Improving the efficiency of nondeterministic indepemndent and-parallel systems

We present the design and implementation of the and-parallel component of ACE. ACE is a computational model for the full Prolog language that simultaneously exploits both or-parallelism and independent and-parallelism. A high performance implementation of the ACE model has been realized and its performance reported in this paper. We discuss how some of the standard problems which appear when implementing and-parallel systems are solved in ACE. We then propose a number of optimizations aimed at reducing the overheads and the increased memory consumption which occur in such systems when using previously proposed solutions. Finally, we present results from an implementation of ACE which includes the optimizations proposed. The results show that ACE exploits and-parallelism with high efficiency and high speedups. Furthermore, they also show that the proposed optimizations, which are applicable to many other and-parallel systems, significantly decrease memory consumption and increase speedups and absolute performance both in forwards execution and during backtracking.

A semantic scheduler architecture for federated hybrid clouds

Cloud computing is one the most relevant computing paradigms available nowadays. Its adoption has increased during last years due to the large investment and research from business enterprises and academia institutions. Among all the services cloud providers usually offer, Infrastructure as a Service has reached its momentum for solving HPC problems in a more dynamic way without the need of expensive investments. The integration of a large number of providers is a major goal as it enables the improvement of the quality of the selected resources in terms of pricing, speed, redundancy, etc. In this paper, we propose a system architecture, based on semantic solutions, to build an interoperable scheduler for federated clouds that works with several IaaS (Infrastructure as a Service) providers in a uniform way. Based on this architecture we implement a proof-of-concept prototype and test it with two different cloud solutions to provide some experimental results about the viability of our approach.

Analytic model of a cache-only memory architecture

An approximate analytic model of a shared memory multiprocessor with a Cache Only Memory Architecture (COMA), the busbased Data Difussion Machine (DDM), is presented and validated. It describes the timing and interference in the system as a function of the hardware, the protocols, the topology and the workload. Model results have been compared to results from an independent simulator. The comparison shows good model accuracy specially for non-saturated systems, where the errors in response times and device utilizations are independent of the number of processors and remain below 10% in 90% of the simulations. Therefore, the model can be used as an average performance prediction tool that avoids expensive simulations in the design of systems with many processors.

Recomputation based implementation of and-or parallel prolog

We argüe that in order to exploit both Independent And- and Or-parallelism in Prolog programs there is advantage in recomputing some of the independent goals, as opposed to all their solutions being reused. We present an abstract model, called the Composition- Tree, for representing and-or parallelism in Prolog Programs. The Composition-tree closely mirrors sequential Prolog execution by recomputing some independent goals rather than fully re-using them. We also outline two environment representation techniques for And-Or parallel execution of full Prolog based on the Composition-tree model abstraction. We argüe that these techniques have advantages over earlier proposals for exploiting and-or parallelism in Prolog.

Memory performance of and-parallel prolog on shared-memory architectures

The goal of the RAP-WAM AND-parallel Prolog abstract architecture is to provide inference speeds significantly beyond those of sequential systems, while supporting Prolog semantics and preserving sequential performance and storage efficiency. This paper presents simulation results supporting these claims with special emphasis on memory performance on a two-level sharedmemory multiprocessor organization. Several solutions to the cache coherency problem are analyzed. It is shown that RAP-WAM offers good locality and storage efficiency and that it can effectively take advantage of broadcast caches. It is argued that speeds in excess of 2 ML IPS on real applications exhibiting medium parallelism can be attained with current technology.

Data-Intensive architecture for scientific knowledge discovery

This paper presents a data-intensive architecture that demonstrates the ability to support applications from a wide range of application domains, and support the different types of users involved in defining, designing and executing data-intensive processing tasks. The prototype architecture is introduced, and the pivotal role of DISPEL as a canonical language is explained. The architecture promotes the exploration and exploitation of distributed and heterogeneous data and spans the complete knowledge discovery process, from data preparation, to analysis, to evaluation and reiteration. The architecture evaluation included large-scale applications from astronomy, cosmology, hydrology, functional genetics, imaging processing and seismology.

c&d-learning implementation architecture: Adapting e-learning to developing countries

