Using parsimony to reconstruct ancestral character states on a phylogenetic tree has become a popular method for testing ecological and evolutionary hypotheses. Despite its popularity, the assumptions and uncertainties of reconstructing the ancestral states of a single character have received less attention than the much less challenging endeavor of reconstructing phylogenetic trees from many c...

Parsimony pressure has been increasingly used as a means of controling code growth in genetic programming. However, several published papers have shown that in some cases its use can degrade the performance of the genetic program Koza, 1992, Nordin and Banzhaf, 1995]. In this paper we show that poor average results with parsimony pressure are a result of \failed" populations which overshadow th...

Maximum parsimony and maximum likelihood are two contrasting approaches for reconstructing phylogenetic trees from sequence and character data. We establish analytic links between these methods (extending connections reported earlier) under the simple Poisson model of substitutions in two settings. First, we show that if the underlying state space is sufficiently large then the maximum likeliho...

MOTIVATION Haplotypes have been attracting increasing attention because of their importance in analysis of many fine-scale molecular-genetics data. Since direct sequencing of haplotype via experimental methods is both time-consuming and expensive, haplotype inference methods that infer haplotypes based on genotype samples become attractive alternatives. RESULTS (1) We design and implement an ...

The questions of how to test hypotheses of character evolution, and incorporate character evolution into phylogenetic analysis are considered in this thesis. When a character transformation series is not linear, it is usually decoded into a set of binary characters by various binary coding methods. The disadvantages of such an approach have been discussed extensively in the literature. We propo...

Genetic programming is distinguished from other evolutionary algorithms in that it uses tree representations of variable size instead of linear strings of xed length. The exible representation scheme is very important because it allows the underlying structure of the data to be discovered automatically. One primary diiculty, however, is that the solutions may grow too big without any improvemen...

Computer simulations are increasingly being used to predict the behaviour of crowds. However, the models used are mainly based on video observations, not an understanding of human decision making. Theories of crowd psychology can elucidate the factors underpinning collective behaviour in human crowds. Yet, in contrast to psychology, computer science must rely upon mathematical formulations in o...

Freivalds defined an acceptable programming system independent criterion for learning programs for functions in which the final programs were required to be both correct and “nearly” minimal size, i.e, within a computable function of being purely minimal size. Kinber showed that this parsimony requirement on final programs limits learning power. However, in scientific inference, parsimony is co...