994 resultados para natural computing


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Image segmentation is one of the image processing problems that deserves special attention from the scientific community. This work studies unsupervised methods to clustering and pattern recognition applicable to medical image segmentation. Natural Computing based methods have shown very attractive in such tasks and are studied here as a way to verify it's applicability in medical image segmentation. This work treats to implement the following methods: GKA (Genetic K-means Algorithm), GFCMA (Genetic FCM Algorithm), PSOKA (PSO and K-means based Clustering Algorithm) and PSOFCM (PSO and FCM based Clustering Algorithm). Besides, as a way to evaluate the results given by the algorithms, clustering validity indexes are used as quantitative measure. Visual and qualitative evaluations are realized also, mainly using data given by the BrainWeb brain simulator as ground truth

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We are indebted with Marnix Medema, Paul Straight and Sean Rovito, for useful discussions and critical reading of the manuscript, as well as with Alicia Chagolla and Yolanda Rodriguez of the MS Service of Unidad Irapuato, Cinvestav, and Araceli Fernandez for technical support in high-performance computing. This work was funded by Conacyt Mexico (grants No. 179290 and 177568) and FINNOVA Mexico (grant No. 214716) to FBG. PCM was funded by Conacyt scholarship (No. 28830) and a Cinvestav posdoctoral fellowship. JF and JFK acknowledge funding from the College of Physical Sciences, University of Aberdeen, UK.

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Acknowledgements The authors thank the children, their parents and school staff, who participated in this research, and who so willingly gave us their time, help and support. They also thank Steven Knox and Alan Clelland for their work on programming the mobile phone application. Additional thanks to DynaVox Inc. for supplying the Vmax communication devices to run our system on and Sensory Software Ltd for supplying us with their AAC software. This research was supported by the Research Council UKs Digittal Economy Programme and EPSRC (Grant numbers EP/F067151/1, EP/F066880/1, EP/E011764/1, EP/H022376/1, and EP/H022570 /1).

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Acknowledgements The work of Klaus Nordhausen was supported by the Academy of Finland (grant 268703). Oleksii Pokotylo is supported by the Cologne Graduate School of Management, Economics and Social Sciences. The work of Daniel Vogel was supported by the DFG collaborate research grant SFB 823

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This work was supported by the Spanish Ministry for Economy and Competitiveness (grant TIN2014-56633-C3-1-R) and by the European Regional Development Fund (ERDF/FEDER) and the Galician Ministry of Education (grants GRC2014/030 and CN2012/151). Alejandro Ramos-Soto is supported by the Spanish Ministry for Economy and Competitiveness (FPI Fellowship Program) under grant BES-2012-051878.

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Acknowledgments This work was supported by grants from the European Commission within its FP7 Programme, under the thematic area KBBE.2012.3.2-01 with Grant Number Nos. 311932 SeaBioTech, 311848 BlueGenics, and 312184 PharmaSea.

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The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

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La computacin evolutiva y muy especialmente los algoritmos genticos son cada vez ms empleados en las organizaciones para resolver sus problemas de gestin y toma de decisiones (Apoteker & Barthelemy, 2000). La literatura al respecto es creciente y algunos estados del arte han sido publicados. A pesar de esto, no hay un trabajo explcito que evale de forma sistemtica el uso de los algoritmos genticos en problemas especficos de los negocios internacionales (ejemplos de ello son la logstica internacional, el comercio internacional, el mercadeo internacional, las finanzas internacionales o estrategia internacional). El propsito de este trabajo de grado es, por lo tanto, realizar un estado situacional de las aplicaciones de los algoritmos genticos en los negocios internacionales.

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This paper is concerned with the computational efficiency of fuzzy clustering algorithms when the data set to be clustered is described by a proximity matrix only (relational data) and the number of clusters must be automatically estimated from such data. A fuzzy variant of an evolutionary algorithm for relational clustering is derived and compared against two systematic (pseudo-exhaustive) approaches that can also be used to automatically estimate the number of fuzzy clusters in relational data. An extensive collection of experiments involving 18 artificial and two real data sets is reported and analyzed. (C) 2011 Elsevier B.V. All rights reserved.

