Genetic programming for the automatic design of controllers for a surface ship

In this paper, the implementation of genetic programming (GP) to design a contoller structure is assessed. GP is used to evolve control strategies that, given the current and desired state of the propulsion and heading dynamics of a supply ship as inputs, generate the command forces required to maneuver the ship. The controllers created using GP are evaluated through computer simulations and real maneuverability tests in a laboratory water basin facility. The robustness of each controller is analyzed through the simulation of environmental disturbances. In addition, GP runs in the presence of disturbances are carried out so that the different controllers obtained can be compared. The particular vessel used in this paper is a scale model of a supply ship called CyberShip II. The results obtained illustrate the benefits of using GP for the automatic design of propulsion and navigation controllers for surface ships

Evaluation and development of animal breeding in Ireland

End of project reportThe primary objectives of this study were: 1) to annually evaluate the pertinence of the Irish dairy cattle breeding index, the Economic Breeding Index (EBI) and where necessary modify, 2) to evaluate the potential of do-it-yourself milk recording as an alternative to current supervised methods of milk recording, and 3) to estimate the level and rate of accumulation of inbreeding in Irish dairy and beef cattle, to quantify its effects on traits of economic importance, and to develop remedial measures to minimise the future accumulation of inbreeding in Ireland

Optimization as a design strategy. Considerations based on building simulation-assisted experiments about problem decomposition

In this article the most fundamental decomposition-based optimization method - block coordinate search, based on the sequential decomposition of problems in subproblems - and building performance simulation programs are used to reason about a building design process at micro-urban scale and strategies are defined to make the search more efficient. Cyclic overlapping block coordinate search is here considered in its double nature of optimization method and surrogate model (and metaphore) of a sequential design process. Heuristic indicators apt to support the design of search structures suited to that method are developed from building-simulation-assisted computational experiments, aimed to choose the form and position of a small building in a plot. Those indicators link the sharing of structure between subspaces ("commonality") to recursive recombination, measured as freshness of the search wake and novelty of the search moves. The aim of these indicators is to measure the relative effectiveness of decomposition-based design moves and create efficient block searches. Implications of a possible use of these indicators in genetic algorithms are also highlighted.Comment: 48 pages. 12 figures, 3 table

Detection of recombination in DNA multiple alignments with hidden markov models

CConventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets from certain bacteria and viruses due to recombination, a process that leads to the creation of mosaic sequences from different strains and, if undetected, causes systematic errors in phylogenetic tree estimation. In the current work, a hidden Markov model (HMM) is employed to detect recombination events in multiple alignments of DNA sequences. The emission probabilities in a given state are determined by the branching order (topology) and the branch lengths of the respective phylogenetic tree, while the transition probabilities depend on the global recombination probability. The present study improves on an earlier heuristic parameter optimization scheme and shows how the branch lengths and the recombination probability can be optimized in a maximum likelihood sense by applying the expectation maximization (EM) algorithm. The novel algorithm is tested on a synthetic benchmark problem and is found to clearly outperform the earlier heuristic approach. The paper concludes with an application of this scheme to a DNA sequence alignment of the argF gene from four Neisseria strains, where a likely recombination event is clearly detected

Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure

Background: Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting trees. Different parameter combinations chosen for the multiple alignment may result in different phylogenies. A new non-alignment based approach, Relative Complexity Measure (RCM), has been introduced to tackle this problem and proven to work in fungi and mitochondrial DNA. Result: In this work, we present an application of the RCM method to reconstruct robust phylogenetic trees using sequence data for genus Galanthus obtained from different regions in Turkey. Phylogenies have been analyzed using nuclear and chloroplast DNA sequences. Results showed that, the tree obtained from nuclear ribosomal RNA gene sequences was more robust, while the tree obtained from the chloroplast DNA showed a higher degree of variation. Conclusions: Phylogenies generated by Relative Complexity Measure were found to be robust and results of RCM were more reliable than the compared techniques. Particularly, to overcome MSA-based problems, RCM seems to be a reasonable way and a good alternative to MSA-based phylogenetic analysis. We believe our method will become a mainstream phylogeny construction method especially for the highly variable sequence families where the accuracy of the MSA heavily depends on the alignment parameters

A metaheuristic particle swarm optimization approach to nonlinear model predictive control

This paper commences with a short review on optimal control for nonlinear systems, emphasizing the Model Predictive approach for this purpose. It then describes the Particle Swarm Optimization algorithm and how it could be applied to nonlinear Model Predictive Control. On the basis of these principles, two novel control approaches are proposed and anal- ysed. One is based on optimization of a numerically linearized perturbation model, whilst the other avoids the linearization step altogether. The controllers are evaluated by simulation of an inverted pendulum on a cart system. The results are compared with a numerical linearization technique exploiting conventional convex optimization methods instead of Particle Swarm Opti- mization. In both approaches, the proposed Swarm Optimization controllers exhibit superior performance. The methodology is then extended to input constrained nonlinear systems, offering a promising new paradigm for nonlinear optimal control design.peer-reviewe