MOTIVATION A quantitative study of molecular evolutionary events such as substitutions, insertions and deletions from closely related genomes requires (1) an accurate multiple sequence alignment program and (2) a method to annotate the insertions and deletions that explain the 'gaps' in the alignment. Although the former requirement has been extensively addressed, the latter problem has receive...

This paper introduces clustering as a tool to improve the eeects of recombination and incorporate niching in evolutionary algorithms. Instead of processing the entire set of parent solutions, the set is rst clustered and the solutions in each of the clusters are processed separately. This alleviates the problem of symmetry which is often a major diiculty of many evolutionary algorithms in combi...

We have developed a new approach (MDLEP) to learning Bayesian network structures based on the Minimum Description Length (MDL) principle and Evolutionary Programming (EP). It integrates a MDL metric founded on information theory and several new genetic operators including structure-guided operators, a knowledge-guided operator, a freeze operator, and a defrost operator for the discovery process...

Discussions of “chance” and related concepts (such as “stochasticity,” “randomness,” “indeterminism,” etc.) are found throughout philosophical work on evolutionary theory. By drawing attention to three very commonly-recognized distinctions, I separate four independent concepts falling under the broad heading of “chance”: randomness (as a property of sequences), epistemic unpredictability, causa...

This paper introduces clustering as a tool to improve the e ects of recombination and in corporate niching in evolutionary algorithms Instead of processing the entire set of parent solutions the set is rst clustered and the solutions in each of the clusters are processed sep arately This alleviates the problem of symmetry which is often a major di culty of many evolutionary algorithms in combin...

Classic parsing methods are based on complete search techniques to find the different interpretations of a sentence. However, the size of the search space increases exponentially with the length of the sentence or text to be parsed, so that exhaustive search methods can fail to reach a solution in a reasonable time. Nevertheless, large problems can be solved approximately by some kind of stocha...

Evolutionary algorithms commonly search for the best solutions by maintaining a population of individuals that evolves from one generation to the next. The evolution consists of selecting a set of individuals from the population and applying, to some subsets of it, recombination operators that create new solutions. In this paper, Estimation of distribution algorithms arise as an alternative to ...

SUMMARY Phylogenetics, likelihood, evolution and complexity (PLEX) is a flexible and fast Bayesian Markov chain Monte Carlo software program for large-scale analysis of nucleotide and amino acid data using complex evolutionary models in a phylogenetic framework. The program gains large speed improvements over standard approaches by implementing 'partial sampling of substitution histories', a da...

Topological quantum computing is an alternative framework for avoiding the quantum decoherence problem in quantum computation. The problem of executing a gate in this framework can be posed as the problem of braiding quasiparticles. Because these are not Abelian, the problem can be reduced to finding an optimal product of braid generators where the optimality is defined in terms of the gate app...

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understandin...