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Este artigo apresenta uma breve reviso de alguns dos mais recentes mtodos bioinspirados baseados no comportamento de populaes para o desenvolvimento de tcnicas de soluo de problemas. As metaheursticas tratadas aqui correspondem s estratgias de otimizao por colnia de formigas, otimizao por enxame de partculas, algoritmo shuffled frog-leaping, coleta de alimentos por bactrias e colnia de abelhas. Os princpios biolgicos que motivaram o desenvolvimento de cada uma dessas estratgias, assim como seus respectivos algoritmos computacionais, so introduzidos. Duas aplicaes diferentes foram conduzidas para exemplificar o desempenho de tais algoritmos. A finalidade enfatizar perspectivas de aplicao destas abordagens em diferentes problemas da rea de engenharia.

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Em muitos problemas de otimizao h dificuldades em alcanar um resultado timo ou mesmo um resultado prximo ao valor timo em um tempo vivel, principalmente quando se trabalha em grande escala. Por isso muitos desses problemas so abordados por heursticas ou metaheursticas que executam buscas por melhores solues dentro do espao de busca definido. Dentro da computao natural esto os Algoritmos Culturais e os Algoritmos Genticos, que so considerados metaheursticas evolutivas que se complementam devido ao mecanismo dual de herana cultura/gentica. A proposta do presente trabalho estudar e utilizar tais mecanismos acrescentando tanto heursticas de busca local como multipopulaes aplicados em problemas de otimizao combinatria (caixeiro viajante e mochila), funes multimodais e em problemas restritos. Sero executados alguns experimentos para efetuar uma avaliao em relao ao desempenho desses mecanismos hbridos e multipopulacionais com outros mecanismos dispostos na literatura de acordo com cada problema de otimizao aqui abordado.

