8 research outputs found

    A multi-view approach to cDNA micro-array analysis

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    The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

    Aspects of algorithms and dynamics of cellular paradigms

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    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

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    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

    Split and Shift Methodology: Overcoming Hardware Limitations on Cellular Processor Arrays for Image Processing

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    Na era multimedia, o procesado de imaxe converteuse nun elemento de singular importancia nos dispositivos electrónicos. Dende as comunicacións (p.e. telemedicina), a seguranza (p.e. recoñecemento retiniano) ou control de calidade e de procesos industriais (p.e. orientación de brazos articulados, detección de defectos do produto), pasando pola investigación (p.e. seguimento de partículas elementais) e diagnose médica (p.e. detección de células estrañas, identificaciónn de veas retinianas), hai un sinfín de aplicacións onde o tratamento e interpretación automáticas de imaxe e fundamental. O obxectivo último será o deseño de sistemas de visión con capacidade de decisión. As tendencias actuais requiren, ademais, a combinación destas capacidades en dispositivos pequenos e portátiles con resposta en tempo real. Isto propón novos desafíos tanto no deseño hardware como software para o procesado de imaxe, buscando novas estruturas ou arquitecturas coa menor area e consumo de enerxía posibles sen comprometer a funcionalidade e o rendemento

    Reservoir Computing: computation with dynamical systems

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    In het onderzoeksgebied Machine Learning worden systemen onderzocht die kunnen leren op basis van voorbeelden. Binnen dit onderzoeksgebied zijn de recurrente neurale netwerken een belangrijke deelgroep. Deze netwerken zijn abstracte modellen van de werking van delen van de hersenen. Zij zijn in staat om zeer complexe temporele problemen op te lossen maar zijn over het algemeen zeer moeilijk om te trainen. Recentelijk zijn een aantal gelijkaardige methodes voorgesteld die dit trainingsprobleem elimineren. Deze methodes worden aangeduid met de naam Reservoir Computing. Reservoir Computing combineert de indrukwekkende rekenkracht van recurrente neurale netwerken met een eenvoudige trainingsmethode. Bovendien blijkt dat deze trainingsmethoden niet beperkt zijn tot neurale netwerken, maar kunnen toegepast worden op generieke dynamische systemen. Waarom deze systemen goed werken en welke eigenschappen bepalend zijn voor de prestatie is evenwel nog niet duidelijk. Voor dit proefschrift is onderzoek gedaan naar de dynamische eigenschappen van generieke Reservoir Computing systemen. Zo is experimenteel aangetoond dat de idee van Reservoir Computing ook toepasbaar is op niet-neurale netwerken van dynamische knopen. Verder is een maat voorgesteld die gebruikt kan worden om het dynamisch regime van een reservoir te meten. Tenslotte is een adaptatieregel geïntroduceerd die voor een breed scala reservoirtypes de dynamica van het reservoir kan afregelen tot het gewenste dynamisch regime. De technieken beschreven in dit proefschrift zijn gedemonstreerd op verschillende academische en ingenieurstoepassingen

    Graphical and Topological Analysis of the Cell Nucleus

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    It is well known that our genetic material influences our tendency to develop certain conditions. Finding the causes behind these predispositions assumes the understanding of mechanisms handling and maintaining the genome. While the problem is important from the biological point of view, being one of the basic riddles of life, it also poses interesting questions which may only be answered by physics. Topics include transport, reaction-diffusion, polymer physics, equilibrium and non-equilibrium dynamics and chaos, amongst others. Experimental techniques, like microscopy or molecular biology approaches provide an ever improving insight in the structure of the nucleus, however, computational and modelling approaches are still needed to explain unknown aspects of genetics. % Evidence is accumulating that our genetic material not only influences our resemblance to relatives and the chances that we may have a tendency to develop certain diseases, but also our predisposition to contract viral infections or to develop conditions like depression, obesity or substance dependence. It has become clear that understanding how the genetic material is organized and how it is being handled might be the key to revolutionize medicine. Experimental techniques, like microscopy or molecular biology approaches provide an ever improving insight in the structure of the nucleus, however, computational and modelling approaches are still needed to explain unknown aspects of genetics. In this thesis we tackle the problem of understanding the structure of the nucleus from the two opposite sides of the experimental ``blind-spot''. We develop alternative image modelling and analysis tools which are able to capture and recreate the ``large scale'' density patterns observed in confocal microscopy images of the nucleus. For this, we introduce a generalized Potts model which is extensively analysed also from the statistical mechanics point of view. Furthermore, we apply statistical mechanics and graph theory calculations to study patterns registered with super resolution microscopy techniques. We investigate the effect of irradiation and light stress on the structure of the chromatin, and are able to quantitatively support prior experimental observations regarding structural changes. Understanding the interaction and classification of proteins, structures which perform vastly different functions on molecular scales, is also important to achieve the final picture. We contribute to this by elaborating a framework to assess topological similarity among these chemicals. Our approach is based on recently developed computational topology algorithms used to calculate fingerprints of the molecules. We discuss three different modifications of the framework and investigate them on real-world datasets. In addition, we recognize that the mentioned fingerprints can be used to calculate the fractal dimension of certain objects, and offer an intuitive explanation for the observed relation
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