1,733 research outputs found

    Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures

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    The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.This work is jointly supported by the FundaciónSéneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants 15290/PI/2010 and 18946/JLI/13, by the Spanish MEC and European Commission FEDER under grant with reference TEC2012-37945-C02-02 and TIN2012-31345, by the Nils Coordinated Mobility under grant 012-ABEL-CM-2014A, in part financed by the European Regional Development Fund (ERDF). We also thank NVIDIA for hardware donation within UCAM GPU educational and research centers.Ingeniería, Industria y Construcció

    Optimización de algoritmos bioinspirados en sistemas heterogéneos CPU-GPU.

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    Los retos científicos del siglo XXI precisan del tratamiento y análisis de una ingente cantidad de información en la conocida como la era del Big Data. Los futuros avances en distintos sectores de la sociedad como la medicina, la ingeniería o la producción eficiente de energía, por mencionar sólo unos ejemplos, están supeditados al crecimiento continuo en la potencia computacional de los computadores modernos. Sin embargo, la estela de este crecimiento computacional, guiado tradicionalmente por la conocida “Ley de Moore”, se ha visto comprometido en las últimas décadas debido, principalmente, a las limitaciones físicas del silicio. Los arquitectos de computadores han desarrollado numerosas contribuciones multicore, manycore, heterogeneidad, dark silicon, etc, para tratar de paliar esta ralentización computacional, dejando en segundo plano otros factores fundamentales en la resolución de problemas como la programabilidad, la fiabilidad, la precisión, etc. El desarrollo de software, sin embargo, ha seguido un camino totalmente opuesto, donde la facilidad de programación a través de modelos de abstracción, la depuración automática de código para evitar efectos no deseados y la puesta en producción son claves para una viabilidad económica y eficiencia del sector empresarial digital. Esta vía compromete, en muchas ocasiones, el rendimiento de las propias aplicaciones; consecuencia totalmente inadmisible en el contexto científico. En esta tesis doctoral tiene como hipótesis de partida reducir las distancias entre los campos hardware y software para contribuir a solucionar los retos científicos del siglo XXI. El desarrollo de hardware está marcado por la consolidación de los procesadores orientados al paralelismo masivo de datos, principalmente GPUs Graphic Processing Unit y procesadores vectoriales, que se combinan entre sí para construir procesadores o computadores heterogéneos HSA. En concreto, nos centramos en la utilización de GPUs para acelerar aplicaciones científicas. Las GPUs se han situado como una de las plataformas con mayor proyección para la implementación de algoritmos que simulan problemas científicos complejos. Desde su nacimiento, la trayectoria y la historia de las tarjetas gráficas ha estado marcada por el mundo de los videojuegos, alcanzando altísimas cotas de popularidad según se conseguía más realismo en este área. Un hito importante ocurrió en 2006, cuando NVIDIA (empresa líder en la fabricación de tarjetas gráficas) lograba hacerse con un hueco en el mundo de la computación de altas prestaciones y en el mundo de la investigación con el desarrollo de CUDA “Compute Unified Device Arquitecture. Esta arquitectura posibilita el uso de la GPU para el desarrollo de aplicaciones científicas de manera versátil. A pesar de la importancia de la GPU, es interesante la mejora que se puede producir mediante su utilización conjunta con la CPU, lo que nos lleva a introducir los sistemas heterogéneos tal y como detalla el título de este trabajo. Es en entornos heterogéneos CPU-GPU donde estos rendimientos alcanzan sus cotas máximas, ya que no sólo las GPUs soportan el cómputo científico de los investigadores, sino que es en un sistema heterogéneo combinando diferentes tipos de procesadores donde podemos alcanzar mayor rendimiento. En este entorno no se pretende competir entre procesadores, sino al contrario, cada arquitectura se especializa en aquella parte donde puede explotar mejor sus capacidades. Donde mayor rendimiento se alcanza es en estos clústeres heterogéneos, donde múltiples nodos son interconectados entre sí, pudiendo dichos nodos diferenciarse no sólo entre arquitecturas CPU-GPU, sino también en las capacidades computacionales dentro de estas arquitecturas. Con este tipo de escenarios en mente, se presentan nuevos retos en los que lograr que el software que hemos elegido como candidato se ejecuten de la manera más eficiente y obteniendo los mejores resultados posibles. Estas nuevas plataformas hacen necesario un rediseño del software para aprovechar al máximo los recursos computacionales disponibles. Se debe por tanto rediseñar y optimizar los algoritmos existentes para conseguir que las aportaciones en este campo sean relevantes, y encontrar algoritmos que, por su propia naturaleza sean candidatos para que su ejecución en dichas plataformas de alto rendimiento sea óptima. Encontramos en este punto una familia de algoritmos denominados bioinspirados, que utilizan la inteligencia colectiva como núcleo para la resolución de problemas. Precisamente esta inteligencia colectiva es la que les hace candidatos perfectos para su implementación en estas plataformas bajo el nuevo paradigma de computación paralela, puesto que las soluciones pueden ser construidas en base a individuos que mediante alguna forma de comunicación son capaces de construir conjuntamente una solución común. Esta tesis se centrará especialmente en uno de estos algoritmos bioinspirados que se engloba dentro del término metaheurísticas bajo el paradigma del Soft Computing, el Ant Colony Optimization “ACO”. Se realizará una contextualización, estudio y análisis del algoritmo. Se detectarán las partes más críticas y serán rediseñadas buscando su optimización y paralelización, manteniendo o mejorando la calidad de sus soluciones. Posteriormente se pasará a implementar y testear las posibles alternativas sobre diversas plataformas de alto rendimiento. Se utilizará el conocimiento adquirido en el estudio teórico-práctico anterior para su aplicación a casos reales, más en concreto se mostrará su aplicación sobre el plegado de proteínas. Todo este análisis es trasladado a su aplicación a un caso concreto. En este trabajo, aunamos las nuevas plataformas hardware de alto rendimiento junto al rediseño e implementación software de un algoritmo bioinspirado aplicado a un problema científico de gran complejidad como es el caso del plegado de proteínas. Es necesario cuando se implementa una solución a un problema real, realizar un estudio previo que permita la comprensión del problema en profundidad, ya que se encontrará nueva terminología y problemática para cualquier neófito en la materia, en este caso, se hablará de aminoácidos, moléculas o modelos de simulación que son desconocidos para los individuos que no sean de un perfil biomédico.Ingeniería, Industria y Construcció

