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Modeling and simulation of parallel adaptive divide-and-conquer algorithms

Barros, Fernando
Fonte: Universidade de Coimbra Publicador: Universidade de Coimbra
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
290.27277%
Abstract Conventional modeling and simulation formalisms only give support to the representation of model behavior, providing no constructs for describing changes in model structure. However, some systems are better modeled by self-reconfigurable formalisms. We have developed the Discrete Flow System Specification (DFSS) to exploit dynamic structure, component-based and hierarchical model construction. Due to structural similarity, dynamic self-configuring DFSS models offer a good description of systems, like adaptive algorithms and reconfigurable computer architectures. In this paper, we present the modeling and simulation of a parallel adaptive divide-and-conquer integration algorithm in the CaosTalk modeling and simulation framework, a realization of the DFSS formalism.; http://dx.doi.org/10.1007/s11227-007-0143-3

Modeling formalisms for dynamic structure systems

Barros, Fernando J.
Fonte: Association for Computing Machinery Publicador: Association for Computing Machinery
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
599.03062%
We present a new concept for a system network to represent systems that are able to undergo structural change. Change in structure is defined in general terms, and includes the addition and deletion of systems and the modification of the relations among components. The structure of a system network is stored in the network executive. Any change in structure-related information is mapped into modifications in the network structure.Based on these concepts, we derive three new system specifications that provide a shorthand notation to specify classes of dynamic structure systems. These new formalisms are: dynamic structure discrete time system, dynamic structure differential equation specified systems, and dynamic structure discrete event system specification. We demonstrate that these formalisms are closed under coupling, making hierarchical model construction possible. formalisms are described using set theoretic notation and general systems theory concepts.; http://doi.acm.org/10.1145/268403.268423

Técnicas de modelagem para a análise de desempenho de processos de negócio; Modeling techniques for business process performance analysis

Braghetto, Kelly Rosa
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 21/09/2011 PT
Relevância na Pesquisa
375.6131%
As recentes pesquisas na área de Gestão de Processos de Negócio (GPN) vêm contribuindo para aumentar a eficiência nas organizações. A GPN pode ser compreendida como o conjunto de métodos, técnicas e ferramentas computacionais desenvolvidas para amparar os processos de negócios. Tipicamente, a GPN é fundamentada por modelos de processos. Esses modelos, além de permitirem a automação da configuração e execução, aumentam a capacidade de análise dos processos de negócio. Apesar de auxiliar os especialistas de negócio nas diferentes fases envolvidas no ciclo de vida de um processo de negócio (projeto, configuração, implantação/execução e a análise), os modelos definidos em linguagens específicas de domínio, como a BPMN (Business Process Model and Notation), não são os mais apropriados para amparar a fase de análise. De formal geral, esses modelos não possuem uma semântica operacional formalmente definida (o que limita o seu uso para a verificação e validação dos processos) e nem mecanismos para quantificar o comportamento modelado (o que impossibilita a análise de desempenho). Neste trabalho de doutorado, nós desenvolvemos um arcabouço que ampara e automatiza os principais passos envolvidos na análise de desempenho de processos de negócio via modelagem analítica. Nós estudamos a viabilidade da aplicação de três formalismos Markovianos na modelagem de processos de negócio: as Redes de Petri Estocásticas...

Derivação eficiente e utilização de filtros de Volterra de referência na avaliação de formalismos não-lineares.; Efficient derivation and use of reference Volterra filters for the evaluation of non-linear formalisms.

Goulart, José Henrique de Morais
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 03/08/2012 PT
Relevância na Pesquisa
390.27277%
O modelamento matemático de sistemas físicos é fundamental para diversas aplicações de processamento digital de sinais (PDS). Em muitos dos problemas enfrentados nesse contexto, para que um modelo seja útil, é necessário que ele represente seu análogo físico com precisão e possua características favoráveis para implementação, como estabilidade e compacidade. A obtenção de um modelo que atenda a estes requisitos depende da escolha de um formalismo matemático apropriado. Em se tratando do modelamento de sistemas (significativamente) não-lineares, tal decisão é particularmente desafiadora, uma vez que muitos formalismos com propriedades diferentes foram propostos na literatura. Basicamente, isto se deve à inexistência de uma teoria completa e geral para sistemas não-lineares, diferentemente do que ocorre no caso linear. Porém, em diversos trabalhos que lidam com aplicações nas quais é necessário modelar dispositivos não-lineares, adota-se alguma representação sem que sejam fornecidas justificativas claras e fundamentadas em características físicas do sistema a ser modelado. Ao invés disso, esse importante aspecto é discutido apenas superficialmente, com base em argumentos informais ou heurísticos. Adicionalmente...

