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检索条件"机构=Parallel Computing Systems group"

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Distributed computing and modeling & simulation: Speeding up simulations and creating large models 11

Distributed computing and modeling & simulation: Speeding up...

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Simulation Winter Conference

作者： Simon J. E. Taylor Mohammadmersad Ghorbani Navonil Mustafee Stephen J. Turner Tamas Kiss Daniel Farkas Shane Kite Steffen Straßburger ICT Innovation Group School of Information Systems Computing and Mathematics Brunei University Uxbridge UK Centre for Parallel Computing University of Westminster London UK School of Business and Economics Swansea University Swansea UK Upper Courtyard Saker Solutions Alcester UK Parallel & Distributed Computing Centre School of Computer Engineering Nanyang Technological University Singapore Singapore School of Economic Sciences Ilmenau University of Technology Ilmenau Germany

Distributed computing has many opportunities for Modeling and Simulation (M&S). Grid computing approaches have been developed that can use multiple computers to reduce the processing time of an application. In terms of M&S this means simulations can be run very quickly by distributing individual runs over locally or remotely available computing resources. Distributed simulation techniques allow us to link together models over a network enabling the creation of large models and/or models that could not be developed due to data sharing or model reuse problems. Using real-world examples, this advanced tutorial discusses how both approaches can be used to benefit M&S researchers and practitioners alike.

关键词： Computational modeling Biological system modeling Data models Educational institutions Computers Grid computing Software

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A parameter-adaptive dynamic programming approach for inferring cophylogenies

A parameter-adaptive dynamic programming approach for inferr...

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8th Asia-Pacific Bioinformatics Conference, APBC 2010

作者： Merkle, Daniel Middendorf, Martin Wieseke, Nicolas Department of Mathematics and Computer Science University of Southern Denmark Odense Denmark Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Germany

Background: Coevolutionary systems like hosts and their parasites are commonly used model systems for evolutionary studies. Inferring the coevolutionary history based on given phylogenies of both groups is often done by employing a set of possible types of events that happened during coevolution. Costs are assigned to the different types of events and a reconstruction of the common history with a minimal sum of event costs is sought. Results: This paper introduces a new algorithm and a corresponding tool called CoRe-PA, that can be used to infer the common history of coevolutionary systems. The proposed method utilizes an event-based concept for reconciliation analyses where the possible events are cospeciations, sortings, duplications, and (host) switches. All known event-based approaches so far assign costs to each type of cophylogenetic events in order to find a cost-minimal reconstruction. CoRe-PA uses a new parameter-adaptive approach, i.e., no costs have to be assigned to the coevolutionary events in advance. Several biological coevolutionary systems that have already been studied intensely in literature are used to show the performance of CoRe-PA. Conclusion: From a biological point of view reasonable cost values for event-based reconciliations can often be estimated only very roughly. CoRe-PA is very useful when it is difficult or impossible to assign exact cost values to different types of coevolutionary events in advance. © 2010 Yeturu et al;licensee BioMed Central Ltd.

关键词： Costs

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Improving simulation through advanced computing techniques: Grid computing and simulation interoperability 10

Improving simulation through advanced computing techniques: ...

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Simulation Winter Conference

作者： Simon J. E. Taylor Navonil Mustafee Shane Kite Chris Wood Stephen J. Turner Steffen Straßburger ICT Innovation Group School of Information Systems Computing and Mathematics Uxbridge UK School of Business and Economics Swansea University Swansea UK Saker Solutions Upper Courtyard Alcester UK Saker Solutions Alcester UK Swansea University School of Business and Economics Wales UK Nanyang Technological University Parallel & Distributed Computing Centre School of Computer Engineering Singapore SINGAPORE Technische Universitat Ilmenau Ilmenau ThÃ¼ringen DE

ISBN: (纸本)9781424498642

Today, due to exciting developments in advanced computing techniques and technologies, many scientists can now make use of dedicated high speed networks and high performance computing. This so-called `e-Science' in enabling scientist across many fields to work together in global virtual research communities. What do these advancements mean for modeling and simulation? This advanced tutorial instigates two key areas that are affecting the way M&S projects are being developed and deployed. Grid computing addresses the use of many computers to speed up applications. Simulation Interoperability deals with linking together remote simulations and/or speeding up the execution of a single run. Through the use of case studies we hope to show that both these areas are making a major impact on the practice of M&S in both industry and science, as well as in turn supporting the future capabilities of e-Science.