From the educational point of view, the most widespread method in developing countries is on-site education. Technical and economic resources cannot support conventional distance learning infrastructures and it is even worse for courses in universities. They usually suffer a lack of qualified faculty staff, especially in technical degrees. The literature suggest that e-learning is a suitable solution for this problem, but its methods are developed attending to educational necessities of the First World and cannot be applied directly to other contexts. The proposed methodology is a variant of traditional e-learning adapted to the needs of developing countries. E-learning for Cooperation and Development (c&d-learning) is oriented to be used for educational institutions without adequate technical or human resources. In this paper we describe the c&d-learning implementation architecture based on three main phases: hardware, communication and software; e.g. computer and technical equipping, internet accessing and e-learning platform adaptation. Proper adaptation of educational contents to c&d-learning is discussed and a real case of application in which the authors are involved is described: the Ngozi University at Burundi.

A multi-agent system with distributed bayesian reasoning for network fault diagnosis

In this paper, an innovative approach to perform distributed Bayesian inference using a multi-agent architecture is presented. The final goal is dealing with uncertainty in network diagnosis, but the solution can be of applied in other fields. The validation testbed has been a P2P streaming video service. An assessment of the work is presented, in order to show its advantages when it is compared with traditional manual processes and other previous systems.

Molecular basis of salt tolerance in Physcomitrella Patens model plant: potassium homeostasis and physiological roles of chx transporters

