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

Clustering of solutions in hard satisfiability problems

We study the structure of the solution space and behavior of local search methods on random 3-SAT problems close to the SAT/UNSAT transition. Using the overlap measure of similarity between different solutions found on the same problem instance we show that the solution space is shrinking as a function of alpha. We consider chains of satisfiability problems, where clauses are added sequentially. In each such chain, the overlap distribution is first smooth, and then develops a tiered structure, indicating that the solutions are found in well separated clusters. On chains of not too large instances, all solutions are eventually observed to be in only one small cluster before vanishing. This condensation transition point is estimated to be alpha_c = 4.26. The transition approximately obeys finite-size scaling with an apparent critical exponent of about 1.7. We compare the solutions found by a local heuristic, ASAT, and the Survey Propagation algorithm up to alpha_c.Comment: 8 pages, 9 figure

Two Decades of Maude

This paper is a tribute to José Meseguer, from the rest of us in the Maude team, reviewing the past, the present, and the future of the language and system with which we have been working for around two decades under his leadership. After reviewing the origins and the language's main features, we present the latest additions to the language and some features currently under development. This paper is not an introduction to Maude, and some familiarity with it and with rewriting logic are indeed assumed.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Steklov Spectral Geometry for Extrinsic Shape Analysis

We propose using the Dirichlet-to-Neumann operator as an extrinsic alternative to the Laplacian for spectral geometry processing and shape analysis. Intrinsic approaches, usually based on the Laplace-Beltrami operator, cannot capture the spatial embedding of a shape up to rigid motion, and many previous extrinsic methods lack theoretical justification. Instead, we consider the Steklov eigenvalue problem, computing the spectrum of the Dirichlet-to-Neumann operator of a surface bounding a volume. A remarkable property of this operator is that it completely encodes volumetric geometry. We use the boundary element method (BEM) to discretize the operator, accelerated by hierarchical numerical schemes and preconditioning; this pipeline allows us to solve eigenvalue and linear problems on large-scale meshes despite the density of the Dirichlet-to-Neumann discretization. We further demonstrate that our operators naturally fit into existing frameworks for geometry processing, making a shift from intrinsic to extrinsic geometry as simple as substituting the Laplace-Beltrami operator with the Dirichlet-to-Neumann operator.Comment: Additional experiments adde

Modeling vitreous silica bilayers

We computer model a free-standing vitreous silica bilayer which has recently been synthesized and characterized experimentally in landmark work. Here we model the bilayer using a computer assembly procedure that starts from a single layer of amorphous graphene, generated using a bond switching algorithm from an initially crystalline graphene structure. Next each bond is decorated with an oxygen atom and the carbon atoms are relabeled as silicon. This monolayer can be now thought of as a two dimensional network of corner sharing triangles. Next each triangle is made into a tetrahedron, by raising the silicon atom above each triangle and adding an additional singly coordinated oxygen atom at the apex. The final step is to mirror reflect this layer to form a second layer and then attach the two layers together to form the bilayer. We show that this vitreous silica bilayer has the additional macroscopic degrees of freedom to easily form a network of identical corner sharing tetrahedra if there is a symmetry plane through the center of the bilayer going through the layer of oxygen ions that join the upper and lower layers. This has the consequence that the upper rings lie exactly above the lower rings, which are tilted in general. The assumption of a network of perfect corner sharing tetrahedra leads to a range of possible densities that we have previously characterized in three dimensional zeolites as a flexibility window. Finally, using a realistic potential, we have relaxed the bilayer to determine the density, and other structural characteristics such as the Si-Si pair distribution functions and the Si-O-Si bond angle distribution, which are compared to the experimental results obtained by direct imaging