Due to the vast success of bioengineering techniques, a series of large-scale analysis tools has been developed to discover the functional organization of cells. Among them, cDNA microarray has emerged as a powerful technology that enables biologists to cDNA microarray technology has enabled biologists to study thousands of genes simultaneously within an entire organism, and thus obtain a better understanding of the gene interaction and regulation mechanisms involved. Although microarray technology has been developed so as to offer high tolerances, there exists high signal irregularity through the surface of the microarray image. The imperfection in the microarray image generation process causes noises of many types, which contaminate the resulting image. These errors and noises will propagate down through, and can significantly affect, all subsequent processing and analysis. Therefore, to realize the potential of such technology it is crucial to obtain high quality image data that would indeed reflect the underlying biology in the samples. One of the key steps in extracting information from a microarray image is segmentation: identifying which pixels within an image represent which gene. This area of spotted microarray image analysis has received relatively little attention relative to the advances in proceeding analysis stages. But, the lack of advanced image analysis, including the segmentation, results in sub-optimal data being used in all downstream analysis methods. Although there is recently much research on microarray image analysis with many methods have been proposed, some methods produce better results than others. In general, the most effective approaches require considerable run time (processing) power to process an entire image. Furthermore, there has been little progress on developing sufficiently fast yet efficient and effective algorithms the segmentation of the microarray image by using a highly sophisticated framework such as Cellular Neural Networks (CNNs). It is, therefore, the aim of this thesis to investigate and develop novel methods processing microarray images. The goal is to produce results that outperform the currently available approaches in terms of PSNR, k-means and ICC measurements.

This thesis is divided into two parts. In the first part, a general problem of the robust template decomposition with restricted weights for cellular neural networks (CNNs) implementing an arbitrary Boolean function is investigated. In the second part, some primary study of the novel Wilcoxon learning machines is made. In the first part of the thesis for the robust CNN template design, the geometric margin of a linear classifier with respect to a training data set, a notion borrowed from the machine learning theory, is used to define the robustness of an uncoupled CNN implementing a linearly separable Boolean function. Consequently, the so-called maximal margin classifiers can be devised via support vector machines (SVMs) to provide the most robust template design for uncoupled CNNs implementing linearly separable Boolean functions. Some general properties of robust CNNs with or without restricted weights are discussed. Moreover, all robust CNNs with restricted weights are characterized. For an arbitrarily given Boolean function, we propose an algorithm, which is the generalized version of the well known CFC algorithm, to find a sequence of robust uncoupled CNNs implementing the given Boolean function. In the second part of the thesis, we investigate the novel Wilcoxon learning machines (WLMs). The invention of these learning machines was motivated by the Wilcoxon approach to linear regression problems in statistics. The resulting linear regressors are quits robust against outliers, as is well known in statistics. The Wilcoxon learning machines investigated in this thesis include Wilcoxon Neural Network (WNN), Wilcoxon Generalized Radial Basis Function Network (WGRBFN), Wilcoxon Fuzzy Neural Network (WFNN), and Kernel-based Wilcoxon Regressor (KWR).

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Nessa dissertação, é investigado o armazenamento e a recuperação de padrões de forma biologicamente inspirada no cérebro. Os modelos estudados consistiram de redes neurais realimentadas, que tentam modelar certos aspectos dinâmicos do funcionamento do cérebro. Em particular, atenção especial foi dada às Redes Neurais Celulares, que constituem uma versão localmente acoplada do já clássico modelo de Hopfield. Além da análise de estabilidade das redes consideradas, foi realizado um teste com o intuito de avaliar o desempenho de diversos métodos de construção de memórias endereçáveis por conteúdo (memórias associativas) em Redes Neurais Celulares. / In this dissertation we investigate biologically inspired models of pattern storage and retrieval, by means of feedback neural networks. These networks try to model some of the dynamical aspects of brain functioning. The study concentrated in Cellular Neural Networks, a local coupled version of the classical Hopfield model. The research comprised stability analysis of the referred networks, as well as performance tests of various methods for content-addressable (associative) memory design in Cellular Neural Networks.

Nessa dissertação, é investigado o armazenamento e a recuperação de padrões de forma biologicamente inspirada no cérebro. Os modelos estudados consistiram de redes neurais realimentadas, que tentam modelar certos aspectos dinâmicos do funcionamento do cérebro. Em particular, atenção especial foi dada às Redes Neurais Celulares, que constituem uma versão localmente acoplada do já clássico modelo de Hopfield. Além da análise de estabilidade das redes consideradas, foi realizado um teste com o intuito de avaliar o desempenho de diversos métodos de construção de memórias endereçáveis por conteúdo (memórias associativas) em Redes Neurais Celulares. / In this dissertation we investigate biologically inspired models of pattern storage and retrieval, by means of feedback neural networks. These networks try to model some of the dynamical aspects of brain functioning. The study concentrated in Cellular Neural Networks, a local coupled version of the classical Hopfield model. The research comprised stability analysis of the referred networks, as well as performance tests of various methods for content-addressable (associative) memory design in Cellular Neural Networks.