El suelo salino impone un estrés abiótico importante que causa graves problemas en la agricultura ya que la mayoría de los cultivos se ven afectados por la salinidad debido a efectos osmóticos y tóxicos. Por ello, la contaminación y la escasez de agua dulce, la salinización progresiva de tierras y el aumento exponencial de la población humana representan un grave problema que amenaza la seguridad alimentaria mundial para las generaciones futuras. Por lo tanto, aumentar la tolerancia a la salinidad de los cultivos es un objetivo estratégico e ineludible para garantizar el suministro de alimentos en el futuro. Mantener una óptima homeostasis de K+ en plantas que sufren estrés salino es un objetivo importante en el proceso de obtención de plantas tolerantes a la salinidad. Aunque el modelo de la homeostasis de K+ en las plantas está razonablemente bien descrito en términos de entrada de K+, muy poco se sabe acerca de los genes implicados en la salida de K+ o de su liberación desde la vacuola. En este trabajo se pretende aclarar algunos de los mecanismos implicados en la homeostasis de K+ en plantas. Para ello se eligió la briofita Physcomitrella patens, una planta no vascular de estructura simple y de fase haploide dominante que, entre muchas otras cualidades, hacen que sea un modelo ideal. Lo más importante es que no sólo P. patens es muy tolerante a altas concentraciones de Na+, sino que también su posición filogenética en la evolución de las plantas abre la posibilidad de estudiar los cambios claves que, durante el curso de la evolución, se produjeron en las diversas familias de los transportadores de K+. Se han propuesto varios transportadores de cationes como candidatos que podrían tener un papel en la salida de K+ o su liberación desde la vacuola, especialmente miembros de la familia CPA2 que contienen las familias de transportadores KEA y CHX. En este estudio se intenta aumentar nuestra comprensión de las funciones de los transportadores de CHX en las células de las plantas usando P. patens, como ya se ha dicho. En esta especie, se han identificado cuatro genes CHX, PpCHX1-4. Dos de estos genes, PpCHX1 y PpCHX2, se expresan aproximadamente al mismo nivel que el gen PpACT5, y los otros dos genes muestran una expresión muy baja. La expresión de PpCHX1 y PpCHX2 en mutantes de Escherichia coli defectivos en el transporte de K+ restauraron el crecimiento de esta cepa en medios con bajo contenido de K+, lo que viii sugiere que la entrada de K+ es energizada por un mecanismo de simporte con H+. Por otra parte, estos transportadores suprimieron el defecto asociado a la mutación kha1 en Saccharomyces cerevisiae, lo que sugiere que podrían mediar un antiporte en K+/H+. La proteína PpCHX1-GFP expresada transitoriamente en protoplastos de P. patens co-localizó con un marcador de Golgi. En experimentos similares, la proteína PpCHX2-GFP localizó aparentemente en la membrana plasmática y tonoplasto. Se construyeron las líneas mutantes simples de P. patens ΔPpchx1 y ΔPpchx2, y también el mutante doble ΔPpchx2 ΔPphak1. Los mutantes simples crecieron normalmente en todas las condiciones ensayadas y mostraron flujos de entrada normales de K+ y Rb+; la mutación ΔPpchx2 no aumentó el defecto de las plantas ΔPphak1. En experimentos a largo plazo, las plantas ΔPpchx2 mostraron una retención de Rb+ ligeramente superior que las plantas silvestres, lo que sugiere que PpCHX2 promueve la transferencia de Rb+ desde la vacuola al citosol o desde el citosol al medio externo, actuando en paralelo con otros transportadores. Sugerimos que transportadores de K+ de varias familias están involucrados en la homeostasis de pH de orgánulos ya sea mediante antiporte K+/H+ o simporte K+-H+.ix ABSTRACT Soil salinity is a major abiotic stress causing serious problems in agriculture as most crops are affected by it. Moreover, the contamination and shortage of freshwater, progressive land salinization and exponential increase of human population aggravates the problem implying that world food security may not be ensured for the next generations. Thus, a strategic and an unavoidable goal would be increasing salinity tolerance of plant crops to secure future food supply. Maintaining an optimum K+ homeostasis in plants under salinity stress is an important trait to pursue in the process of engineering salt tolerant plants. Although the model of K+ homeostasis in plants is reasonably well described in terms of K+ influx, very little is known about the genes implicated in K+ efflux or release from the vacuole. In this work, we aim to clarify some of the mechanisms involved in K+ homeostasis in plants. For this purpose, we chose the bryophyte plant Physcomitrella patens, a nonvascular plant of simple structure and dominant haploid phase that, among many other characteristics, makes it an ideal model. Most importantly, not only P. patens is very tolerant to high concentrations of Na+, but also its phylogenetic position in land plant evolution opens the possibility to study the key changes that occurred in K+ transporter families during the course of evolution. Several cation transporter candidates have been proposed to have a role in K+ efflux or release from the vacuole especially members of the CPA2 family which contains the KEA and CHX transporter families. We intended in this study to increase our understanding of the functions of CHX transporters in plant cells using P. patens, in which four CHX genes have been identified, PpCHX1-4. Two of these genes, PpCHX1 and PpCHX2, are expressed at approximately the same level as the PpACT5 gene, but the other two genes show an extremely low expression. PpCHX1 and PpCHX2 restored growth of Escherichia coli mutants on low K+-containing media, suggesting they mediated K+ uptake that may be energized by symport with H+. In contrast, these genes suppressed the defect associated to the kha1 mutation in Saccharomyces cerevisiae, which suggest that they might mediate K+/H+ antiport. PpCHX1-GFP protein transiently expressed in P. patens protoplasts co-localized with a Golgi marker. In similar experiments, the PpCHX2-GFP protein appeared to localize to tonoplast and plasma x membrane. We constructed the ΔPpchx1 and ΔPpchx2 single mutant lines, and the ΔPpchx2 ΔPphak1 double mutant. Single mutant plants grew normally under all the conditions tested and exhibited normal K+ and Rb+ influxes; the ΔPpchx2 mutation did not increase the defect of ΔPphak1 plants. In long-term experiments, ΔPpchx2 plants showed a slightly higher Rb+ retention than wild type plants, which suggests that PpCHX2 mediates the transfer of Rb+ from either the vacuole to the cytosol or from the cytosol to the external medium in parallel with other transporters. We suggest that K+ transporters of several families are involved in the pH homeostasis of organelles by mediating either K+/H+ antiport or K+-H+ symport.

Photonic processing subsystem based on visual cortex architecture

Optical signal processing in any living being is more complex than the one obtained in artificial systems. Cortex architecture, although only partly known, gives some useful ideas to be employed in communications. To analyze some of these structures is the objective of this paper. One of the main possibilities reported is handling signals in a parallel way. As it is shown, according to the signal characteristics each signal impinging onto a single input may be routed to a different output. At the same time, identical signals, coming to different inputs, may be routed to the same output without internal conflicts. This is due to the change of some of their characteristics in the way out when going through the intermediate levels. The simulation of this architecture is based on simple logic cells. The basis for the proposed architecture is the five layers of the mammalian retina and the first levels of the visual cortex.

