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Specification-correct and scalable coordination of scientific applications in grid environments 07

Specification-correct and scalable coordination of scientifi...

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7th IEEE international symposium on Cluster Computing and the Grid

作者： Prodan, Radu Univ Innsbruck Inst Comp Sci Tech Str 21A A-6020 Innsbruck Austria

ISBN: (纸本)9780769528335

the workflow model for composing Grid applications is based on an imperative model of computation prone to programming errors, which is an issue yet to consider in the Grid community. In this paper, we propose a new unconventional model for programming Grid applications based on two programming phases: (1) formal functional specification, written by the application scientist not interested in any Grid-related issues and representing "what" has to be computed;(2) imperative workflow-based coordination, written by the computer scientist which indicates "how" to efficiently execute the specification on the Grid. A correctness checker automatically connects both parts at compile-time and ensures the correct execution of the workflow coordination with respect to the formal specification. We validate our approach for three real-world applications and show experimental results that demonstrate the correctness and scalability of our coordination model.

关键词： programming profession functional programming Application software Grid computing Computational modeling Formal specifications Scalability Middleware Switches Computer science

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Solving satisfiability in ground logic with equality by efficient conversion to propositional logic

Solving satisfiability in ground logic with equality by effi...

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7th international symposium on Abstraction, Reformulation and Approximation

作者： Gammer, Igor Amir, Eyal Univ Illinois Dept Comp Sci Urbana IL USA

ISBN: (纸本)9783540735793

Ground logic with Equality (GL(=)) is a subset of First-Order logic (FOL) in which functions or quantifiers are excluded, but equality is preserved. We argue about GL(=) 's unique position (in terms of expressiveness and ease of decidability) between FOL and Propositional logic (PL). We aim to solve satisfiability (SAT) problems formulated in GL(=) by converting them into PL using a satisfiability-preserving conversion algorithms, and running a general SAT solver on the resulting PL Knowledge Base (KB). We introduce two conversion algorithms, with the latter utilizing the former as a subroutine, and prove their correctness - that is, that the translation preserves satisfiability. the main contribution of this work is in utilizing input fragmentation to yield PL KBs that are smaller than possible prior to our work, thus resulting in the ability to solve GL(=) SAT problems faster than was possible before.

关键词： logic programming

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Differential Scoring for Systolic Sequence Alignment

Differential Scoring for Systolic Sequence Alignment

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IEEE symposium on Bioinformatics and Bioengineering (BIBE)

作者： Antonio E. de la Serna Member IEEE serna@***

Systolic implementations of dynamic programming solutions that utilize a similarity matrix can achieve appreciable performance with both course-and fine-grain parallelization. A limitation of systolic array design is that score routing between array elements, array I/O bandwidth, and score memory capacity are dependent upon the length of the sequence that can be processed. A novel approach of differential scoring is presented that exploits adjacency and decouples the complexity of score routing and systolic array bandwidth to sequence length. Instead, these design parameters become a function of algorithm sensitivity. As a consequence, the Simile implementation of differential scoring for sequence alignment has reduced score routing, I/O bandwidth, and score storage by 82% for sequences of length 10 and has significantly improved gate count, clock rate, and power utilization per systolic processing element.

关键词： Systolic arrays Dynamic programming Routing Bandwidth Heuristic algorithms Concurrent computing Algorithm design and analysis Matrices Computational complexity logic programming

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IEEE 7th BIBE Research Tutorial Lecture: Decoding Novel Genomes: From Microbiomes to the Eukaryota

IEEE 7th BIBE Research Tutorial Lecture: Decoding Novel Geno...

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IEEE symposium on Bioinformatics and Bioengineering (BIBE)

作者： Mark Borodovsky Department of Biomedical Engineering and Division of Computational Science Georgia Institute of Technology Atlanta GA USA

One of the main goals of computational genomics is fast and accurate biological interpretation of newly sequenced genomic DNA. the complexity of the task varies among genomes but is never simple. Currently, for a new genome a custom built annotation pipeline is constructed by integration of ab initio and comparative genomic methods. Still, a consistent solution of the jigsaw puzzle of genome annotation frequently requires additional experimental efforts (such as EST/cDNA sequencing, etc.) Current ab initio gene finding algorithms use statistical analysis and optimization to solve the gene identification problem restated as search for the optimal parse of the genomic sequence into fragments with distinct statistical characteristics. this problem setting leads to a classic task for dynamic programming: search for an optimal path through a network with weights/scores assigned to nodes and vertices. Obviously, assignment of weights/scores plays a critical role and may present a significant challenge. this task is equivalent to estimation of parameters of statistical models (hidden Markov models) representing a mosaic of functional sequences and sites in a given genome. the task is rather easy when large sets of validated training sequences are available. However, it is not the case for hundreds of currently unfolding genome sequencing and annotation projects. In the lecture we will consider the general schemes of ab initio gene prediction. We will discuss estimation of model parameters without a training set. We will show that this unsupervised approach is possible and is becoming very important for two rapidly developing branches of genomics: i/ for prokaryotic metagenomes that are becoming a rich source of information about non-cultivated microbial species and ii/ for "compact" eukaryotic genomes, such as fungi, which relatively short genome size (less than 50 MB) allows to obtain complete genome sequence in a relatively short time.

关键词： Genomics Bioinformatics Sequences Parameter estimation Hidden Markov models Biology computing DNA computing Pipelines Statistical analysis Dynamic programming

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Environmentally superior implementation of electronic hardware through modular programmable logic devices & eco design

Environmentally superior implementation of electronic hardwa...