    Benchmarking Inverse Optimization Algorithms for Molecular Materials Discovery

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    Machine learning-based molecular materials discovery has attracted enormous attention recently due to its flexibility in dealing with black box models. Yet, metaheuristic algorithms are not as widely applied to materials discovery applications. We comprehensively compare 11 different optimization algorithms for molecular materials design with targeted properties. These algorithms include Bayesian Optimization (BO) and multiple metaheuristic algorithms. We performed 5000 material evaluations repeated 5 times with different randomized initialization to optimize defined target properties. By maximizing the bulk modulus and minimizing the Fermi energy through perturbing parameterized molecular representations, we estimated the unique counts of molecular materials, mean density scan of the objectives space, mean objectives, and frequency distributed over the materials' representations and objectives. GA, GWO, and BWO exhibit higher variances for materials count, density scan, and mean objectives; and BO and Runge Kutta optimization (RUN) display generally lower variances. These results unveil that nature-inspired algorithms contain more uncertainties in the defined molecular design tasks, which correspond to their dependency on multiple hyperparameters. RUN exhibits higher mean objectives whereas BO displayed low mean objectives compared with other benchmarked methods. Combined with materials count and density scan, we propose that BO strives to approximate a more accurate surrogate of the design space by sampling more molecular materials and hence have lower mean objectives, yet RUN will repeatedly sample the targeted molecules with higher objective values. Our work shed light on automated digital molecular materials design and is expected to elicit future studies on materials optimization such as composite and alloy design based on specific desired properties.Comment: 15 pages, 5 figures, for the main manuscrip

    Inference of hidden structures in complex physical systems by multi-scale clustering

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    We survey the application of a relatively new branch of statistical physics--"community detection"-- to data mining. In particular, we focus on the diagnosis of materials and automated image segmentation. Community detection describes the quest of partitioning a complex system involving many elements into optimally decoupled subsets or communities of such elements. We review a multiresolution variant which is used to ascertain structures at different spatial and temporal scales. Significant patterns are obtained by examining the correlations between different independent solvers. Similar to other combinatorial optimization problems in the NP complexity class, community detection exhibits several phases. Typically, illuminating orders are revealed by choosing parameters that lead to extremal information theory correlations.Comment: 25 pages, 16 Figures; a review of earlier work

    Hybrid Honey Bees Mating Optimization Algorithm for Identifying the Near-Optimal Solution in Web Service Composition

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    This paper addresses the problem of optimality in semantic Web service composition by proposing a hybrid nature-inspired method for selecting the optimal or near-optimal solution in semantic Web Service Composition. The method hybridizes the Honey-Bees Mating Optimization algorithm with components inspired from genetic algorithms, reinforcement learning, and tabu search. To prove the necessity of hybridization, we have analyzed comparatively the experimental results provided by our hybrid selection algorithm versus the ones obtained with the classical Honey Bees Mating Optimization algorithm and with the genetic-inspired algorithm of Canfora et al