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Con el surgir de los problemas irresolubles de forma eficiente en tiempo polinomial en base al dato de entrada, surge la Computacin Natural como alternativa a la computacin clsica. En esta disciplina se trata de o bien utilizar la naturaleza como base de cmputo o bien, simular su comportamiento para obtener mejores soluciones a los problemas que los encontrados por la computacin clsica. Dentro de la computacin natural, y como una representacin a nivel celular, surge la Computacin con Membranas. La primera abstraccin de las membranas que se encuentran en las clulas, da como resultado los P sistemas de transicin. Estos sistemas, que podran ser implementados en medios biolgicos o electrnicos, son la base de estudio de esta Tesis. En primer lugar, se estudian las implementaciones que se han realizado, con el fin de centrarse en las implementaciones distribuidas, que son las que pueden aprovechar las caractersticas intrnsecas de paralelismo y no determinismo. Tras un correcto estudio del estado actual de las distintas etapas que engloban a la evolucin del sistema, se concluye con que las distribuciones que buscan un equilibrio entre las dos etapas (aplicacin y comunicacin), son las que mejores resultados presentan. Para definir estas distribuciones, es necesario definir completamente el sistema, y cada una de las partes que influyen en su transicin. Adems de los trabajos de otros investigadores, y junto a ellos, se realizan variaciones a los proxies y arquitecturas de distribucin, para tener completamente definidos el comportamiento dinmico de los P sistemas. A partir del conocimiento esttico configuracin inicial del P sistema, se pueden realizar distribuciones de membranas en los procesadores de un clster para obtener buenos tiempos de evolucin, con el fin de que la computacin del P sistema sea realizada en el menor tiempo posible. Para realizar estas distribuciones, hay que tener presente las arquitecturas o forma de conexin de los procesadores del clster. La existencia de 4 arquitecturas, hace que el proceso de distribucin sea dependiente de la arquitectura a utilizar, y por tanto, aunque con significativas semejanzas, los algoritmos de distribucin deben ser realizados tambin 4 veces. Aunque los propulsores de las arquitecturas han estudiado el tiempo ptimo de cada arquitectura, la inexistencia de distribuciones para estas arquitecturas ha llevado a que en esta Tesis se probaran las 4, hasta que sea posible determinar que en la prctica, ocurre lo mismo que en los estudios tericos. Para realizar la distribucin, no existe ningn algoritmo determinista que consiga una distribucin que satisfaga las necesidades de la arquitectura para cualquier P sistema. Por ello, debido a la complejidad de dicho problema, se propone el uso de metaheursticas de Computacin Natural. En primer lugar, se propone utilizar Algoritmos Genticos, ya que es posible realizar alguna distribucin, y basada en la premisa de que con la evolucin, los individuos mejoran, con la evolucin de dichos algoritmos, las distribuciones tambin mejorarn obtenindose tiempos cercanos al ptimo terico. Para las arquitecturas que preservan la topologa arbrea del P sistema, han sido necesarias realizar nuevas representaciones, y nuevos algoritmos de cruzamiento y mutacin. A partir de un estudio ms detallado de las membranas y las comunicaciones entre procesadores, se ha comprobado que los tiempos totales que se han utilizado para la distribucin pueden ser mejorados e individualizados para cada membrana. As, se han probado los mismos algoritmos, obteniendo otras distribuciones que mejoran los tiempos. De igual forma, se han planteado el uso de Optimizacin por Enjambres de Partculas y Evolucin Gramatical con reescritura de gramticas (variante de Evolucin Gramatical que se presenta en esta Tesis), para resolver el mismo cometido, obteniendo otro tipo de distribuciones, y pudiendo realizar una comparativa de las arquitecturas. Por ltimo, el uso de estimadores para el tiempo de aplicacin y comunicacin, y las variaciones en la topologa de rbol de membranas que pueden producirse de forma no determinista con la evolucin del P sistema, hace que se deba de monitorizar el mismo, y en caso necesario, realizar redistribuciones de membranas en procesadores, para seguir obteniendo tiempos de evolucin razonables. Se explica, cmo, cundo y dnde se deben realizar estas modificaciones y redistribuciones; y cmo es posible realizar este reclculo. Abstract Natural Computing is becoming a useful alternative to classical computational models since it its able to solve, in an efficient way, hard problems in polynomial time. This discipline is based on biological behaviour of living organisms, using nature as a basis of computation or simulating nature behaviour to obtain better solutions to problems solved by the classical computational models. Membrane Computing is a sub discipline of Natural Computing in which only the cellular representation and behaviour of nature is taken into account. Transition P Systems are the first abstract representation of membranes belonging to cells. These systems, which can be implemented in biological organisms or in electronic devices, are the main topic studied in this thesis. Implementations developed in this field so far have been studied, just to focus on distributed implementations. Such distributions are really important since they can exploit the intrinsic parallelism and non-determinism behaviour of living cells, only membranes in this case study. After a detailed survey of the current state of the art of membranes evolution and proposed algorithms, this work concludes that best results are obtained using an equal assignment of communication and rules application inside the Transition P System architecture. In order to define such optimal distribution, it is necessary to fully define the system, and each one of the elements that influence in its transition. Some changes have been made in the work of other authors: load distribution architectures, proxies definition, etc., in order to completely define the dynamic behaviour of the Transition P System. Starting from the static representation initial configuration of the Transition P System, distributions of membranes in several physical processors of a cluster is algorithmically done in order to get a better performance of evolution so that the computational complexity of the Transition P System is done in less time as possible. To build these distributions, the cluster architecture or connection links must be considered. The existence of 4 architectures, makes that the process of distribution depends on the chosen architecture, and therefore, although with significant similarities, the distribution algorithms must be implemented 4 times. Authors who proposed such architectures have studied the optimal time of each one. The non existence of membrane distributions for these architectures has led us to implement a dynamic distribution for the 4. Simulations performed in this work fix with the theoretical studies. There is not any deterministic algorithm that gets a distribution that meets the needs of the architecture for any Transition P System. Therefore, due to the complexity of the problem, the use of meta-heuristics of Natural Computing is proposed. First, Genetic Algorithm heuristic is proposed since it is possible to make a distribution based on the premise that along with evolution the individuals improve, and with the improvement of these individuals, also distributions enhance, obtaining complexity times close to theoretical optimum time. For architectures that preserve the tree topology of the Transition P System, it has been necessary to make new representations of individuals and new algorithms of crossover and mutation operations. From a more detailed study of the membranes and the communications among processors, it has been proof that the total time used for the distribution can be improved and individualized for each membrane. Thus, the same algorithms have been tested, obtaining other distributions that improve the complexity time. In the same way, using Particle Swarm Optimization and Grammatical Evolution by rewriting grammars (Grammatical Evolution variant presented in this thesis), to solve the same distribution task. New types of distributions have been obtained, and a comparison of such genetic and particle architectures has been done. Finally, the use of estimators for the time of rules application and communication, and variations in tree topology of membranes that can occur in a non-deterministic way with evolution of the Transition P System, has been done to monitor the system, and if necessary, perform a membrane redistribution on processors to obtain reasonable evolution time. How, when and where to make these changes and redistributions, and how it can perform this recalculation, is explained.