Fault isolation schemes for a class of continuous-time stochastic dynamical systems

In this paper a new method for fault isolation in a class of continuous-time stochastic dynamical systems is proposed. The method is framed in the context of model-based analytical redundancy, consisting in the generation of a residual signal by means of a diagnostic observer, for its posterior analysis. Once a fault has been detected, and assuming some basic a priori knowledge about the set of possible failures in the plant, the isolation task is then formulated as a type of on-line statistical classification problem. The proposed isolation scheme employs in parallel different hypotheses tests on a statistic of the residual signal, one test for each possible fault. This isolation method is characterized by deriving for the unidimensional case, a sufficient isolability condition as well as an upperbound of the probability of missed isolation. Simulation examples illustrate the applicability of the proposed scheme.

Simulating Metabolic Processes Using an Architecture Based on Networks of Bio-inspired Processors.

In this work, we propose the Networks of Evolutionary Processors (NEP) [2] as a computational model to solve problems related with biological phenomena. In our first approximation, we simulate biological processes related with cellular signaling and their implications in the metabolism, by using an architecture based on NEP (NEP architecture) and their specializations: Networks of Polarized Evolutionary Processors (NPEP) [1] and NEP Transducers (NEPT) [3]. In particular, we use this architecture to simulate the interplay between cellular processes related with the metabolism as the Krebs cycle and the malate-aspartate shuttle pathway (MAS) both being altered by signaling by calcium.

An Architecture forRepresenting Biological Processes based on Networks of Bio-inspired Processors

n this paper we propose the use of Networks of Bio-inspired Processors (NBP) to model some biological phenomena within a computational framework. In particular, we propose the use of an extension of NBP named Network Evolutionary Processors Transducers to simulate chemical transformations of substances. Within a biological process, chemical transformations of substances are basic operations in the change of the state of the cell. Previously, it has been proved that NBP are computationally complete, that is, they are able to solve NP complete problems in linear time, using massively parallel computations. In addition, we propose a multilayer architecture that will allow us to design models of biological processes related to cellular communication as well as their implications in the metabolic pathways. Subsequently, these models can be applied not only to biological-cellular instances but, possibly, also to configure instances of interactive processes in many other fields like population interactions, ecological trophic networks, in dustrial ecosystems, etc.

Marco computacional para la definición de un modelo bio-inspirado en la señalización celular

