Dirichlet-Neumann inverse spectral problem for a star graph of Stieltjes strings

We solve two inverse spectral problems for star graphs of Stieltjes strings with Dirichlet and Neumann boundary conditions, respectively, at a selected vertex called root. The root is either the central vertex or, in the more challenging problem, a pendant vertex of the star graph. At all other pendant vertices Dirichlet conditions are imposed; at the central vertex, at which a mass may be placed, continuity and Kirchhoff conditions are assumed. We derive conditions on two sets of real numbers to be the spectra of the above Dirichlet and Neumann problems. Our solution for the inverse problems is constructive: we establish algorithms to recover the mass distribution on the star graph (i.e. the point masses and lengths of subintervals between them) from these two spectra and from the lengths of the separate strings. If the root is a pendant vertex, the two spectra uniquely determine the parameters on the main string (i.e. the string incident to the root) if the length of the main string is known. The mass distribution on the other edges need not be unique; the reason for this is the non-uniqueness caused by the non-strict interlacing of the given data in the case when the root is the central vertex. Finally, we relate of our results to tree-patterned matrix inverse problems.Comment: 32 pages, 3 figure

K-Bit-Swap: a new operator for real-coded evolutionary algorithms

There have been a variety of crossover operators proposed for real-coded genetic algorithms (RCGAs). Such operators recombine values from pairs of strings to generate new solutions. In this article, we present a recombination operator for RCGAs that selects the string locations for change separately randomly in the parent and offspring, enabling solution parts to move within a string, and compare it to mainstream crossover operators in a set of experiments on a range of standard multidimensional optimization problems and a real-world clustering problem. We present two variants of the operator, either selecting bits uniformly at random in both strings or sampling the second bit from a normal distribution centered at the selected location in the first string. While the operator is biased toward exploitation of fitness space, the random selection of the second bit for swapping reduces this bias slightly. Statistical analysis of the experimental results using a nonparametric test shows the advantage of the new recombination operators on our test optimization functions

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

Scalability of Genetic Programming and Probabilistic Incremental Program Evolution

This paper discusses scalability of standard genetic programming (GP) and the probabilistic incremental program evolution (PIPE). To investigate the need for both effective mixing and linkage learning, two test problems are considered: ORDER problem, which is rather easy for any recombination-based GP, and TRAP or the deceptive trap problem, which requires the algorithm to learn interactions among subsets of terminals. The scalability results show that both GP and PIPE scale up polynomially with problem size on the simple ORDER problem, but they both scale up exponentially on the deceptive problem. This indicates that while standard recombination is sufficient when no interactions need to be considered, for some problems linkage learning is necessary. These results are in agreement with the lessons learned in the domain of binary-string genetic algorithms (GAs). Furthermore, the paper investigates the effects of introducing utnnecessary and irrelevant primitives on the performance of GP and PIPE.Comment: Submitted to GECCO-200

Around Kolmogorov complexity: basic notions and results

Algorithmic information theory studies description complexity and randomness and is now a well known field of theoretical computer science and mathematical logic. There are several textbooks and monographs devoted to this theory where one can find the detailed exposition of many difficult results as well as historical references. However, it seems that a short survey of its basic notions and main results relating these notions to each other, is missing. This report attempts to fill this gap and covers the basic notions of algorithmic information theory: Kolmogorov complexity (plain, conditional, prefix), Solomonoff universal a priori probability, notions of randomness (Martin-L\"of randomness, Mises--Church randomness), effective Hausdorff dimension. We prove their basic properties (symmetry of information, connection between a priori probability and prefix complexity, criterion of randomness in terms of complexity, complexity characterization for effective dimension) and show some applications (incompressibility method in computational complexity theory, incompleteness theorems). It is based on the lecture notes of a course at Uppsala University given by the author

Highly Scalable Algorithms for Robust String Barcoding

String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher selection based on whole genomic sequences of hundreds of microorganisms of up to bacterial size on a well-equipped workstation, and can be easily parallelized to further extend the applicability range to thousands of bacterial size genomes. Experimental results on both randomly generated and NCBI genomic data show that whole-genome based selection results in a number of distinguishers nearly matching the information theoretic lower bounds for the problem

Optimality program in segment and string graphs

Planar graphs are known to allow subexponential algorithms running in time $2^{O(\sqrt n)}$ or $2^{O(\sqrt n \log n)}$ for most of the paradigmatic problems, while the brute-force time $2^{\Theta(n)}$ is very likely to be asymptotically best on general graphs. Intrigued by an algorithm packing curves in $2^{O(n^{2/3}\log n)}$ by Fox and Pach [SODA'11], we investigate which problems have subexponential algorithms on the intersection graphs of curves (string graphs) or segments (segment intersection graphs) and which problems have no such algorithms under the ETH (Exponential Time Hypothesis). Among our results, we show that, quite surprisingly, 3-Coloring can also be solved in time $2^{O(n^{2/3}\log^{O(1)}n)}$ on string graphs while an algorithm running in time $2^{o(n)}$ for 4-Coloring even on axis-parallel segments (of unbounded length) would disprove the ETH. For 4-Coloring of unit segments, we show a weaker ETH lower bound of $2^{o(n^{2/3})}$ which exploits the celebrated Erd\H{o}s-Szekeres theorem. The subexponential running time also carries over to Min Feedback Vertex Set but not to Min Dominating Set and Min Independent Dominating Set.Comment: 19 pages, 15 figure

LIBOPT - An environment for testing solvers on heterogeneous collections of problems - Version 1.0

The Libopt environment is both a methodology and a set of tools that can be used for testing, comparing, and profiling solvers on problems belonging to various collections. These collections can be heterogeneous in the sense that their problems can have common features that differ from one collection to the other. Libopt brings a unified view on this composite world by offering, for example, the possibility to run any solver on any problem compatible with it, using the same Unix/Linux command. The environment also provides tools for comparing the results obtained by solvers on a specified set of problems. Most of the scripts going with the Libopt environment have been written in Perl