Els paradigmes cel·lulars, com les xarxes neuronals cel·lulars (CNN, en anglès) i els autòmats cel·lulars (CA, en anglès), són una eina excel·lent de càlcul, al ser equivalents a una màquina universal de Turing. La introducció de la màquina universal CNN (CNN-UM, en anglès) ha permès desenvolupar hardware, el nucli computacional del qual funciona segons la filosofia cel·lular; aquest hardware ha trobat aplicació en diversos camps al llarg de la darrera dècada. Malgrat això, encara hi ha moltes preguntes a obertes sobre com definir els algoritmes d'una CNN-UM i com estudiar la dinàmica dels autòmats cel·lulars. En aquesta tesis es tracten els dos problemes: primer, es demostra que es possible acotar l'espai dels algoritmes per a la CNN-UM i explorar-lo gràcies a les tècniques genètiques; i segon, s'expliquen els fonaments de l'estudi dels CA per mitjà de la dinàmica no lineal (segons la definició de Chua) i s'il·lustra com aquesta tècnica ha permès trobar resultats innovadors. / Los paradigmas celulares, como las redes neuronales celulares (CNN, eninglés) y los autómatas celulares (CA, en inglés), son una excelenteherramienta de cálculo, al ser equivalentes a una maquina universal deTuring. La introducción de la maquina universal CNN (CNN-UM, eninglés) ha permitido desarrollar hardware cuyo núcleo computacionalfunciona según la filosofía celular; dicho hardware ha encontradoaplicación en varios campos a lo largo de la ultima década. Sinembargo, hay aun muchas preguntas abiertas sobre como definir losalgoritmos de una CNN-UM y como estudiar la dinámica de los autómatascelular. En esta tesis se tratan ambos problemas: primero se demuestraque es posible acotar el espacio de los algoritmos para la CNN-UM yexplorarlo gracias a técnicas genéticas; segundo, se explican losfundamentos del estudio de los CA por medio de la dinámica no lineal(según la definición de Chua) y se ilustra como esta técnica hapermitido encontrar resultados novedosos. / Cellular paradigms, like Cellular Neural Networks (CNNs) and Cellular Automata (CA) are an excellent tool to perform computation, since they are equivalent to a Universal Turing machine. The introduction of the Cellular Neural Network - Universal Machine (CNN-UM) allowed us to develop hardware whose computational core works according to the principles of cellular paradigms; such a hardware has found application in a number of fields throughout the last decade. Nevertheless, there are still many open questions about how to define algorithms for a CNN-UM, and how to study the dynamics of Cellular Automata. In this dissertation both problems are tackled: first, we prove that it is possible to bound the space of all algorithms of CNN-UM and explore it through genetic techniques; second, we explain the fundamentals of the nonlinear perspective of CA (according to Chua's definition), and we illustrate how this technique has allowed us to find novel results.

Made available in DSpace on 2016-08-17T14:53:04Z (GMT). No. of bitstreams: 1 Werner Borges de Sampaio.pdf: 2991418 bytes, checksum: 1c3fd03c2e6ffea37ed00740d75d2ffd (MD5) Previous issue date: 2009-08-31 / Breast cancer presents high occurrence frequency among the world population and its psychological effects alter the perception of the patient s sexuality and the own personal image. Mammography is an x-ray of the mamma that allows the precocious detection of cancer, since it is capable to showing lesions in their initial stages, typically very small lesions in the order of millimeters. The processing of mammographic images has been contributing to the detection and the diagnosis of mammary nodules, being an important tool, because it reduces the degree of uncertainty of the diagnosis, providing a supplementary source of information to the specialist. This work presents a computational methodology that aids the specialist in the detection of breast masses. The first step of the methodology aims at improvement the mammographic image, which consists of removal of unwanted objects, reduction of noise and enhancement of the breast internal structures. Then, Cellular Neural Networks are used to segment areas suspected of containing masses. These regions have their shapes analyzed by geometry descriptors (eccentricity, circularity, compactness, circular disproportion and circular density) and their textures are analyzed using geostatistical functions (Ripley's K function, Moran's and Geary's indices). Support Vector Machine were trained and used to classify the candidate regions in one of the classes, masses or no-mass, with sensibility of 80.00%, specificity of 85.68%, acuracy of 84.62%, a rate of 0.84 false positive for image and 0.20 false negative for image and an area under the curve ROC of 0.827. / Câncer de mama apresenta alta freqüência de ocorrência entre a população mundial e seus efeitos psicológicos alteram a percepção da sexualidade do paciente e a própria imagem pessoal. A mamografia é uma radiografia da mama que permite a descoberta precoce de câncer, sendo capaz a mostrar lesões nas fases iniciais, tipicamente lesões muito pequenas na ordem de milímetros. O processamento de imagens mamográficas tem contribuído para a descoberta e o diagnóstico de nódulos mamários, sendo uma importante ferramenta, pois reduz o grau de incerteza do diagnóstico, provendo uma fonte adicional de informação ao especialista. Este trabalho apresenta uma metodologia computacional que ajuda o especialista na descoberta de massas mamárias. O primeiro passo da metodologia visa à melhoria da imagem da mamografia que consiste em remoção de objetos externos à mama, redução de ruídos e realce das estruturas internas da mama. Então, Redes Neurais Celulares são usadas para segmentar áreas suspeitadas de conter massas. Estas regiões têm as suas formas analisadas por descritores de geometria (excentricidade, circularidade, densidade, desproporção circular e densidade circular) e as suas texturas analisadas por funções geoestatísticas (função de K de Ripley, e os índices de Moran e Geary). Máquinas de Vetores de Suporte são treinadas para classificar as regiões candidatas em um das classes, massas ou não-massa, com sensibilidade de 80,00%, especificidade de 85,68%, acurácia de 84,62%, uma taxa de 0,84 falsos positivos por imagem e 0,20 falsos negativos por imagem e uma área sob da curva ROC de 0,870.