Volume 17, Issue 4

We aim to search for cellular automata candidates using an automatic system for the demonstration of collision-based universality. Some of these candidates are able to simulate Turing machines in their space-time dynamics using gliders and glider guns.

In this paper, we present an evolutionary algorithm that searches for the simulation of a logic gate by cellular automata. Different parameters are tried and other search techniques are also presented to provide a benchmark.

Results show how a large number of simulations of logic gates were found.

John M. Palmer
Relative Referenced Genetic Programming

This paper presents a linear code referencing approach to the representation of individuals within a genetic programming scheme. This approach has been devised in order to confront various problems associated with genetic programming schemes. These are primarily the size of the available search space, the ability to pass through this search space, the construction of valid individuals after crossover and mutation, and the probability for the use of terminals and subpieces of an individual's solution. A comparison is made with existing methods and for the problems tested the presented method gives the best results.

Ray Goodman, Mihaela T. Matache
Dynamics of Directed Boolean Networks under Generalized Elementary Cellular Automata Rules, with Power-Law Distributions and Popularity Assignment of Parent Nodes

This study provides an analysis of the dynamics of fixed-size directed Boolean networks governed by generalizations of elementary cellular automata rules 22 and 126, under a power-law distribution of parent nodes and a popularity parent assignment. The analysis shows the existence of a two-piece chaotic attractor for smaller values of the power-law parameter which evolves into a "cloud"-like attractor for larger values of the parameter. Values of the parameter for which the system exhibits an ordered behavior are indicated as well. The dynamics are investigated using space-time diagrams, delay plots, bifurcation diagrams, and Lyapunov exponent computations. It is also shown that the children (out)links do not obey a power-law distribution; more precisely, numerical investigations indicate that the children links have a Gaussian-like distribution.

Nava E. Whiteford, Niall J. Haslam, Gerald Weber, Adam Prügel-Bennett, Jonathan W. Essex, Cameron Neylon
Visualizing the Repeat Structure of Genomic Sequences

Repeats are a common feature of genomic sequences and much remains to be understood of their origin and structure. The identification of repeated strings in genomic sequences is therefore of importance for a variety of applications in biology.

In this paper a new method for finding all repeats and visualizing them in a two-dimensional plot is presented. The method is first applied to a set of constructed sequences in order to develop a comparative framework. Several complete genomes are then analyzed, including the whole human genome.

The technique reveals the complex repeat structure of genomic sequences. In particular, interesting differences in the repeat character of the coding and noncoding regions of bacterial genomes are noted.

The method allows fast identification of all repeats and easy inter-genome comparison. In doing this the plot effectively creates a signature of a sequence which allows some classes of repeats present in a sequence to be identified by simple visual inspection.

To our knowledge this is the first time all exact repeats have been visualized in a single plot that highlights the degree to which repeats occur within a genomic sequence, giving an indication of the important role repeats play. From this it is clear that large scale repeat analysis remains an important and unsolved problem in bioinformatics.

Shigeru Ninagawa
Power Spectral Analysis of Elementary Cellular Automata

Spectral analysis of elementary cellular automata is performed. A power spectrum is calculated from the evolution of 88 independent rules starting from random initial configurations. As a result, it is found that rule 110 exhibits 1/f noise during the longest time steps. Rule 110 has proved to be capable of supporting universal computation. These results suggest that there is a relationship between computational universality and 1/f noise in cellular automata.

Ling-Yun He, Feng Zheng
Empirical Evidence of Some Stylized Facts in International Crude Oil Markets

In this paper, based on the time series of Brent and WTI crude oil prices (daily spot), some stylized facts such as autocorrelation and scaling/multiscaling features are investigated as observed in international crude oil price markets.

Miklos N. Szilagyi, Iren Somogyi
Agent-Based Simulation of N-Person Games with Crossing Payoff Functions

We report on computer simulation experiments using our agent-based simulation tool to model uniform N-person games with crossing payoff functions. We study the case when agents are greedy simpletons who imitate the action of their neighbor that received the highest payoff for its previous action.

The individual agents may cooperate with each other for the collective interest or may defect, that is, pursue their selfish interests only. After a certain number of iterations the proportion of cooperators stabilizes to either a constant value or oscillates around such a value.

The payoff (reward/penalty) functions are given as two straight lines: one for the cooperators and another for the defectors. The payoff curves are functions of the ratio of cooperators to the total number of agents. Even if the payoff functions are linear, four free parameters determine them. In this investigation only crossing payoff functions are considered.

We have investigated the behavior of the agents systematically. The results show that the solutions are nontrivial and in some cases quite irregular. They show drastic changes for the Leader Game in the narrow parameter range of 1.72 <= P <= 1.75. This behavior is similar to that observed in [1] for the N-Person Chicken Game. Irregular solutions were also found for the Reversed Stag Hunt Game.