Design of an Interleaver for Turbo Codes using Genetic Algorithms (2009)
Shobha Rekh, Subha Rani, Wim Hordijk, Princy Gift
Turbo codes are a powerful channel coding technique employed in communication systems. Turbo codes emerged in 1993 and have since become a popular area of communications research. The excellent...
Material Representations: From the Genetic Code to the Evolution of Cellular Automata (2008)
Luis Mateus, Wim Hordijk, Informatics Group
We present a definition of the concept of representation that relies on a study of the origin of the types of structures that are used to store memory in evolving systems. This study is based on what...
Correlation analysis of coupled fitness landscapes (2008)
Wim Hordijk, Stuart A. Kauffman
∗ Author for correspondence The correlation structure of fitness landscapes is a much used measure to characterize and classify various types of landscapes. However, analyzing the correlation...
The footprint sorting problem (2008)
Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, Peter F. Stadler
Phylogenetic footprints are short pieces of non-coding DNA sequence in the vicinity of a gene that are conserved between evolutionary distant species. A seemingly simple problem is to sort footprints...
an der Fakultät für Naturwissenschaften und Mathematik (2008)
Claudia Fried, Sonja J. Prohaska, Chi-hua Chiu, Christoph Flamm, Günther P. Wagner, ...
Dank an meine Eltern nicht nur dafür, dass sie mir mein Studium ermöglicht haben An dieser Stelle möchte ich mich herzlich bei all jenen bedanken, die mich bei meiner Arbeit unterstützt haben....
Graph Laplacians, nodal domains, and hyperplane arrangements (2008)
Wim Hordijk, Josef Leydold, Peter F. Stadler
Abstract. Eigenvectors of the Laplacian of a graph G have received increasing attention in the recent past. Here we investigate their so-called nodal domains, i.e., the connected components of the...
Correlation Analysis of Coupled Fitness Landscapes (2008)
Wim Hordijk And, Wim Hordijk, Stuart A. Kauffman
The correlation structure of fitness landscapes is a much used measure to characterize and classify various types of landscapes. However, analyzing the correlation structure of fitness landscapes has...
Graph Laplacians, nodal domains, and hyperplane arrangements (2007)
Wim Hordijk, Josef Leydold, Peter F. Stadler
Abstract. Eigenvectors of the Laplacian of a graph G have received increasing attention in the recent past. Here we investigate their so-called nodal domains, i.e., the connected components of the...
The Structure of the Synchronizing-CA Landscape (2007)
In many complex systems control situations, searching for solutions or alternatives is involved. Searching for solutions can be modeled by a search on a fitness landscape. Knowing the structure of...
Graph Laplacians, Nodal Domains, and Hyperplane Arrangements (2007)
Türker Bıyıkoglu, Wim Hordijk, Josef Leydold, Tomaz Pisanski, Peter F. Stadler
Eigenvectors of the Laplacian of a graph G have received increasing attention in the recent past. Here we investigate their so-called nodal domains, i.e., the connected components of the maximal...
Shapes of Tree Representations of Spin-Glass (2007)
Landscapes Wim Hordijk, Wim Hordijk, Jose F. Fontanari, Peter F. Stadler
Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure { a barrier tree { the leaves and internal nodes of which represent,...
Motivation: Maximum likelihood methods have become very popular for constructing phylogenetic trees from sequence data. However, despite noticeable recent progress, with large and difficult data sets...
Hordijk, Wim, Gascuel, Olivier
Motivation: Maximum likelihood (ML) methods have become very popular for constructing phylogenetic trees from sequence data. However, despite noticeable recent progress, with large and difficult...
Hordijk, Wim, Gascuel, Olivier
Motivation: Maximum likelihood methods have become very popular for constructing phylogenetic trees from sequence data. However, despite noticeable recent progress, with large and difficult data sets...
Graph Laplacians, nodal domains, and hyperplane arrangements. (2004)
Pisanski, Tomaž, BIYIKOGLU, Türker, HORDIJK, Wim, LEYDOLD, Josef, STADLER, Peter
Eigenvectors of the Laplacian of a graph $G$ have received increasing attention in the recent past. Here we investigate their so-called nodal domains, i.e., the connected components of the maximal...
PD. Encoding a post-operative coronary artery bypass surgery care plan (2004)
Luis Mateus Rocha, Wim Hordijk
Abstract We present a new definition of the concept of representation for cognitive science that is based on a study of the origin of structures that are used to store memory in evolving systems....
