Supertree Algorithms for Ancestral Divergence Dates and Nested Taxa (2004)
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 just...
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...
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 (2003)
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,...
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,...
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, (2002)
Turker Bykoglu, 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...
Graph Laplacians, Nodal Domains, and Hyperplane Arrangements and Hyperplane Arrangements (2002)
Turker Bykoglu, 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...
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...
Embedded-Particle Computation in Evolved Cellular Automata (2000)
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...
Mechanisms of Emergent Computation in Cellular Automata (2000)
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...
Fast Fourier Transform for Fitness Landscapes (1999)
Dan Rockmore, Peter Kostelec, Wim Hordijk, 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...
Fast Fourier Transform for Fitness Landscapes (1999)
Dan Rockmore, Peter Kostelec, Wim Hordijk, 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...
Mechanisms of Emergent Computation in Cellular Automata (1999)
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
. 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...
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...
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...
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...
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...
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...
Embedded-Particle Computation in Evolved Cellular Automata (1998)
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...
Embedded-Particle Computation in Evolved Cellular Automata (1997)
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...
Embedded-Particle Computation in Evolved Cellular Automata (1997)
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...
Correlation Analysis of the Synchronizing-CA Landscape (1997)
this paper was to show that the in [6] proposed landscape analysis will still work nicely on less well behaved, non-isotropic landscapes. This turns out to be true, as long as subspaces in the...
A Measure of Landscapes (1997)
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 the...
A Measure of Landscapes (1997)
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 the...
The Structure of the Synchronizing-CA Landscape (1996)
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...
The Structure of the Synchronizing-CA Landscape (1996)
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...
The Structure of the Synchronizing-CA Landscape (1996)
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 (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...
Population Flow on Fitness Landscapes (1996)
Wim Hordijk, Bernard Manderick
Contents 1 Introduction 1 1.1 The goal of this thesis : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 2 1.2 The outline of the thesis : : : : : : : : : : : : : : : : : : : : : : : : : : : :...
A Measure of Landscapes (1995)
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 (1995)
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...
The Usefulness of Recombination (1995)
. 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 Algorithms with...
Population Flow on Fitness Landscapes (1994)
Wim Hordijk, Bernard Manderick, Stuart A. Kauffman
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...