Aspects of algorithms and dynamics of cellular paradigms

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

Microarray image processing: A novel neural network framework

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.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.Aleppo University, Syri

Microarray image processing : a novel neural network framework

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.EThOS - Electronic Theses Online ServiceAleppo University, SyriaGBUnited Kingdo