Supertree algorithms for ancestral divergence dates and nested taxa. Bioinformatics (2004)
Charles Semple, Philip Daniel, Wim Hordijk, Mike Steel
Abstract. Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the `Tree of Life'. However, a limitation of such methods is that, typically,...
Supertree algorithms for ancestral divergence dates and nested taxa. Bioinformatics (2004)
Charles Semple, Philip Daniel, Wim Hordijk, Mike Steel
Abstract. Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the ‘Tree of Life’. However, a limitation of such methods is that, typically,...
Supertree algorithms for ancestral divergence dates and nested taxa. Bioinformatics (2004)
Charles Semple, Philip Daniel, Wim Hordijk, Mike Steel
Abstract. Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the ‘Tree of Life’. However, a limitation of such methods is that, typically,...
The Footprint Sorting Problem (2004)
Fried, Claudia, Hordijk, Wim, Prohaska, Sonja J., Stadler, Claus R., Stadler, Peter F.
Graph Laplacians, Nodal Domains, and Hyperplane Arrangements (2004)
Biyikoglu, Türker, Hordijk, Wim, Leydold, Josef, Pisanski, Tomaz, Stadler, Peter F.
Supertree algorithms for ancestral divergence dates and nested taxa (2004)
Semple, Charles, Daniel, Philip, Hordijk, Wim, Page, Roderic D. M., Steel, Mike
Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the ‘Tree of Life’. However, a limitation of such methods is that, typically, they use...
Supertree algorithms for ancestral divergence dates and nested taxa (2004)
Semple, Charles, Daniel, Philip, Hordijk, Wim, Page, Roderic D.M., Steel, Mike
Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the ‘Tree of Life’. However, a limitation of such methods is that, typically, they use...
Supertree algorithms for ancestral divergence dates and nested taxa (2004)
Semple, Charles, Daniel, Philip, Hordijk, Wim, Page, Roderic D. M., Steel, Mike
Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the ‘Tree of Life’. However, a limitation of such methods is that, typically, they use...
Phase transition and landscape statistics of the number partitioning problem (2003)
Stadler, Peter F., Hordijk, Wim, Fontanari, Jos{é} F.
The phase transition in the number partitioning problem (NPP), i.e., the transition from a region in the space of control parameters in which almost all instances have many solutions to a region in...
Shapes of tree representations of spin-glass landscapes (2003)
Hordijk, Wim, Fontanari, Jose F., Stadler, Peter F.
Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure -- a barrier tree -- the leaves and internal nodes of which represent,...
The ability of systems of molecular reactions to be simultaneously autocatalylic and sustained by some ambient ‘food source ’ of simple molecules may have been an essential step in the origin of...
Catalytic reaction sets, decay, and the preservation of information (2003)
Wim Hordijk, José F. Fontanari
Abstract--- We study the ability to maintain information in a population of protocells that enclose sets of reacting polymers or metabolisms, under the influence of decay, i.e., spontaneous breakdown...
Catalytic Reaction Sets, Decay, and the Preservation of Information (2002)
Hordijk, Wim, Fontanari, Jose F.
We study the ability to maintain information in a population of reacting polymers under the influence of decay, i.e., spontaneous breakdown of large polymers. At a certain decay rate, it becomes...
Graph Laplacians, Nodal Domains, and Hyperplane Arrangements (2002)
Biyikoglu, Türker, Hordijk, Wim, Leydold, Josef, Pisanski, Tomaz, Stadler, Peter F.
Eigenvectors of the Laplacian of a graph G have received increasing attention in the recent past. Here we investigate their so-called nodal domains, i.e., the connected components of the maximal...
Fast Fourier Transform for Fitness Landscapes (2001)
Dan Rockmore, Peter Kostelec, Wim Hordijk, Peter F. Stadler, Peter F
We cast some classes of fitness landscapes as problems in spectral analysis on various Cayley graphs. In particular, landscapes derived from RNA folding are realized on Hamming graphs and analyzed in...
Upper Bound on the Products of Particle Interactions in Cellular Automata (2000)
Hordijk, Wim, Shalizi, Cosma Rohilla, Crutchfield, James P.
Particle-like objects are observed to propagate and interact in many spatially extended dynamical systems. For one of the simplest classes of such systems, one-dimensional cellular automata, we...
Amplitude spectra of fitness landscapes (1998)
Wim Hordijk, W. Hordijk, P. F. Stadler
ABSTRACT. Fitness landscapes can be decomposed into elementary landscapes using a Fourier transform that is determined by the structure of the underlying con guration space. The amplitude spectrum...