Novel modeling formalisms and simulation tools in computational biosystems

Machado, C. D.
Fonte: Universidade do Minho Publicador: Universidade do Minho
Tipo: Tese de Doutorado
Publicado em 23/01/2012 ENG
Relevância na Pesquisa
505.7205%
Tese de doutoramento em Bioengenharia; The goal of Systems Biology is to understand the complex behavior that emerges from the interaction among the cellular components. Industrial biotechnology is one of the areas of application, where new approaches for metabolic engineering are developed, through the creation of new models and tools for simulation and optimization of the microbial metabolism. Although whole-cell modeling is one of the goals of Systems Biology, so far most models address only one kind of biological network independently. This work explores the integration of di erent kinds of biological networks with a focus on the improvement of simulation of cellular metabolism. The bacterium Escherichia coli is the most well characterized model organism and is used as our case-study. An extensive review of modeling formalisms that have been used in Systems Biology is presented in this work. It includes several formalisms, including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, di erential equations, rule-based models, interacting state machines, cellular automata and agent-based models. We compare the features provided by these formalisms and classify the most suitable ones for the creation of a common framework for modeling...

Modeling formalisms in systems biology

Machado, C. D.; Costa, Rafael S.; Rocha, Miguel; Ferreira, E. C.; Tidor, Bruce; Rocha, I.
Fonte: Springer Publicador: Springer
Tipo: Artigo de Revista Científica
Publicado em //2011 ENG
Relevância na Pesquisa
707.6454%
Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future.

Novel modeling formalisms and simulation tools in computational biosystems

Machado, C. D.; Rocha, I.; Tidor, Bruce; Ferreira, E. C.
Fonte: Universidade do Minho Publicador: Universidade do Minho
Tipo: Conferência ou Objeto de Conferência
Publicado em 11/10/2010 ENG
Relevância na Pesquisa
497.95164%
Living organisms are complex systems that emerge from the fundamental building blocks of life. Systems Biology is a recent field of science that studies these complex phenomena at the cellular level (Kitano 2002). Understanding the mechanisms of the cell is essential for research and development in several areas such as drug discovery and biotechnological production. In the latter, metabolic engineering is used for building mutant microbial strains with increased productivity of compounds with industrial interest, such as biofuels (Stephanopoulos 1998). Using computational models of cellular metabolism, it is possible to systematically test and predict the optimal manipulations, such as gene knockouts, that produce the ideal phenotype for a specific application. These models are typically built in an iterative cycle of experiment and refinement, by multidisciplinary research teams that include biologists, engineers and computer scientists. The interconnection between different cellular processes, such as metabolism and genetic regulation, reflects the importance of the holistic approach claimed by the Systems Biology paradigm in replacement of traditional reductionist methods. Although most cellular components have been studied individually...

Dynamic decision modeling in medicine: a critique of existing formalisms.

Leong, T. Y.
Fonte: American Medical Informatics Association Publicador: American Medical Informatics Association
Tipo: Artigo de Revista Científica
Publicado em //1993 EN
Relevância na Pesquisa
395.34305%
Dynamic decision models are frameworks for modeling and solving decision problems that take into explicit account the effects of time. These formalisms are based on structural and semantical extensions of conventional decision models, e.g., decision trees and influence diagrams, with the mathematical definitions of finite-state semi-Markov processes. This paper identifies the common theoretical basis of existing dynamic decision modeling formalisms, and compares and contrasts their applicability and efficiency. It also argues that a subclass of such dynamic decision problems can be formulated and solved more effectively with non-graphical techniques. Some insights gained from this exercise on automating the dynamic decision making process are summarized.

Modeling formalisms in Systems Biology

Machado, Daniel; Costa, Rafael S; Rocha, Miguel; Ferreira, Eugénio C; Tidor, Bruce; Rocha, Isabel
Fonte: Springer Publicador: Springer
Tipo: Artigo de Revista Científica
Publicado em 05/12/2011 EN
Relevância na Pesquisa
502.6771%
Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future.