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14th IEEE international symposium on Electronics and the Environment (ISEE)/7th Electronics Recycling Summit

作者： Fitzpatrick, Colin Walsh, Joseph Grout, Ian Univ Limerick Dept Elect & Comp Engn Limerick Ireland

ISBN: (纸本)1424403510

the inclusion of modular functional units is often used as an example of how environmental considerations can be incorporated in the design stage of electronic products. the assumption is that the functional units can can be reused at end of life to perform the same task in a different product. the environmental benefit from this practice is only accrued if the feedback loop from recovery to remanufacture is completed. the barriers to the completion of this loop are numerous and concern compatability, reliability, functionality, flexibility and cost inter alia. this paper discusses the concept of modular digital electronic circuits based on programmable logic device technology and examines their suitability for use in the scheme of an overall Eco-design methodology based on the re-use of such modular units. A comparative streamlined life cycle assessment between this methodology and conventional digital electronics is also conducted to inspect the environmental benefits across the whole life cycle.

关键词： eco-design programmable logic devices electronics re-use circuit re-use

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A functional tool for fuzzy first order logic evaluation 4

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7th international Conference on Fuzzy logic and Intelligent Technologies in Nuclear Science

作者： Lopez, Victoria Cleva, J. Miguel Montero, Javier Univ Complutense Madrid Fac Informat E-28040 Madrid Spain Nebrija Univ Dept Comp Sci Madrid Spain Univ Complutense Madrid Fac Math E-28040 Madrid Spain

ISBN: (纸本)9812566902

In this paper we present an automatic evaluation tool for fuzzy first order logic formulae. Since different logics can be considered, we allow for such formulae the appearance of syntactic modifiers, in such a way that our tool is designed not only to evaluate formulae in existing logic, but also to evaluate properties in any other logic framework given by the user. Such generalization is performed using Haskell, a functional programming language.

关键词： Syntactics

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Planning effectively with stories: Requirements and planning made easy

Planning effectively with stories: Requirements and planning...

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7th international Conference on eXtreme programming and Agile Processes in Software Engineering: Tutorials, Workshops, Activities, and Keynote Speeches

作者： Hill, Mike Industrial Logic Inc.

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Fast Boolean matching with don't cares

Fast Boolean matching with don't cares

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IEEE international symposium on Quality Electronic Design

作者： Zile Wei D. Chai A. Kuehlmann A.R. Newton University of California Berkeley CA USA Cadence Berkeley Laboratories Berkeley CA USA

this paper describes a fast Boolean matching algorithm which checks the containment relationship between an incompletely specified function and a completely specified function under permutation and negation on the input variables. the algorithm is designed for the pattern matching problem in technology mapping. It exploits functional symmetries of patterns and utilizes a compact data structure: binary permutation matrix. Using this matrix, nonmatching permutations and phase assignments can be pruned efficiently. All legal permutations and phase assignments, leading to a matching, can be obtained, as well. the experimental results on the MCNC benchmarks show that, compared with other Boolean matching approaches, our algorithm is at least 1,500 times faster for a common pattern abed + efgh and 58,000 times faster for another common pattern ab + cd + ef + gh. the matching speed for completely specified functions is also comparable to state-of-the-art matching algorithms

关键词： Libraries Pattern matching Data structures Boolean functions Algorithm design and analysis Input variables Law Legal factors logic circuits Circuit synthesis

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Practical Aspects of Declarative Languages - 7th international symposium, PADL 2005

Practical Aspects of Declarative Languages - 7th Internation...

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7th international symposium on Practical Aspects of Declarative Languages, PADL 2005

the proceedings contain 19 papers from the Practical Aspects of Declarative Languages - 7th international symposium, PADL 2005. the topics discussed include: functional framework for sound synthesis;specializing narrowing for time table generation;character-based cladistics and answer set programming;role-based declarative synchronization for reconfigurable systems;towards a more practical hybrid probabilistic logic;safe programming with pointers through stateful views;a provably correct compiler for efficient model checking of mobile processes;an ordered logic program solver;improving memory usage in the BEAM;and solving constraints on sets of spatial objects.

关键词： Computer programming languages

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Specializing narrowing for timetable generation: A case study

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7th international symposium on Practical Aspects of Declarative Languages (PADL)

作者： Brauner, N Echahed, R Finke, G Gregor, H Prost, F Inst Informat & Math Appl Grenoble Lab Leibniz F-38000 Grenoble France

ISBN: (纸本)3540243623

An important property of strategies used to solve goals in functional logic programming (FLP) languages is the complete exploration of the solution space. Integrating constraints into FLP proved to be useful in many cases, as the resulting constraint functional logic programming (CFLP) offers more facilities and more efficient operational semantics. CFLP can be achieved by means of conditional rewrite systems with a narrowing-based operational semantics. A common idea to improve the efficiency of such operational semantics is to use specific algorithms from operations research as constraint solvers. If the algorithm does not return a complete set of solutions, the property of completeness might be lost. We present a real world timetabling problem illustrating this approach. We propose an algorithm, obtained as an integration of three known optimization algorithms for the linear assignment problem (LAP), enumerating solutions to the LAP in order of increasing weight, such that resolution of goals is complete again. We show, how the narrowing process can be tailored to use this algorithm and provide an efficient way to solve the timetable generation problem.

关键词： functional-logic programming constraints narrowing timetable generation

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