关键词： Biological system modeling Computational modeling Grid computing Analytical models Middleware Mathematical model Software

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Evolved cooperation and emergent communication structures in learning classifier based organic computing systems 09

Evolved cooperation and emergent communication structures in...

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11th Annual Genetic and Evolutionary Computation Conference, GECCO-2009

作者： Scheidler, Alexander Middendorf, Martin Parallel Computing and Complex Systems Group Faculty of Mathematics and Computer Science University of Leipzig Germany

ISBN: (纸本)9781605583259

In this paper we look at systems consisting of many autonomous components or agents which have only limited amount of resources (e.g. memory) but are able to communicate with each other. The aim of these systems is to solve classification problems (usually to classify binary strings). We incorporate a pittsburgh style learning classifier system into the agents and extend its possible actions by actions for passing the classification requests to other agents. We show that the system is able to overcome the limited resources of its parts by evolving cooperation between them. We take a deeper look at the structure of the generated rule sets and investigate the occurring communication patterns. © 2009 ACM.

关键词： Genetic algorithms

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Efficiency and Benefits of Wireless Network Segregation

Efficiency and Benefits of Wireless Network Segregation

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International Conference on Networking and Services (ICNS)

作者： Athanasios Paraskelidis Mo Adda School of Computing Parallel Systems and Networks Research Group University of Portsmouth UK

This paper examines the performance of segregate networks with single and multiple channels. It compares the simulation results to the location-aware channel assignment protocol named GRID. The term segregated means that the network is divided into smaller domains and each one operates on different radios. Each node is assigned a predefined pool of radios, per segregate. The results show that the average delay of the segregate is comparable to GRID topology, in some instances. We also demonstrate that the effect of single channel interference has been minimised and the throughput of the network has been increased, far more when multiple channel allocations are deployed within the segregate. Segregate networks are more robust in harsh environments and provide better data reliability.

关键词： Wireless networks Interference Protocols Telecommunication traffic Computer networks Wireless LAN Concurrent computing Wireless mesh networks Routing Switches

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Finding All sorting tandem duplication random loss operations

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20th Annual Symposium on Combinatorial Pattern Matching, CPM 2009

作者： Bernt, Matthias Chen, Ming-Chiang Merkle, Daniel Wang, Hung-Lung Chao, Kun-Mao Middendorf, Martin Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Germany Department of Computer Science and Information Engineering National Taiwan University Taiwan Department of Mathematics and Computer Science University of Southern Denmark Odense Denmark

ISBN: (纸本)3642024408

A tandem duplication random loss (TDRL) operation duplicates a contiguous segment of genes, followed by the loss of one copy of each of the duplicated genes. Although the importance of this operation is founded by several recent biological studies, it has been investigated only rarely from a theoretical point of view. Of particular interest are sorting TDRLs which are TDRLs that, when applied to a permutation representing a genome, reduce the distance towards another given permutation. The identification of sorting genome rearrangement operations in general is a key ingredient of many algorithms for reconstructing the evolutionary history of a set of species. In this paper we present methods to compute all sorting TDRLs for two given gene orders. In addition, a closed formula for the number of sorting TDRLs is derived and further properties of sorting TDRLs are investigated. It is also shown that the theoretical findings are useful for identifying unique sorting TDRL scenarios for mitochondrial gene orders. © 2009 Springer Berlin Heidelberg.

关键词： Genes

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On the Design of RNA Sequences for Realizing Extended Shapes

On the Design of RNA Sequences for Realizing Extended Shapes

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International Joint Conference on Bioinformatics, systems Biology and Intelligent computing, IJCBS

作者： Marc Hellmuth Daniel Merkle Martin Middendorf Interdisciplinary Centre of Bioinformatics Department of Computer Science University of Leipzig Leipzig Germany Department of Mathematics and Computer Science University of Southern Denmark Odense Denmark Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Leipzig Germany