Las Redes de Procesadores Evolutivos-NEP propuestas en [Mitrana et al., 2001], son un modelo computacional bio-inspirado a partir de la evolución de poblaciones de células, definiendo a nivel sintáctico algunas propiedades biológicas. En este modelo, las células están representadas por medio de palabras que describen secuencias de ADN. Informalmente, en algún instante de tiempo, el sistema evolutivo está representado por una colección de palabras cada una de las cuales representa una célula. El espacio genotipo de las especies, es un conjunto que recoge aquellas palabras que son aceptadas como sobrevivientes (es decir, como \correctas"). Desde el punto de vista de la evolución, las células pertenecen a especies y su comunidad evoluciona de acuerdo a procesos biológicos como la mutación y la división celular. éstos procesos representan el proceso natural de evolución y ponen de manifiesto una característica intrínseca de la naturaleza: el paralelismo. En este modelo, estos procesos son vistos como operaciones sobre palabras. Formalmente, el modelo de las NEP constituyen una arquitectura paralela y distribuida de procesamiento simbólico inspirada en la Máquina de conexión [Hillis, 1981], en el Paradigma de Flujo Lógico [Errico and Jesshope, 1994] y en las Redes de Procesadores Paralelos de Lenguajes (RPPL) [Csuhaj-Varju and Salomaa, 1997]. Al modelo NEP se han ido agregando nuevas y novedosas extensiones hasta el punto que actualmente podemos hablar de una familia de Redes de Procesadores Bio-inspirados (NBP) [Mitrana et al., 2012b]. Un considerable número de trabajos a lo largo de los últimos años han demostrado la potencia computacional de la familia NBP. En general, éstos modelos son computacionalmente completos, universales y eficientes [Manea et al., 2007], [Manea et al., 2010b], [Mitrana and Martín-Vide, 2005]. De acuerdo a lo anterior, se puede afirmar que el modelo NEP ha adquirido hasta el momento un nivel de madurez considerable. Sin embargo, aunque el modelo es de inspiración biológica, sus metas siguen estando motivadas en la Teoría de Lenguajes Formales y las Ciencias de la Computación. En este sentido, los aspectos biológicos han sido abordados desde una perspectiva cualitativa y el acercamiento a la realidad biológica es de forma meramente sintáctica. Para considerar estos aspectos y lograr dicho acercamiento es necesario que el modelo NEP tenga una perspectiva más amplia que incorpore la interacción de aspectos tanto cualitativos como cuantitativos. La contribución de esta Tesis puede considerarse como un paso hacia adelante en una nueva etapa de los NEPs, donde el carácter cuantitativo del modelo es de primordial interés y donde existen posibilidades de un cambio visible en el enfoque de interés del dominio de los problemas a considerar: de las ciencias de la computación hacia la simulación/modelado biológico y viceversa, entre otros. El marco computacional que proponemos en esta Tesis extiende el modelo de las Redes de Procesadores Evolutivos (NEP) y define arquitectura inspirada en la definición de bloques funcionales del proceso de señalización celular para la solución de problemas computacionales complejos y el modelado de fenómenos celulares desde una perspectiva discreta. En particular, se proponen dos extensiones: (1) los Transductores basados en Redes de Procesadores Evolutivos (NEPT), y (2) las Redes Parametrizadas de Procesadores Evolutivos Polarizados (PNPEP). La conservación de las propiedades y el poder computacional tanto de NEPT como de PNPEP se demuestra formalmente. Varias simulaciones de procesos relacionados con la señalización celular son abordadas sintáctica y computacionalmente, con el _n de mostrar la aplicabilidad e idoneidad de estas dos extensiones. ABSTRACT Network of Evolutionary Processors -NEP was proposed in [Mitrana et al., 2001], as a computational model inspired by the evolution of cell populations, which might model some properties of evolving cell communities at the syntactical level. In this model, cells are represented by words which encode their DNA sequences. Informally, at any moment of time, the evolutionary system is described by a collection of words, where each word represents one cell. Cells belong to species and their community evolves according to mutations and division which are defined by operations on words. Only those cells accepted as survivors (correct) are represented by a word in a given set of words, called the genotype space of the species. This feature is analogous with the natural process of evolution. Formally, NEP is based on an architecture for parallel and distributed processing inspired from the Connection Machine [Hillis, 1981], the Flow Logic Paradigm [Errico and Jesshope, 1994] and the Networks of Parallel Language Processors (RPPL) [Csuhaj-Varju and Salomaa, 1997]. Since the date when NEP was proposed, several extensions and variants have appeared engendering a new set of models named Networks of Bio-inspired Processors (NBP) [Mitrana et al., 2012b]. During this time, several works have proved the computational power of NBP. Specifically, their efficiency, universality, and computational completeness have been thoroughly investigated [Manea et al., 2007, Manea et al., 2010b, Mitrana and Martín-Vide, 2005]. Therefore, we can say that the NEP model has reached its maturity. Nevertheless, although the NEP model is biologically inspired, this model is mainly motivated by mathematical and computer science goals. In this context, the biological aspects are only considered from a qualitative and syntactical perspective. In view of this lack, it is important to try to keep the NEP theory as close as possible to the biological reality, extending their perspective incorporating the interplay of qualitative and quantitative aspects. The contribution of this Thesis, can be considered as a starting point in a new era of the NEP model. Then, the quantitative character of the NEP model is mandatory and it can address completely new different types of problems with respect to the classical computational domain (e.g. from the computer science to system biology). Therefore, the computational framework that we propose extends the NEP model and defines an architecture inspired by the functional blocks from cellular signaling in order to solve complex computational problems and cellular phenomena modeled from a discrete perspective. Particularly, we propose two extensions, namely: (1) Transducers based on Network of Evolutionary Processors (NEPT), and (2) Parametrized Network of Polarized Evolutionary Processors (PNPEP). Additionally, we have formally proved that the properties and computational power of NEP is kept in both extensions. Several simulations about processes related with cellular signaling both syntactical and computationally have been considered to show the model suitability.

