Evolutionary approaches for feature selection in biological data

Data mining techniques have been used widely in many areas such as business, science, engineering and medicine. The techniques allow a vast amount of data to be explored in order to extract useful information from the data. One of the foci in the health area is finding interesting biomarkers from biomedical data. Mass throughput data generated from microarrays and mass spectrometry from biological samples are high dimensional and is small in sample size. Examples include DNA microarray datasets with up to 500,000 genes and mass spectrometry data with 300,000 m/z values. While the availability of such datasets can aid in the development of techniques/drugs to improve diagnosis and treatment of diseases, a major challenge involves its analysis to extract useful and meaningful information. The aims of this project are: 1) to investigate and develop feature selection algorithms that incorporate various evolutionary strategies, 2) using the developed algorithms to find the “most relevant” biomarkers contained in biological datasets and 3) and evaluate the goodness of extracted feature subsets for relevance (examined in terms of existing biomedical domain knowledge and from classification accuracy obtained using different classifiers). The project aims to generate good predictive models for classifying diseased samples from control

Contribución a la Aplicación de Técnicas de Inteligencia Artificial para el diseño efectivo de Sistemas Adaptativos de Aprendizaje Competitivo

El objetivo principal de esta tesis consiste en la propuesta y validación de métodos basados en técnicas de Inteligencia Artificial para la estimación del nivel de dificultad de los desafíos propuestos en el entorno On-line de Aprendizaje Competitivo QUESTTOURnament, que permita el posterior establecimiento de concursos o itinerarios de aprendizaje para grupos de alumnos según su nivel de conocimiento. QUESTOURnament es una herramienta telemática que permite el desarrollo de concursos on-line. Mediante estudios de estado de arte de sistemas de aprendizaje competitivo y de sistemas de aprendizaje adaptativos se han identificado las características de estos últimos que permitirían potenciar las ventajas e inconvenientes que presentan los sistemas competitivos y, en concreto, el sistema QUESTOURnament. Así, se propone el sistema QUESTOURnament adaptativo y se diseña y valida una solución basada en algoritmos genéticos y lógica difusa que permite estimar el nivel de dificultad de las preguntas en QUESTOURnament.Departamento de Teoría de la Señal y Comunicaciones e Ingeniería Telemátic

Hybrid Optimisation Algorithms for Two-Objective Design of Water Distribution Systems

Multi-objective design or extended design of Water Distribution Systems (WDSs) has received more attention in recent years. It is of particular interest for obtaining the trade-offs between cost and hydraulic benefit to support the decision-making process. The design problem is usually formulated as a multi-objective optimisation problem, featuring a huge search space associated with a great number of constraints. Multi-objective evolutionary algorithms (MOEAs) are popular tools for addressing this kind of problem because they are capable of approximating the Pareto-optimal front effectively in a single run. However, these methods are often held by the “No Free Lunch” theorem (Wolpert and Macready 1997) that there is no guarantee that they can perform well on a wide range of cases. To overcome this drawback, many hybrid optimisation methods have been proposed to take advantage of multiple search mechanisms which can synergistically facilitate optimisation. In this thesis, a novel hybrid algorithm, called Genetically Adaptive Leaping Algorithm for approXimation and diversitY (GALAXY), is proposed. It is a dedicated optimiser for solving the discrete two-objective design or extended design of WDSs, minimising the total cost and maximising the network resilience, which is a surrogate indicator of hydraulic benefit. GALAXY is developed using the general framework of MOEAs with substantial improvements and modifications tailored for WDS design. It features a generational framework, a hybrid use of the traditional Pareto-dominance and the epsilon-dominance concepts, an integer coding scheme, and six search operators organised in a high-level teamwork hybrid paradigm. In addition, several important strategies are implemented within GALAXY, including the genetically adaptive strategy, the global information sharing strategy, the duplicates handling strategy and the hybrid replacement strategy. One great advantage of GALAXY over other state-of-the-art MOEAs lies in the fact that it eliminates all the individual parameters of search operators, thus providing an effective and efficient tool to researchers and practitioners alike for dealing with real-world cases. To verify the capability of GALAXY, an archive of benchmark problems of WDS design collected from the literature is first established, ranging from small to large cases. GALAXY has been applied to solve these benchmark design problems and its achievements in terms of both ultimate and dynamic performances are compared with those obtained by two state-of-the-art hybrid algorithms and two baseline MOEAs. GALAXY generally outperforms these MOEAs according to various numerical indicators and a graphical comparison tool. For the largest problem considered in this thesis, GALAXY does not perform as well as its competitors due to the limited computational budget in terms of number of function evaluations. All the algorithms have also been applied to solve the challenging Anytown rehabilitation problem, which considers both the design and operation of a system from the extended period simulation perspective. The performance of each algorithm is sensitive to the quality of the initial population and the random seed used. GALAXY and the Pareto-dominance based MOEAs are superior to the epsilon-dominance based methods; however, there is a tie between GALAXY and the Pareto-dominance based approaches. At the end, a summary of this thesis is provided and relevant conclusions are drawn. Recommendations for future research work are also made

Computational complexity of evolutionary algorithms, hybridizations, and swarm intelligence

Bio-inspired randomized search heuristics such as evolutionary algorithms, hybridizations with local search, and swarm intelligence are very popular among practitioners as they can be applied in case the problem is not well understood or when there is not enough knowledge, time, or expertise to design problem-specific algorithms. Evolutionary algorithms simulate the natural evolution of species by iteratively applying evolutionary operators such as mutation, recombination, and selection to a set of solutions for a given problem. A recent trend is to hybridize evolutionary algorithms with local search to refine newly constructed solutions by hill climbing. Swarm intelligence comprises ant colony optimization as well as particle swarm optimization. These modern search paradigms rely on the collective intelligence of many single agents to find good solutions for the problem at hand. Many empirical studies demonstrate the usefulness of these heuristics for a large variety of problems, but a thorough understanding is still far away. We regard these algorithms from the perspective of theoretical computer science and analyze the random time these heuristics need to optimize pseudo-Boolean problems. This is done in a mathematically rigorous sense, using tools known from the analysis of randomized algorithms, and it leads to asymptotic bounds on their computational complexity. This approach has been followed successfully for evolutionary algorithms, but the theory of hybrid algorithms and swarm intelligence is still in its very infancy. Our results shed light on the asymptotic performance of these heuristics, increase our understanding of their dynamic behavior, and contribute to a rigorous theoretical foundation of randomized search heuristics