Search results for "Theoretical Computer Science"
showing 10 items of 1151 documents
A distance metric on binary trees using lattice-theoretic measures
1990
A so called height function which is a strictly antitone supervaluation is defined on binary trees. Via lattice-theoretic results and using the height function, we can define a distance metric on binary trees of size n which can be computed in expected time O(n 3/2 )
Efficient lower and upper bounds of the diagonal-flip distance between triangulations
2006
There remains today an open problem whether the rotation distance between binary trees or equivalently the diagonal-flip distance between triangulations can be computed in polynomial time. We present an efficient algorithm for computing lower and upper bounds of this distance between a pair of triangulations.
An efficient upper bound of the rotation distance of binary trees
2000
A polynomial time algorithm is developed for computing an upper bound for the rotation distance of binary trees and equivalently for the diagonal-flip distance of convex polygons triangulations. Ordinal tools are used.
On the Locality of Standard Search Operators in Grammatical Evolution
2014
Offspring should be similar to their parents and inherit their relevant properties. This general design principle of search operators in evolutionary algorithms is either known as locality or geometry of search operators, respectively. It takes a geometric perspective on search operators and suggests that the distance between an offspring and its parents should be less than or equal to the distance between both parents. This paper examines the locality of standard search operators used in grammatical evolution (GE) and genetic programming (GP) for binary tree problems. Both standard GE and GP search operators suffer from low locality since a substantial number of search steps result in an o…
The Myriad Virtues of Wavelet Trees
2009
Wavelet Trees have been introduced in [Grossi, Gupta and Vitter, SODA '03] and have been rapidly recognized as a very flexible tool for the design of compressed full-text indexes and data compressors. Although several papers have investigated the beauty and usefulness of this data structure in the full-text indexing scenario, its impact on data compression has not been fully explored. In this paper we provide a complete theoretical analysis of a wide class of compression algorithms based on Wavelet Trees. We also show how to improve their asymptotic performance by introducing a novel framework, called Generalized Wavelet Trees, that aims for the best combination of binary compressors (like,…
A bio-inspired approach to attack graphs analysis
2018
Computer security has recently become more and more important as the world economy dependency from data has kept growing. The complexity of the systems that need to be kept secure calls for new models capable of abstracting the interdependencies among heterogeneous components that cooperate at providing the desired service. A promising approach is attack graph analysis, however the manual analysis of attack graphs is tedious and error prone. In this paper we propose to apply the metabolic network model to attack graphs analysis, using three interacting bio-inspired algorithms: topological analysis, flux balance analysis, and extreme pathway analysis. A developed framework for graph building…
Protein-protein interaction network querying by a "focus and zoom" approach
2008
We propose an approach to network querying in protein-protein interaction networks based on bipartite graph weighted matching. An algorithm is presented that first “focuses” the potentially relevant portion of the target graph by performing a global alignment of this one with the query graph, and then “zooms” on the actual matching nodes by considering their topological arrangement, hereby obtaining a (possibly) approximated occurrence of the query graph within the target graph. Approximation is related to node insertions, node deletions and edge deletions possibly intervening in the query graph. The technique manages networks of arbitrary topology. Moreover, edge labels are used to represe…
Textual data compression in computational biology: Algorithmic techniques
2012
Abstract In a recent review [R. Giancarlo, D. Scaturro, F. Utro, Textual data compression in computational biology: a synopsis, Bioinformatics 25 (2009) 1575–1586] the first systematic organization and presentation of the impact of textual data compression for the analysis of biological data has been given. Its main focus was on a systematic presentation of the key areas of bioinformatics and computational biology where compression has been used together with a technical presentation of how well-known notions from information theory have been adapted to successfully work on biological data. Rather surprisingly, the use of data compression is pervasive in computational biology. Starting from…
Iterative sparse matrix-vector multiplication for accelerating the block Wiedemann algorithm over GF(2) on multi-graphics processing unit systems
2012
SUMMARY The block Wiedemann (BW) algorithm is frequently used to solve sparse linear systems over GF(2). Iterative sparse matrix–vector multiplication is the most time-consuming operation. The necessity to accelerate this step is motivated by the application of BW to very large matrices used in the linear algebra step of the number field sieve (NFS) for integer factorization. In this paper, we derive an efficient CUDA implementation of this operation by using a newly designed hybrid sparse matrix format. This leads to speedups between 4 and 8 on a single graphics processing unit (GPU) for a number of tested NFS matrices compared with an optimized multicore implementation. We further present…
A New Universal Cellular Automaton Discovered by Evolutionary Algorithms
2004
In Twenty Problems in the Theory of Cellular Automata, Stephen Wolfram asks “how common computational universality and undecidability [are] in cellular automata.” This papers provides elements of answer, as it describes how another universal cellular automaton than the Game of Life (Life) was sought and found using evolutionary algorithms. This paper includes a demonstration that consists in showing that the presented R automaton can both implement any logic circuit (logic universality) and a simulation of Life (universality in the Turing sense).