On the Mean Convergence Time of Multi-parent Genetic Algorithms Without Selection

Abstract. This paper investigates genetic drift in multi-parent genetic algorithms (MPGAs). An exact model based on Markov chains is pro-posed to formulate the variation of gene frequency. This model iden-tifies the correlation between the adopted number of parents and the mean convergence time. Moreover, it reveals the pairwise equivalence phenomenon in the number of parents and indicates the acceleration of genetic drift in MPGAs. The good fit between theoretical and experi-mental results further verifies the capability of this model.

Multi-membership gene regulation in pathway based microarray analysis

This article is available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. Results: We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. Conclusions: We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.The work was sponsored by the studentship scheme of the School of Information Systems, Computing and Mathematics, Brunel Universit

On the evolutionary optimisation of many conflicting objectives

This inquiry explores the effectiveness of a class of modern evolutionary algorithms, represented by Non-dominated Sorting Genetic Algorithm (NSGA) components, for solving optimisation tasks with many conflicting objectives. Optimiser behaviour is assessed for a grid of mutation and recombination operator configurations. Performance maps are obtained for the dual aims of proximity to, and distribution across, the optimal trade-off surface. Performance sweet-spots for both variation operators are observed to contract as the number of objectives is increased. Classical settings for recombination are shown to be suitable for small numbers of objectives but correspond to very poor performance for higher numbers of objectives, even when large population sizes are used. Explanations for this behaviour are offered via the concepts of dominance resistance and active diversity promotion

Memetic Multilevel Hypergraph Partitioning

Hypergraph partitioning has a wide range of important applications such as VLSI design or scientific computing. With focus on solution quality, we develop the first multilevel memetic algorithm to tackle the problem. Key components of our contribution are new effective multilevel recombination and mutation operations that provide a large amount of diversity. We perform a wide range of experiments on a benchmark set containing instances from application areas such VLSI, SAT solving, social networks, and scientific computing. Compared to the state-of-the-art hypergraph partitioning tools hMetis, PaToH, and KaHyPar, our new algorithm computes the best result on almost all instances