The application of artificial intelligence techniques to a sequencing problem in the biological domain

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Nature-inspired algorithms for solving some hard numerical problems

Optimisation is a branch of mathematics that was developed to find the optimal solutions, among all the possible ones, for a given problem. Applications of optimisation techniques are currently employed in engineering, computing, and industrial problems. Therefore, optimisation is a very active research area, leading to the publication of a large number of methods to solve specific problems to its optimality. This dissertation focuses on the adaptation of two nature inspired algorithms that, based on optimisation techniques, are able to compute approximations for zeros of polynomials and roots of non-linear equations and systems of non-linear equations. Although many iterative methods for finding all the roots of a given function already exist, they usually require: (a) repeated deflations, that can lead to very inaccurate results due to the problem of accumulating rounding errors, (b) good initial approximations to the roots for the algorithm converge, or (c) the computation of first or second order derivatives, which besides being computationally intensive, it is not always possible. The drawbacks previously mentioned served as motivation for the use of Particle Swarm Optimisation (PSO) and Artificial Neural Networks (ANNs) for root-finding, since they are known, respectively, for their ability to explore high-dimensional spaces (not requiring good initial approximations) and for their capability to model complex problems. Besides that, both methods do not need repeated deflations, nor derivative information. The algorithms were described throughout this document and tested using a test suite of hard numerical problems in science and engineering. Results, in turn, were compared with several results available on the literature and with the well-known Durand–Kerner method, depicting that both algorithms are effective to solve the numerical problems considered.A Optimização é um ramo da matemática desenvolvido para encontrar as soluções óptimas, de entre todas as possíveis, para um determinado problema. Actualmente, são várias as técnicas de optimização aplicadas a problemas de engenharia, de informática e da indústria. Dada a grande panóplia de aplicações, existem inúmeros trabalhos publicados que propõem métodos para resolver, de forma óptima, problemas específicos. Esta dissertação foca-se na adaptação de dois algoritmos inspirados na natureza que, tendo como base técnicas de optimização, são capazes de calcular aproximações para zeros de polinómios e raízes de equações não lineares e sistemas de equações não lineares. Embora já existam muitos métodos iterativos para encontrar todas as raízes ou zeros de uma função, eles usualmente exigem: (a) deflações repetidas, que podem levar a resultados muito inexactos, devido ao problema da acumulação de erros de arredondamento a cada iteração; (b) boas aproximações iniciais para as raízes para o algoritmo convergir, ou (c) o cálculo de derivadas de primeira ou de segunda ordem que, além de ser computacionalmente intensivo, para muitas funções é impossível de se calcular. Estas desvantagens motivaram o uso da Optimização por Enxame de Partículas (PSO) e de Redes Neurais Artificiais (RNAs) para o cálculo de raízes. Estas técnicas são conhecidas, respectivamente, pela sua capacidade de explorar espaços de dimensão superior (não exigindo boas aproximações iniciais) e pela sua capacidade de modelar problemas complexos. Além disto, tais técnicas não necessitam de deflações repetidas, nem do cálculo de derivadas. Ao longo deste documento, os algoritmos são descritos e testados, usando um conjunto de problemas numéricos com aplicações nas ciências e na engenharia. Os resultados foram comparados com outros disponíveis na literatura e com o método de Durand–Kerner, e sugerem que ambos os algoritmos são capazes de resolver os problemas numéricos considerados

Birds and people in towns and cities : an exploration of human-bird relations in urban areas

Urban nature conservation and sustainability discourses regularly state a desire to bring more ‘nature’ and wildlife into towns and cities - for the perceived good of both people and wildlife. Yet many wildlife species that already live in urban areas are often seen as undesirable by people, and are caught up in the parallel discourses and practices of pest control. This partial disparity between the types of wildlife successfully inhabiting urban areas and the types that, put simplistically, different people want or don’t want in urban areas is further complicated by the heterogeneity of humans, nonhumans, ideas, practices and space-times that co-constitute the character of, and the uneven geographies of, different human-wildlife relations in urban areas. This heterogeneity, and these uneven relations, creates practical and ethical issues, not only for those directly involved in policy and management, but also for the constitution and potential implementation of a diverse body of social science theory that is concerned with developing an expanded political collective and fostering better relations between humans and nonhumans.In light of these issues, this thesis has examined and compared the specific constitution of particular, different, and uneven human-wildlife relations in urban areas in the cases of different bird species, with a particular focus on the built environment. It has subsequently considered the problems and opportunities that arise in seeking better relations. Using an approach derived from relational thinking, the contingent knowledges/ideas, practices, and human and nonhuman agencies involved in these relations have been assessed, revealing how diverse human-bird relations, and certain urban-space times, are produced. In spite of the problems that the heterogeneity and complexity of these relations presents for living with wildlife in urban areas, this thesis concludes that creatively experimenting with the form and practice of diverse urban landscapes offers opportunities for better relations

Birds and people in towns and cities : an exploration of human-bird relations in urban areas

Urban nature conservation and sustainability discourses regularly state a desire to bring more ‘nature’ and wildlife into towns and cities - for the perceived good of both people and wildlife. Yet many wildlife species that already live in urban areas are often seen as undesirable by people, and are caught up in the parallel discourses and practices of pest control. This partial disparity between the types of wildlife successfully inhabiting urban areas and the types that, put simplistically, different people want or don’t want in urban areas is further complicated by the heterogeneity of humans, nonhumans, ideas, practices and space-times that co-constitute the character of, and the uneven geographies of, different human-wildlife relations in urban areas. This heterogeneity, and these uneven relations, creates practical and ethical issues, not only for those directly involved in policy and management, but also for the constitution and potential implementation of a diverse body of social science theory that is concerned with developing an expanded political collective and fostering better relations between humans and nonhumans. In light of these issues, this thesis has examined and compared the specific constitution of particular, different, and uneven human-wildlife relations in urban areas in the cases of different bird species, with a particular focus on the built environment. It has subsequently considered the problems and opportunities that arise in seeking better relations. Using an approach derived from relational thinking, the contingent knowledges/ideas, practices, and human and nonhuman agencies involved in these relations have been assessed, revealing how diverse human-bird relations, and certain urban-space times, are produced. In spite of the problems that the heterogeneity and complexity of these relations presents for living with wildlife in urban areas, this thesis concludes that creatively experimenting with the form and practice of diverse urban landscapes offers opportunities for better relations