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Membrane computing is a recent area that belongs to natural computing. This field works on computational models based on nature's behavior to process the information. Recently, numerous models have been developed and implemented with this purpose. P-systems are the structures which have been defined,developed and implemented to simulate the behavior and the evolution of membrane systems which we find in nature. What we show in this paper is a new model that deals with encrypted information which provides security the membrane systems communication. Moreover we find non deterministic and random applications in nature that are suitable to MEIA systems. The inherent parallelism and non determinism make this applications perfect object to implement MEIA systems.

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La caracterstica fundamental de la Computacin Natural se basa en el empleo de conceptos, principios y mecanismos del funcionamiento de la Naturaleza. La Computacin Natural -y dentro de sta, la Computacin de Membranas- surge como una posible alternativa a la computacin clsica y como resultado de la bsqueda de nuevos modelos de computacin que puedan superar las limitaciones presentes en los modelos convencionales. En concreto, la Computacin de Membranas se origin como un intento de formular un nuevo modelo computacional inspirado en la estructura y el funcionamiento de las clulas biolgicas: los sistemas basados en este modelo constan de una estructura de membranas que actan a la vez como separadores y como canales de comunicacin, y dentro de esa estructura se alojan multiconjuntos de objetos que evolucionan de acuerdo a unas determinadas reglas de evolucin. Al conjunto de dispositivos contemplados por la Computacin de Membranas se les denomina genricamente como Sistemas P. Hasta el momento los Sistemas P slo han sido estudiados a nivel terico y no han sido plenamente implementados ni en medios electrnicos, ni en medios bioqumicos, slo han sido simulados o parcialmente implementados. Por tanto, la implantacin de estos sistemas es un reto de investigacin abierto. Esta tesis aborda uno de los problemas que debe ser resuelto para conseguir la implantacin de los Sistemas P sobre plataformas hardware. El problema concreto se centra en el modelo de los Sistemas P de Transicin y surge de la necesidad de disponer de algoritmos de aplicacin de reglas que, independientemente de la plataforma hardware sobre la que se implementen, cumplan los requisitos de ser no deterministas, masivamente paralelos y adems su tiempo de ejecucin est estticamente acotado. Como resultado se ha obtenido un conjunto de algoritmos (tanto para plataformas secuenciales, como para plataformas paralelas) que se adecan a las diferentes configuraciones de los Sistemas P. ABSTRACT The main feature of Natural Computing is the use of concepts, principles and mechanisms inspired by Nature. Natural Computing and within it, Membrane Computing emerges as an potential alternative to conventional computing and as from the search for new models of computation that may overcome the existing limitations in conventional models. Specifically, Membrane Computing was created to formulate a new computational paradigm inspired by the structure and functioning of biological cells: it consists of a membrane structure, which acts as separators as well as communication channels, and within this structure are stored multisets of objects that evolve according to certain evolution rules. The set of computing devices addressed by Membrane Computing are generically known P systems. Up to now, no P systems have been fully implemented yet in electronic or biochemical means. They only have been studied in theory, simulated or partially implemented. Therefore, the implementation of these systems is an open research challenge. This thesis addresses one of the problems to be solved in order to deploy P systems on hardware platforms. This specific problem is focused on the Transition P System model and emerges from the need of providing application rules algorithms that independently on the hardware platform on which they are implemented, meets the requirements of being nondeterministic, massively parallel and runtime-bounded. As a result, this thesis has developed a set of algorithms for both platforms, sequential and parallel, adapted to all possible configurations of P systems.