It is known that for two given secondary structures (defined by position of base pairings) an RNA string can easily be found that can fold into both structures. But for more than two secondary structures this is not necessarily possible. Moreover, when four or more secondary structures are given the problem to determine the least number of positions, such that after the removal of all incident base pairs, a compatible RNA sequence can be found, is known to be NP-complete (\cite{real_shapes}). In this paper we introduce pseudo edges that are used to forbid that certain base pairs can bind and therefore can be used to define the properties of possible RNA secondary structures. We study the complexity of the problem to design an RNA sequence that can fold into different secondary structures each of them is described by a set of required and forbidden base pairs. We refine the NP-completeness results of \cite{real_shapes} and show an analoguous NP-completeness result for the realization problem concerning the removal of (pseudo) edges. We also present a polynomial time method for checking the realizability of extended shape graphs. Furthermore, we empirically analyze the influence of pseudo edges on the realizability for sets of random RNA sequences and for sets of aptamers.

关键词： RNA Shape Switches Computer science Bioinformatics Sequences systems biology Intelligent systems Biology computing Concurrent computing

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SPP1148 booth: Hyperreconfigurable architectures

SPP1148 booth: Hyperreconfigurable architectures

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International Conference on Field Programmable Logic and Applications

作者： Sebastian Lange Martin Middendorf Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Germany

ISBN: (纸本)9781424419606

Dynamically reconfigurable hardware offers promising possibilities for flexible, computation intensive applications. With the technological advance of reconfigurable hardware came a rapid growth in the number of resources per chip requiring large amounts of data transfer per reconfiguration. Especially run-time reconfigurable applications, which make frequent use of reconfiguration, suffer from the growing overhead induced thereby. In this project, we investigate novel concepts for reconfigurable architectures that can dynamically reconfigure the actual reconfiguration potential to reduce the total amount of reconfiguration data that is necessary for a computation.

关键词： Computer architecture Computational modeling Hardware Reconfigurable architectures Polynomials Control systems Conferences

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On the Reconfiguration Costs of Models for Partially Reconfigurable FPGAs

On the Reconfiguration Costs of Models for Partially Reconfi...

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Southern Conference on Programmable Logic

作者： Sebastian Lange Martin Middendorf Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Leipzig Germany

ISBN: (纸本)9781424419920

There exists several FPGA architectures that can be partially reconfigured at run-time. The advantage of partial run-time reconfiguration is that it allows to develop new algorithmic solutions for many applications. But a limiting factor for using frequent dynamic reconfiguration could be the reconfiguration overhead. In order to study the potential of frequent run-time reconfiguration it is interesting to investigate its costs and benefits from an abstract point of view and to develop new architectural concepts. In this paper, we provide a formal treatment of the reconfiguration costs and compare them for models of standard partially reconfigurable FPGAs and 2-level reconfigurable FPGAs.

关键词： Costs Field programmable gate arrays Switches Runtime Computer architecture Reconfigurable architectures Reconfigurable logic parallel processing Computer science Application software

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Swarm controlled emergence - Designing an anti-clustering ant system

Swarm controlled emergence - Designing an anti-clustering an...

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2007 IEEE Swarm Intelligence Symposium, SIS 2007

作者： Merkle, Daniel Middendorf, Martin Scheidler, Alexander Parallel Computing and Complex Systems Group University of Leipzig Johannisgasse 26 04103 Leipzig Germany

ISBN: (纸本)1424407087

A new approach to prevent negative emergent behaviors of adaptive or organic computing systems is presented. One characteristic of such computing systems is the use self-organisation principles from nature and components that make decentralized decisions. To control such systems is a difficult task. In this paper we propose to control by introducing a swarm of so called anti-components to the system that can prevent the negative emergence. As an example serves a model that is inspired by the emergent behavior of ants to cluster different items. This model system has been used for several applications in computer science already. Different types of anti-components (or anti-agents) that can prevent a clustering behavior are designed for this system. Several cluster validity measures are used to investigate the clustering behavior of a system that contains standard clustering agents together with anti-clustering agents. It is shown that such systems can show a complex behavior over time where a phase of item distributions with increasing order is followed by distributions with increasing degree of clustering. It is also shown that a medium number of certain anti-clustering agents (which in a larger number completely prevent any clustering) may even help the system to perform a good clustering faster. © 2007 IEEE.

关键词： Global optimization

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