinatorial optimization problem on a graph asking to assign a label from $\{\pm{}1,2,3\}$ to each vertex feasibly, such that the total sum of assigned labels is minimized. Here feasibility is given whenever (i) vertices labeled $\pm{}1$ have at least one neighbor with label in $\{2,3\}$; (ii) each vertex labeled $-1$ has one $3$-labeled neighbor or at least two $2$-labeled neighbors; and (iii) the sum of labels over the closed neighborhood of any vertex is positive. The cumulative weight of an optimal labeling is called signed double Roman domination number (SDRDN). In this work, we first consider the problem on general cubic graphs of order $n$ for which we present a sharp $n/2+\Theta(1)$ lower bound for the SDRDN by means of the discharging method. Moreover, we derive a new best upper bound. Observing that we are often able to minimize the SDRDN over the class of cubic graphs of a fixed order, we then study in this context generalized Petersen graphs for independent interest, for which we propose a constraint programming guided proof. We then use these insights to determine the SDRDNs of subcubic $2\times m$ grid graphs, among other results

Solving the Railway Traveling Salesman Problem via a Transformation into the Classical Traveling Salesman Problem

Abstract Th

A brief survey on hybrid metaheuristics

The combination of components from different algorithms is currently one of most successful trends in optimization. The hybridization of metaheuristics, such as ant colony optimization, evolutionary algorithms, and variable neighborhood search, with techniques from operations research and artificial intelligence plays hereby an important role. The resulting hybrid algorithms are generally labelled hybrid metaheuristics. The rising of this new research field was due to the fact that the focus of research in optimization has shifted form an algorithm-oriented point of view. In this brief survey on hybrid metaheuristics we provide an overview on some of the most interesting and representative developments.Peer ReviewedPostprint (published version

Semi-Automated Location Planning for Urban Bike-Sharing Systems

Bike-sharing has developed into an established part of many urban transportation systems. However, new bikesharing systems (BSS) are still built and existing ones are extended. Particularly for large BSS, location planning is complex since factors determining potential usage are manifold. We propose a semi-automatic approach for creating or extending real-world sized BSS during general planning. Our approach optimizes locations such that the number of trips is maximized for a given budget respecting construction as well as operation costs. The approach consists of four steps: (1) collecting and preprocessing required data, (2) estimating a demand model, (3) calculating optimized locations considering estimated redistribution costs, and (4) presenting the solution to the planner in a visualization and planning front end. The full approach was implemented and evaluated positively with BSS and planning experts