The Layer-Oriented Approach to Declarative Languages for Biological Modeling

Raikov, Ivan; De Schutter, Erik
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
292.03988%
We present a new approach to modeling languages for computational biology, which we call the layer-oriented approach. The approach stems from the observation that many diverse biological phenomena are described using a small set of mathematical formalisms (e.g. differential equations), while at the same time different domains and subdomains of computational biology require that models are structured according to the accepted terminology and classification of that domain. Our approach uses distinct semantic layers to represent the domain-specific biological concepts and the underlying mathematical formalisms. Additional functionality can be transparently added to the language by adding more layers. This approach is specifically concerned with declarative languages, and throughout the paper we note some of the limitations inherent to declarative approaches. The layer-oriented approach is a way to specify explicitly how high-level biological modeling concepts are mapped to a computational representation, while abstracting away details of particular programming languages and simulation environments. To illustrate this process, we define an example language for describing models of ionic currents, and use a general mathematical notation for semantic transformations to show how to generate model simulation code for various simulation environments. We use the example language to describe a Purkinje neuron model and demonstrate how the layer-oriented approach can be used for solving several practical issues of computational neuroscience model development. We discuss the advantages and limitations of the approach in comparison with other modeling language efforts in the domain of computational biology and outline some principles for extensible...

Cellular Potts Modeling of Tumor Growth, Tumor Invasion, and Tumor Evolution

Szabó, András; Merks, Roeland M. H.
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 16/04/2013 EN
Relevância na Pesquisa
379.62145%
Despite a growing wealth of available molecular data, the growth of tumors, invasion of tumors into healthy tissue, and response of tumors to therapies are still poorly understood. Although genetic mutations are in general the first step in the development of a cancer, for the mutated cell to persist in a tissue, it must compete against the other, healthy or diseased cells, for example by becoming more motile, adhesive, or multiplying faster. Thus, the cellular phenotype determines the success of a cancer cell in competition with its neighbors, irrespective of the genetic mutations or physiological alterations that gave rise to the altered phenotype. What phenotypes can make a cell “successful” in an environment of healthy and cancerous cells, and how? A widely used tool for getting more insight into that question is cell-based modeling. Cell-based models constitute a class of computational, agent-based models that mimic biophysical and molecular interactions between cells. One of the most widely used cell-based modeling formalisms is the cellular Potts model (CPM), a lattice-based, multi particle cell-based modeling approach. The CPM has become a popular and accessible method for modeling mechanisms of multicellular processes including cell sorting...

Integrative Analysis of Metabolic Models – from Structure to Dynamics

Hartmann, Anja; Schreiber, Falk
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 26/01/2015 EN
Relevância na Pesquisa
283.42516%
The characterization of biological systems with respect to their behavior and functionality based on versatile biochemical interactions is a major challenge. To understand these complex mechanisms at systems level modeling approaches are investigated. Different modeling formalisms allow metabolic models to be analyzed depending on the question to be solved, the biochemical knowledge and the availability of experimental data. Here, we describe a method for an integrative analysis of the structure and dynamics represented by qualitative and quantitative metabolic models. Using various formalisms, the metabolic model is analyzed from different perspectives. Determined structural and dynamic properties are visualized in the context of the metabolic model. Interaction techniques allow the exploration and visual analysis thereby leading to a broader understanding of the behavior and functionality of the underlying biological system. The System Biology Metabolic Model Framework (SBM2 – Framework) implements the developed method and, as an example, is applied for the integrative analysis of the crop plant potato.

Alternativas de alto desempenho para a multiplicação vetor-descritor

Campos Velho, Pedro Antônio Madeira de
Fonte: Pontifícia Universidade Católica do Rio Grande do Sul; Porto Alegre Publicador: Pontifícia Universidade Católica do Rio Grande do Sul; Porto Alegre
Tipo: Dissertação de Mestrado
PORTUGUêS
Relevância na Pesquisa
287.66416%
A modelagem analítica pode ser utilizada para prever desempenho, detectar deficiências e avaliar estratégias para melhorar sistemas. No contexto da modelagem computacional, diversos formalismos para a modelagem analítica estão se popularizando devido ao fato de proverem alto-nível de abstração e modularidade. No entanto, para inferir estimativas de desempenho destes modelos, é necessário resolver um sistema de equações. Em modelos analíticos estruturados, tais sistemas não se apresentam na forma tradicional, Ax = b, pois a matriz de coeficientes (A) é trocada por uma expressão algébrica (Q), denominada Descritor Markoviano (ou só descritor). Logo, a multiplicação convencional, Ax é substituída pela multiplicação vetor-descritor (MVD), Qx. Dois algoritmos foram propostos recentemente para implementar a MVD: shuffle e slice. Ambos apresentam um alto custo computacional, que eleva drasticamente o tempo necessário para resolver modelos complexos. O objetivo do presente trabalho está relacionado com a utilização de técnicas de alto desempenho para propor versões mais rápidas, tanto para o algoritmo shuffle quanto para o slice.; Analytical modeling can be used to predict performance, detect unexpected behavior and evaluate strategies in order to enhance systems. In the subject of modeling computational environments...

