Woven string kernels are a form of evolvable, directed, acyclic graphs specialized to perform DNA classification. They are introduced in this thesis, given a rigorous theoretical treatment as a mathematical object, and shown to have a number of interesting properties. Two forms of woven string kernels, uniform and non-uniform, are discussed. The non-uniform woven string kernels are repurposed for use as updating rules for cellular automata. The details of their representation and implementation are presented. A chapter of this thesis is devoted to a visualization technique called non-linear projection, an evolvable form of multidimensional scaling that is used in the analysis of experimental results. The woven string kernels are tested on simple and complex synthetic data as well as biological data, using an evolutionary algorithm to find woven string kernels that are acceptable solutions for classification. They perform marginally on the simplest synthetic data - based on GC content - for which they are not entirely appropriate. They exhibit perfect classification on the more complex synthetic data and on the biological data. Woven string kernels have a number of parameters including their height, the number of initial strings from which they are built, and the amount of weaving used to generate the final structure. A parameter study shows that these parameters must be set based on the type of data under analysis. Experimentation with woven string kernels as rules for updating cellular automata show that having a larger population and more available colour states are correlated with an increase in performance as apoptotic one dimensional cellular automata. This thesis concludes with directions for future work related to theory and experimentation, for both uniform and non-uniform woven string kernels.

No description available.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

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No description available.

This thesis provides a framework for describing a canonical evolutionary system. Populations of individuals are envisaged as traversing a search space structured by genetic and developmental operators under the influence of selection. Selection acts on individuals' phenotypic expressions, guiding the population over an evaluation landscape, which describes an idealised evaluation surface over the phenotypic space. The corresponding valuation landscape describes evaluations over the genotypic space and may be transformed by within generation adaptive (learning) or maladaptive (fault induction) local search. Populations subjected to particular genetic and selection operators are claimed to evolve towards a region of the valuation landscape with a characteristic local ruggedness, as given by the runtime operator correlation coefficient. This corresponds to the view of evolution discovering an evolutionarily stable population, or quasi-species, held in a state of dynamic equilibrium by the operator set and evaluation function. This is demonstrated by genetic algorithm experiments using the NK landscapes and a novel, evolvable evaluation function, The Tower of Babel. In fluctuating environments of varying temporal ruggedness, different operator sets are correspondingly more or less adapted. Quantitative genetics analyses of populations in sinusoidally fluctuating conditions are shown to describe certain well known electronic filters. This observation suggests the notion of Evolutionary Signal Processing. Genetic algorithm experiments in which a population tracks a sinusoidally fluctuating optimum support this view. Using a self-adaptive mutation rate, it is possible to tune the evolutionary filter to the environmental frequency. For a time varying frequency, the mutation rate reacts accordingly. With local search, the valuation landscape is transformed through temporal smoothing. By coevolving modifier genes for individual learning and the rate at which the benefits may be directly transmitted to the next generation, the relative adaptedness of individual learning and cultural inheritance according to the rate of environmental change is demonstrated.

Thesis (Ph.D.)--University of Missouri-Columbia, 2007. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on March 23, 2009) Vita. Includes bibliographical references.

published_or_final_version / abstract / Industrial and Manufacturing Systems Engineering / Doctoral / Doctor of Philosophy

Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (leaves 160-171).

This research deals with production scheduling of manufacturing systems that predominantly consist of hybrid flowshops. Hybrid Flowshop Scheduling (HFS) problems are common in metal working industries. Their solution has significant inferences on company performance in a globally competitive market in terms of production cycle time, delivery dates, warehouse and work-in-process inventory management. HFS problems have attracted considerable research efforts on examining their scientific complexity and practical solution algorithms. In conventional HFS systems, an individual job goes through the flowshop with its own processing route, which has no influence on other jobs. However, in many metal working HFS systems, jobs have interdependent relationships during the process. This thesis focuses on addressing two classes of HFS problems with job interdependence that have been motivated by real-life industrial problems observed from our collaborating companies. The first class of HFS problems with job interdependence are faced by manufacturers of typically standard metal components where jobs are organized in families according to their machine settings and tools. Family setup times arise when a machine shifts from processing one job family to another. This problem is compounded by the challenges that the formation of job families is different in different stages and only a limited number of jobs can be processed within one setup. This class of problems is defined as HFS with family setup and inconsistent family formation. The second class of HFS problems with job interdependence is typically faced in a production process consisting of divergent operations where a single input item is converted into multiple output items. Two important challenges have been investigated. One is that one product can be produced following different process routes. The other is that the total inventory capacity is very limited in the company in the sense that the inventory spaces are commonly shared by raw materials, work-in-process items and finished products. This class of problems is defined as HFS with divergent production and common inventory. The aim is to analyze the general characteristics of HFS with job interdependence and develop effective and practical methodologies that can tackle real-world constraints and reduce the scheduling effort in daily production. This research has made the following contributions: (1) A V-A-X structural classification has been proposed to represent the divergent (V), convergent (A) and mixed (X) job interdependent relations during the production. (2) A genetic algorithm based approach and a particle swarm optimization based approach have been developed to solve two classes of HFS problems with job interdependence, respectively. The computational results based on actual production data have shown that the proposed solutions are robust, efficient and advantageous for solving the practical problems. (3) A waiting factor approach and delay timetable approach have been developed to extend the solutions space of two classes of HFS problems by inserting intentional idle times into original schedules. The computational results have indicated that better schedules can be obtained in the extended solution spaces. / published_or_final_version / Industrial and Manufacturing Systems Engineering / Doctoral / Doctor of Philosophy