    Biomimetic Engineering

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    Humankind is a privileged animal species for many reasons. A remarkable one is its ability to conceive and manufacture objects. Human industry is indeed leading the various winning strategies (along with language and culture) that has permitted this primate to extraordinarily increase its life expectancy and proliferation rate. (It is indeed so successful, that it now threatens the whole planet.) The design of this industry kicks off in the brain, a computing machine particularly good at storing, recognizing and associating patterns. Even in a time when human beings tend to populate non-natural, man-made environments, the many forms, colorings, textures and behaviors of nature continuously excite our senses and blend in our thoughts, even more deeply during childhood. Then, it would be exaggerated to say that Biomimetics is a brand new strategy. As long as human creation is based on previously acquired knowledge and experiences, it is not surprising that engineering, the arts, and any form of expression, is influenced by nature’s way to some extent. The design of human industry has evolved from very simple tools, to complex engineering devices. Nature has always provided us with a rich catalog of excellent materials and inspiring designs. Now, equipped with new machinery and techniques, we look again at Nature. We aim at mimicking not only its best products, but also its design principles. Organic life, as we know it, is indeed a vast pool of diversity. Living matter inhabits almost every corner of the terrestrial ecosphere. From warm open-air ecosystems to the extreme conditions of hot salt ponds, living cells have found ways to metabolize the sources of energy, and get organized in complex organisms of specialized tissues and organs that adapt themselves to the environment, and can modify the environment to their own needs as well. Life on Earth has evolved such a diverse portfolio of species that the number of designs, mechanisms and strategies that can actually be abstracted is astonishing. As August Krogh put it: "For a large number of problems there will be some animal of choice, on which it can be most conveniently studied". The scientific method starts with a meticulous observation of natural phenomena, and humans are particularly good at that game. In principle, the aim of science is to understand the physical world, but an observer’s mind can behave either as an engineer or as a scientist. The minute examination of the many living forms that surround us has led to the understanding of new organizational principles, some of which can be imported in our production processes. In practice, bio-inspiration can arise at very different levels of observation: be it social organization, the shape of an organism, the structure and functioning of organs, tissular composition, cellular form and behavior, or the detailed structure of molecules. Our direct experience of the wide portfolio of species found in nature, and their particular organs, have clearly favored that the initial models would come from the organism and organ levels. But the development of new techniques (on one hand to observe the micro- and nanostructure of living beings, and on the other to simulate the complex behavior of social communities) have significantly extended the domain of interest

    Modified Intelligent Water Drops with perturbation operators for atomic cluster optimization

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    A modified version of the Intelligent Water Drops algorithm (MIWD) was developed then used to determine the most stable configurations of Lennard-Jones (LJ), Binary Lennard-Jones (BLJ) and Morse Clusters. The algorithm is unbiased in that it uses no a priori cluster geometry information or cluster seeds. Results for LJ clusters show that the algorithm is effective and efficient in rediscovering all clusters up to size N = 104 with better success rates specially on difficult clusters compared to previous best methodologies reported in literature. Results on more difficult systems, such as the Binary Lennard Jones clusters up to size 50 (with 5 different atomic size ratios) and Morse clusters up to size 60 (with 2 interparticle range potentials), also showed the ability of MIWD to handle more complex systems. MIWD was then applied to predict the most stable structures of Janus clusters up to size 50 and on size 100 using a LJ potential model with a modulated angular term suited for two-patched Janus particles. Results show that MIWD is able to find well-structured geometries of Janus clusters. It is believed that this has been the first time that a nature-inspired stochastic algorithm and a variant of the IWD algorithm has been applied to the configurational optimization of Janus clusters

    Applying autonomy to distributed satellite systems: Trends, challenges, and future prospects

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    While monolithic satellite missions still pose significant advantages in terms of accuracy and operations, novel distributed architectures are promising improved flexibility, responsiveness, and adaptability to structural and functional changes. Large satellite swarms, opportunistic satellite networks or heterogeneous constellations hybridizing small-spacecraft nodes with highperformance satellites are becoming feasible and advantageous alternatives requiring the adoption of new operation paradigms that enhance their autonomy. While autonomy is a notion that is gaining acceptance in monolithic satellite missions, it can also be deemed an integral characteristic in Distributed Satellite Systems (DSS). In this context, this paper focuses on the motivations for system-level autonomy in DSS and justifies its need as an enabler of system qualities. Autonomy is also presented as a necessary feature to bring new distributed Earth observation functions (which require coordination and collaboration mechanisms) and to allow for novel structural functions (e.g., opportunistic coalitions, exchange of resources, or in-orbit data services). Mission Planning and Scheduling (MPS) frameworks are then presented as a key component to implement autonomous operations in satellite missions. An exhaustive knowledge classification explores the design aspects of MPS for DSS, and conceptually groups them into: components and organizational paradigms; problem modeling and representation; optimization techniques and metaheuristics; execution and runtime characteristics and the notions of tasks, resources, and constraints. This paper concludes by proposing future strands of work devoted to study the trade-offs of autonomy in large-scale, highly dynamic and heterogeneous networks through frameworks that consider some of the limitations of small spacecraft technologies.Postprint (author's final draft
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