Aprendizaje colaborativo en enseñanza a distancia: entorno genérico para configurar, realizar y analizar actividades en grupo

En esta tesis se ha profundizado en el estudio y desarrollo de modelos de soporte para el aprendizaje colaborativo a distancia, que ha permitido proponer una arquitectura fundamentada en los principios del paradigma CSCL (Computer Supported Collaborative Learning). La arquitectura propuesta aborda un tipo de problema concreto que requiere el uso de técnicas derivadas del Trabajo Colaborativo, la Inteligencia Artificial, Interfaces de Usuario así como ideas tomadas de la Pedagogía y la Psicología. Se ha diseñado una solución completa, abierta y genérica. La arquitectura aprovecha las nuevas tecnologías para lograr un sistema efectivo de apoyo a la educación a distancia. Está organizada en cuatro niveles: el de Configuración, el de Experiencia, el de Organización y el de Análisis. A partir de ella se ha implementado un sistema llamado DEGREE. En DEGREE, cada uno de los niveles de la arquitectura da lugar a un subsistema independiente pero relacionado con los otros. La aplicación saca partido del uso de espacios de trabajo estructurados. El subsistema Configurador de Experiencias permite definir los elementos de un espacio de trabajo y una experiencia y adaptarlos a cada tipo de usuario. El subsistema Manejador de Experiencias recoge las contribuciones de los usuarios para construir una solución conjunta de un problema. Las intervenciones de los alumnos se estructuran basándose en un grafo conversacional genérico. Además, se registran todas las acciones de los usuarios para representar explícitamente el proceso completo que lleva a la solución. Estos datos también se almacenan en una memoria común que constituye el subsistema llamado Memoria Organizativa de Experiencias. El subsistema Analizador estudia las intervenciones de los usuarios. Este análisis permite inferir conclusiones sobre la forma en que trabajan los grupos y sus actitudes frente a la colaboración, teniendo en cuenta además el conocimiento subjetivo del observador. El proceso de desarrollo en paralelo de la arquitectura y el sistema ha seguido un ciclo de refinamiento en cinco fases con sucesivas etapas de prototipado y evaluación formativa. Cada fase de este proceso se ha realizado con usuarios reales y se han considerado las opiniones de los usuarios para mejorar las funcionalidades de la arquitectura así como la interfaz del sistema. Esta aproximación ha permitido, además, comprobar la utilidad práctica y la validez de las propuestas que sustentan este trabajo.---ABSTRACT---In this thesis, we have studied in depth the development of support models for distance collaborative learning and subsequently devised an architecture based on the Computer Supported Collaborative Learning paradigm principles. The proposed architecture addresses a specific problem: coordinating groups of students to perform collaborative distance learning activities. Our approach uses Cooperative Work, Artificial Intelligence and Human-Computer Interaction techniques as well as some ideas from the fields of Pedagogy and Psychology. We have designed a complete, open and generic solution. Our architecture exploits the new information technologies to achieve an effective system for education purposes. It is organised into four levels: Configuration, Experience, Organisation and Reflection. This model has been implemented into a system called DEGREE. In DEGREE, each level of the architecture gives rise to an independent subsystem related to the other ones. The application benefits from the use of shared structured workspaces. The configuration subsystem allows customising the elements that define an experience and a workspace. The experience subsystem gathers the users' contributions to build joint solutions to a given problem. The students' interventions build up a structure based on a generic conversation graph. Moreover, all user actions are registered in order to represent explicitly the complete process for reaching the group solution. Those data are also stored into a common memory, which constitutes the organisation subsystem. The user interventions are studied by the reflection subsystem. This analysis allows us inferring conclusions about the way in which the group works and its attitudes towards collaboration. The inference process takes into account the observer's subjective knowledge. The process of developing both the architecture and the system in parallel has run through a five-pass cycle involving successive stages of prototyping and formative evaluation. At each stage of that process, we have considered the users' feedback for improving the architecture's functionalities as well as the system interface. This approach has allowed us to prove the usability and validity of our proposal.