Amplitude spectra of fitness landscapes (1998)
Wim Hordijk, Peter F. Stadler, W. Hordijk, P. F. Stadler
ABSTRACT. Fitness landscapes can be decomposed into elementary landscapes using a Fourier transform that is determined by the structure of the underlying configuration space. The amplitude spectrum...
Mechanisms of Emergent Computation in Cellular Automata (1998)
Wim Hordijk, James P. Crutchfield, Melanie Mitchell
. We introduce a class of embedded-particle models for describing the emergent computational strategies observed in cellular automata (CAs) that were evolved for performing certain computational...
Amplitude Spectra of Fitness Landscapes (1998)
Fitness landscapes can be decomposed into elementary landscapes using a Fourier transform that is determined by the structure of the underlying configuration space. The amplitude spectrum obtained...
Mechanisms of emergent computation in cellular automata (1998)
Wim Hordijk, James P. Crutchfield, Melanie Mitchell
Abstract. We introduce a class of embedded-particle models for describing the emergent computational strategies observed in cellular automata (CAs) that were evolved for performing certain...
Correlation Analysis of the Synchronizing-CA Landscape (1997)
A correlation analysis will be applied to subspaces of the fitness landscape generated by the synchronization task for onedimensional cellular automata. This results in a stochastic model that can be...
A measure of landscapes (1996)
The structure of a fitness landscape is still an ill-defined concept. This paper introduces a statistical fitness landscape analysis, that can be used on a multitude of fitness landscapes. The result...
A measure of landscapes (1996)
This paper introduces a statistical fitness landscape analysis, based on Weinberger's random walk method and on a time series analysis known as the Box-Jenkins approach, to measure and express...
Embedded-Particle Computation in Evolved Cellular Automata (1996)
Wim Hordijk, James P. Crutchfield, Melanie Mitchell
this paper we focus on how these CAs implement the emergent computational strategies for performing a task. In particular, we develop a class of embedded-particle models to describe the computational...
The usefulness of recombination (1995)
Abstract. In this paper, we examine the usefulness of recombination from two points of view. First, the problem of crossover disruption is investigated. This is done by comparing two Genetic...
Population Flow on Fitness Landscapes (1994)
Wim Hordijk, Bernard Manderick
Contents 1 Introduction 1 1.1 The goal of this thesis : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 2 1.2 The outline of the thesis : : : : : : : : : : : : : : : : : : : : : : : : : : : :...
Upper Bound on the Products of Particle Interactions in Cellular Automata
Wim Hordijk, Cosma Rohilla Shalizi, James P. Crutchfield
Particle-like objects are observed to propagate and interact in many spatially extended dynamical systems. For one of the simplest classes of such systems, one-dimensional cellular automata, we...
Fast Fourier Transform for Fitness Landscapes
Dan Rockmore, Peter Kostelec, Wim Hordijk, Peter F. Stadler
We cast some classes of fitness landscapes as problems in spectral analysis on various Cayley graphs. In particular, landscapes derived from RNA folding are realized on Hamming graphs and analyzed in...
Mechanisms of Emergent Computation in Cellular Automata
Wim Hordijk, James P. Crutchfield, Melanie Mitchell
We introduce a class of embedded-particle models for describing the emergent computational strategies observed in cellular automata (CAs) that were evolved for performing certain computational tasks....
Amplitude Spectra of Fitness Landscapes
Fitness landscapes can be decomposed into elementary landscapes using a Fourier transform that is determined by the structure of the underlying configuration space. The amplitude spectrum obtained...
Correlation Analysis of the Synchronizing-CA Landscape
A correlation analysis will be applied to subspaces of the fitness landscape generated by the synchronization task for one- dimensional cellular automata. This results in a stochastic model that can...
The Structurte of the Synchronizing-CA Landscape
In many complex systems control situations, searching for solutions or alternatives is involved. Searching for solutions can be modeled by a search on a fitness landscape. Knowing the structure of...
Embedded-Particle Computation in Evolved Cellular Automata
Wim Hordijk, James P. Crutchfield, Melanie Mitchell
In our work we are studying how genetic algorithms (GAs) can evolve cellular automata (CAs) to perform computations that require global coordination. The "evolving cellular automata" framework is an...
The structure of a fitness landscape is still an ill-defined concept. This paper introduces a statistical fitness landscape analysis, that can be used on a multitude of fitness landscapes. The result...