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La computacin con membranas surge como una alternativa a la computacin tradicional. Dentro de este campo se sitan los denominados Sistemas P de Transicin que se basan en la existencia de regiones que contienen recursos y reglas que hacen evolucionar a dichos recursos para poder llevar a cada una de las regiones a una nueva situacin denominada configuracin. La sucesin de las diferentes configuraciones conforman la computacin. En este campo, el Grupo de Computacin Natural de la Universidad Politcnica de Madrid lleva a cabo numerosas investigaciones al amparo de las cuales se han publicado numerosos artculos y realizado varias tesis doctorales. Las principales vas de investigacin han sido, hasta el momento, el estudio del modelo terico sobre el que se definen los Sistemas P, el estudio de los algoritmos que se utilizan para la aplicacin de las reglas de evolucin en las regiones, el diseo de nuevas arquitecturas que mejoren las comunicaciones entre las diferentes membranas (regiones) que componen el sistema y la implantacin de estos sistemas en dispositivos hardware que pudiesen definir futuras mquinas basadas en este modelo. Dentro de este ltimo campo, es decir, dentro del objetivo de construir finalmente mquinas que puedan llevar a cabo la funcionalidad de la computacin con Sistemas P, la presente tesis doctoral se centra en el diseo de dos procesadores paralelos que, aplicando variantes de algoritmos existentes, favorezcan el crecimiento en el nivel de intra-paralelismo a la hora de aplicar las reglas. El diseo y creacin de ambos procesadores presentan novedosas aportaciones al entorno de investigacin de los Sistemas P de Transicin en tanto en cuanto se utilizan conceptos que aunque previamente definidos de manera terica, no haban sido introducidos en el hardware diseado para estos sistemas. As, los dos procesadores mantienen las siguientes caractersticas: - Presentan un alto rendimiento en la fase de aplicacin de reglas, manteniendo por otro lado una flexibilidad y escalabilidad medias que son dependientes de la tecnologa final sobre la que se sinteticen dichos procesadores. - Presentan un alto nivel de intra-paralelismo en las regiones al permitir la aplicacin simultnea de reglas. - Tienen carcter universal en tanto en cuanto no depende del carcter de las reglas que componen el Sistema P. - Tienen un comportamiento indeterminista que es inherente a la propia naturaleza de estos sistemas. El primero de los circuitos utiliza el conjunto potencia del conjunto de reglas de aplicacin as como el concepto de mxima aplicabilidad para favorecer el intra-paralelismo y el segundo incluye, adems, el concepto de dominio de aplicabilidad para determinar el conjunto de reglas que son aplicables en cada momento con los recursos existentes. Ambos procesadores se disean y se prueban mediante herramientas de diseo electrnico y se preparan para ser sintetizados sobre FPGAs. ABSTRACT Membrane computing appears as an alternative to traditional computing. P Systems are placed inside this field and they are based upon the existence of regions called membranes that contain resources and rules that describe how the resources may vary to take each of these regions to a new situation called "configuration". Successive configurations conform computation. Inside this field, the Natural Computing Group of the Universidad Politcnica of Madrid develops a large number of works and researches that provide a lot of papers and some doctoral theses. Main research lines have been, by the moment, the study of the theoretical model over which Transition P Systems are defined, the study of the algorithms that are used for the evolution rules application in the regions, the design of new architectures that may improve communication among the different membranes (regions) that compose the whole system and the implementation of such systems over hardware devices that may define machines based upon this new model. Within this last research field, this is, within the objective of finally building machines that may accomplish the functionality of computation with P Systems, the present thesis is centered on the design of two parallel processors that, applying several variants of some known algorithms, improve the level of the internal parallelism at the evolution rule application phase. Design and creation of both processors present innovations to the field of Transition P Systems research because they use concepts that, even being known before, were never used for circuits that implement the applying phase of evolution rules. So, both processors present the following characteristics: - They present a very high performance during the application rule phase, keeping, on the other hand, a level of flexibility and scalability that, even known it is not very high, it seems to be acceptable. - They present a very high level of internal parallelism inside the regions, allowing several rule to be applied at the same time. - They present a universal character meaning this that they are not dependent upon the active rules that compose the P System. - They have a non-deterministic behavior that is inherent to this systems nature. The first processor uses the concept of "power set of the application rule set" and the concept of "maximal application" number to improve parallelism, and the second one includes, besides the previous ones, the concept of "applicability domain" to determine the set of rules that may be applied in each moment with the existing resources.. Both processors are designed and tested with the design software by Altera Corporation and they are ready to be synthetized over FPGAs.