Utilização de diagramas de decisão multi-valorada para representação do espaço de estados atingível em redes de autômatos estocásticos

Scolari, Ana Paula Salengui
Fonte: Pontifícia Universidade Católica do Rio Grande do Sul; Porto Alegre Publicador: Pontifícia Universidade Católica do Rio Grande do Sul; Porto Alegre
Tipo: Dissertação de Mestrado
PORTUGUêS
Relevância na Pesquisa
291.10406%
Formalismos de modelagem são linguagens capazes de descrever sistemas de forma não ambígüa, permitindo a sua avaliação quantitativa. Os formalismos conhecidos como estruturados permitem a representação sistemática de modelos grandes e complexos. Entretanto, na prática, a modelagem de sistemas de tal porte pode apresentar o problema de explosão do espaço de estados. Em geral, a modelagem de sistemas através de formalismos estruturados, com espaço de estados discreto, resulta em um grande número de estados inatingíveis. A geração e armazenamento dos estados não atingíveis é um ônus não desejado ao processo de modelagem. Este trabalho apresenta um algoritmo capaz de gerar e armazenar somente o espaço de estados atingível (RSS) para o formalismo de Redes de Autômatos Estocásticos (SAN) utilizando Diagramas de Decisão Multi-Valorada (MDD). A idéia principal é apresentar uma primeira versão desse algoritmo, a m de comprovar a sua viabilidade para o formalismo SAN.; Modeling formalisms are languages capable of describing a system behavior in a non ambiguous way, allowing its quantitative evaluation. The structured formalisms can represent large and complex models in a systematic manner. However, the modeling of systems with such characteristics is still a problem...

Complementary use of BG and EMR formalisms for multiphysics systems analysis and control

CHIKHAOUI, Zeineb; GOMAND, Julien; MALBURET, François; BARRE, Jean-Pierre
Fonte: ASME Publicador: ASME
EN
Relevância na Pesquisa
383.42516%
In this paper, a complex multiphysics system is modeled using two different energy-based graphical techniques: Bond Graph and Energetic Macroscopic Representation. These formalisms can be used together to analyze, model and control a system. The BG is used to support physical, lumped-parameter modeling and analysis processes, and then EMR is used to facilitate definition of a control structure through inversion-based methodology. This complementarity between both of these tools is set out through a helicopter flight control subsystem.

Using restriction to extend parsing algorithms for complex-feature-based formalisms

Shieber, Stuart
Fonte: Association for Computational Linguistics Publicador: Association for Computational Linguistics
Tipo: Conference Paper
EN_US
Relevância na Pesquisa
290.938%
Grammar formalisms based on the encoding of grammatical information in complex-valued feature systems enjoy some currency both in linguistics and natural-language-processing research. Such formalisms can be thought of by analogy to context-free grammars as generalizing the notion of nonterminal symbol from a finite domain of atomic elements to a possibly infinite domain of directed graph structures of a certain sort. Unfortunately, in moving to an infinite nonterminal domain, standard methods of parsing may no longer be applicable to the formalism. Typically, the problem manifests itself as gross inefficiency or even nontermination of the algorithms. In this paper, we discuss a solution to the problem of extending parsing algorithms to formalisms with possibly infinite nonterminal domains, a solution based on a general technique we call restriction. As a particular example of such an extension, we present a complete, correct, terminating extension of Earley's algorithm that uses restriction to perform top-down filtering. Our implementation of this algorithm demonstrates the drastic elimination of chart edges that can be achieved by this technique. Finally, we describe further uses for the technique---including parsing other grammar formalisms...

Dispositivos adaptativos cooperantes: formulação e aplicação.; Cooperative adaptive devices : design and implementation.

