Exploring the effect of sex on empirical fitness landscapes

The nature of epistasis has important consequences for the evolutionary significance of sex and recombination. Recent efforts to find negative epistasis as a source of negative linkage disequilibrium and associated long-term advantage to sex have yielded little support. Sign epistasis, where the sign of the fitness effects of alleles varies across genetic backgrounds, is responsible for the ruggedness of the fitness landscape, with several unexplored implications for the evolution of sex. Here, we describe fitness landscapes for two sets of strains of the asexual fungus Aspergillus niger involving all combinations of five mutations. We find that 30% of the single-mutation fitness effects are positive despite their negative effect in the wild-type strain and that several local fitness maxima and minima are present. We then compare adaptation of sexual and asexual populations on these empirical fitness landscapes by using simulations. The results show a general disadvantage of sex on these rugged landscapes, caused by the breakdown by recombination of genotypes on fitness peaks. Sex facilitates movement to the global peak only for some parameter values on one landscape, indicating its dependence on the landscape’s topography. We discuss possible reasons for the discrepancy between our results and the reports of faster adaptation of sexual population

Adaptive Approaches Towards Better GA Performance in Dynamic Fitness Landscapes

We review different techniques for improving GA performance. By analysing the fitness landscape, a correlation measure between parents and offspring can be provided, and we can estimate effectively which genetic operator to use in the GA for a given fitness landscape. The response to selection equation further tells us how well the GA will do, and combining the two approaches gives us a powerful tool to automatically ensure the selection of the right parameter settings for a given problem. In dynamic environments the fitness landscape changes over time, and the evolved systems should be able to adapt to such changes. By introducing evolvable mutation rates and evolvable fitness formulae, we obtain such systems. The systems are shown to be able to adapt to both internal and external constraints and changes

On the locality of Representations

Darstellungsschich

Addressing stability issues in mediated complex contract negotiations for constraint-based, non-monotonic utility spaces

Negotiating contracts with multiple interdependent issues may yield non- monotonic, highly uncorrelated preference spaces for the participating agents. These scenarios are specially challenging because the complexity of the agents’ utility functions makes traditional negotiation mechanisms not applicable. There is a number of recent research lines addressing complex negotiations in uncorrelated utility spaces. However, most of them focus on overcoming the problems imposed by the complexity of the scenario, without analyzing the potential consequences of the strategic behavior of the negotiating agents in the models they propose. Analyzing the dynamics of the negotiation process when agents with different strategies interact is necessary to apply these models to real, competitive environments. Specially problematic are high price of anarchy situations, which imply that individual rationality drives the agents towards strategies which yield low individual and social welfares. In scenarios involving highly uncorrelated utility spaces, “low social welfare” usually means that the negotiations fail, and therefore high price of anarchy situations should be avoided in the negotiation mechanisms. In our previous work, we proposed an auction-based negotiation model designed for negotiations about complex contracts when highly uncorrelated, constraint-based utility spaces are involved. This paper performs a strategy analysis of this model, revealing that the approach raises stability concerns, leading to situations with a high (or even infinite) price of anarchy. In addition, a set of techniques to solve this problem are proposed, and an experimental evaluation is performed to validate the adequacy of the proposed approaches to improve the strategic stability of the negotiation process. Finally, incentive-compatibility of the model is studied.Spain. Ministerio de Educación y Ciencia (grant TIN2008-06739-C04-04

An Empirical Study on the Influence of Genetic Operators for Molecular Docking Optimization

Evolutionary approaches to molecular docking typically use a real-value encoding with standard genetic operators. Mutation is usually based on Gaussian and Cauchy distributions whereas for crossover no special considerations are made. The choice of operators is important for an efficient algorithm for this problem. We investigate their effect by performing a locality, heritability and heuristic bias analysis. Our investigation focus on encoding properties and how the different variation operators affect them. It is important to understand the behavior and influence of these components in order to design new and more efficient evolutionary algorithms for the molecular docking problem. Results confirm that high locality is important and explain the behavior of different crossover and mutation operators. In addition, the heritability and heuristic bias study provides some insights in how the different crossover operators perform. Optimization runs in different instances of the problem support the analysis findings. The performance and behavior of the variation operators are consistent on several molecules