Santos, José Maria Novaes dos
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 26/11/2014 PT
Relevância na Pesquisa
291.10406%
Com a crescente complexidade das aplicações e sistemas computacionais, atualmente tem se tornado importante o uso de formalismos de várias naturezas na representação e modelagem de problemas complexos, como os sistemas reativos e concorrentes. Este trabalho apresenta uma contribuição na Tecnologia Adaptativa e uma nova técnica no desenvolvimento de uma aplicação para execução de alguns tipos de jogos, (General Game Playing), cuja característica está associada à capacidade de o sistema tomar conhecimento das regras do jogo apenas em tempo de execução. Com esse trabalho, amplia-se a classe de problemas que podem ser estudados e analisados sob a perspectiva da Tecnologia Adaptativa, através dos Dispositivos Adaptativos Cooperantes. A aplicação desenvolvida como exemplo neste trabalho introduz uma nova ótica no desenvolvimento de aplicações para jogos gerais (GGP) e abre novos horizontes para a aplicação da Tecnologia Adaptativa, como a utilização das regras para extração de informação e inferência.; The complexity of computer applications has grown so much that several formalisms of different kinds became important nowadays. Many systems (e.g. reactive and concurrent ones) employ such formalisms to represent and model actual complex problems. This work contributes to the field of Adaptive Technology...

Modeling Time in Computing: A Taxonomy and a Comparative Survey

Furia, Carlo A.; Mandrioli, Dino; Morzenti, Angelo; Rossi, Matteo
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
302.67713%
The increasing relevance of areas such as real-time and embedded systems, pervasive computing, hybrid systems control, and biological and social systems modeling is bringing a growing attention to the temporal aspects of computing, not only in the computer science domain, but also in more traditional fields of engineering. This article surveys various approaches to the formal modeling and analysis of the temporal features of computer-based systems, with a level of detail that is suitable also for non-specialists. In doing so, it provides a unifying framework, rather than just a comprehensive list of formalisms. The paper first lays out some key dimensions along which the various formalisms can be evaluated and compared. Then, a significant sample of formalisms for time modeling in computing are presented and discussed according to these dimensions. The adopted perspective is, to some extent, historical, going from "traditional" models and formalisms to more modern ones.; Comment: More typos fixed

Relation between ab initio molecular dynamics and electron-phonon interaction formalisms

Prasanna, T. R. S.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
290.938%
The relation between ab initio molecular dynamics formalism and the electron-phonon interaction formalism [P.B. Allen and V. Heine, J. Phys. C 9, 2305 (1976)] is explored. The fundamental quantity obtained in the AIMD formalism - total energy for any configuration - is also obtained from the formalism (ES-DWF) that incorporates the role of Debye-Waller Factor in electronic structure calculations. The two formalisms are exactly equivalent and represent the direct and perturbation theory approaches to determine total energy. This equivalence allows either formalism to be used depending on the requirement - ES-DWF for a priori theoretical analysis and AIMD for ab initio modeling of the effect of thermal vibrations. Combining the two formalisms makes the ES-DWF formalism into an ab initio method and increases the range of problems that can be modeled ab initio. It is also theoretically possible to obtain self-consistent band structures from AIMD calculations. This study clarifies the incorrect assumptions regarding the two formalisms that exist in published literature. By combining the two formalisms and including self-energy effects, more accurate results can be obtained, ab initio, within the adiabatic approximation, than by using AIMD alone.; Comment: 16 pages...

Integrated Modeling and Verification of Real-Time Systems through Multiple Paradigms

Bersani, Marcello M.; Furia, Carlo A.; Pradella, Matteo; Rossi, Matteo
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 29/07/2009
Relevância na Pesquisa
387.66414%
Complex systems typically have many different parts and facets, with different characteristics. In a multi-paradigm approach to modeling, formalisms with different natures are used in combination to describe complementary parts and aspects of the system. This can have a beneficial impact on the modeling activity, as different paradigms an be better suited to describe different aspects of the system. While each paradigm provides a different view on the many facets of the system, it is of paramount importance that a coherent comprehensive model emerges from the combination of the various partial descriptions. In this paper we present a technique to model different aspects of the same system with different formalisms, while keeping the various models tightly integrated with one another. In addition, our approach leverages the flexibility provided by a bounded satisfiability checker to encode the verification problem of the integrated model in the propositional satisfiability (SAT) problem; this allows users to carry out formal verification activities both on the whole model and on parts thereof. The effectiveness of the approach is illustrated through the example of a monitoring system.; Comment: 27 pages