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graph Transformations - Third international Conference, ICGT 2006, Proceedings

3rd international Conference on graph Transformations, ICGT 2006

ISBN: (纸本)3540388702

The proceedings contain 34 papers. The topics discussed include: nested quantification in graph transformation rules;new algorithms and applications of cyclic reference counting;narrowing data-structures with pointers;string generating hypergraph grammars with word order restrictions;process bisimulation via a graphical encoding;dynamic graph transformation systems;transition analysis of model transformations by petri nets;temporal graph queries to support software evolution;on the use of alloy to analyze graph transformation systems;model view management with triple graph transformation systems;heuristic search for the analysis of graph transition systems;weakest preconditions for high-level programs;introductory tutorial on foundations and applications of graph transformation;workshop on graph computation models;and workshop on petri nets and graph transformations.

关键词： graph theory

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An approximate de bruijn graph approach to multiple local alignment and motif discovery in protein sequences

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1st international workshop on Data Mining and Bioinformatics, VDMB 2006

作者： Patwardhan, Rupali Haixu, Tang Sun, Kim Dalkilic, Mehmet Center for Genomics and Bioinformatics Indiana University 1001 E. 3rd Street Bloomington IN 47405 United States School of Informatics Indiana University 901 E. 10th Street Bloomington IN 47408 United States

ISBN: (纸本)3540689702

Motif discovery is an important problem in protein sequence analysis. Computationally, it can be viewed as an application of the more general multiple local alignment problem, which often encounters the difficulty of computer time when aligning many sequences. We introduce a new algorithm for multiple local alignment for protein sequences, based on the de Bruijn graph approach first proposed by Zhang and Waterman for aligning DNA sequence. We generalize their approach to aligning protein sequences by building an approximate de Bruijn graph to allow gluing similar but not identical amino acids. We implement this algorithm and test it on motif discovery of 100 sets of protein sequences. The results show that our method achieved comparable results as other popular motif discovery programs, while offering advantages in terms of speed. © Springer-Verlag Berlin Heidelberg 2006.

关键词： Proteins

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Closure properties of linear context-free tree languages with an application to optimality theory

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THEORETICAL computer science 2006年第1期354卷 82-97页

作者： Kepser, S Mönnich, U Univ Tubingen D-72074 Tubingen Germany

Context-free tree grammars, originally introduced by Rounds [Math. Systems Theory 4(3) (1970) 257-287], are powerful grammar devices for the definition of tree languages. The properties of the class of context-free tree languages have been studied for more than three decades now. Particularly important here is the work by Engelfriet and Schmidt [J. Comput. System Sci. 15(3) (1977) 328-353, 16(1) (1978) 67-99]. In the present paper, we consider a subclass of the class of context-free tree languages, namely the class of linear context-free tree languages. A context-free tree grammar is linear, if no rule permits the copying of subtrees. For this class of linear context-free tree languages we show that the grammar derivation mode, which is very important for the general class of context-free tree languages, is immaterial. The main result we present is the closure of the class of linear context-free tree languages under linear frontier-to-root tree transduction mappings. Two further results are the closure of this class under linear root-to-frontier tree transduction mappings and under intersection with regular tree languages. The results of the first part of the paper are applied to the formalisation of optimality theory. Optimality theory (OT), introduced by Prince and Smolensky [Tech. Report 1993], is a linguistic framework in which the mapping of one level of linguistic representation to another is based on rules and filters. The rules generate candidate expressions in the target representation, which are subsequently checked against the filters, so that only those candidates remain that survive this filtering process. A proposal to formalise the description of OT using formal language theory and in particular automata theory was presented by Karttumen [Proceedings of international workshop on Finite-State Methods in Natural Language Processing, 1998, pp. 1-12] and Frank and Satta [Comput. Linguistics 24 (1998) 307-315]. The main result of these papers is that if th

关键词： context-free tree grammar optimality theory finite-state techniques

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Closure properties of linear context-free tree languages with an application to optimality theory

Closure properties of linear context-free tree languages wit...

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3rd international workshop on Algebraic Methods in Language Processing

作者： Kepser, S Mönnich, U Univ Tubingen D-72074 Tubingen Germany

关键词： context-free tree grammar optimality theory finite-state techniques

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Automatically retargetable pre-processor and assembler generation for ASIPs

Automatically retargetable pre-processor and assembler gener...

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Annual IEEE Northeast workshop on Circuits and Systems (NEWCAS)

作者： L. Taglietti J.O.C. Filho D.C. Casarotto O.J.V. Furtado L.C.V. dos Santos Computer Science Department Federal University of Santa Catarina Florianopolis Santa Catarina Brazil

During design space exploration, alternative CPUs are evaluated for an envisaged SoC, thereby requiring fast CPU models and efficient code generation tools. Candidate CPUs may be general-purpose processors, DSPs, micro-controllers or ASIPs. The ASIP is a particularly challenging alternative: since instruction-set architecture (ISA) tailoring is allowed, an ASIP cannot rely on pre-existent code generation tools. Each target ISA requires a new tool chain. Therefore, an automatically retargetable tool chain is mandatory. This paper focuses on a couple of tools from such a chain: pre-processor and assembler. It proposes robust and efficient techniques allowing retargetability through automatic tool generation from a given target ISA, which is formally described by architecture description language (ADL) constructs. Tool robustness results from formal techniques based on context-free grammars. Tool efficiency evidence is provided by experiments targeting three CPUs: MIPS, PowerPC 405 and PIC 16F84.

关键词： Assembly application specific processors Instruction sets Space exploration Robustness Architecture description languages computer science Microelectronics Digital signal processing Hardware

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Ygdrasil - a framework for composing shared virtual worlds

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FUTURE GENERATION computer SYSTEMS-THE international JOURNAL OF Escience 2003年第6期19卷 1041-1049页

作者： Pape, D Anstey, J Dolinsky, M Dambik, EJ Univ Buffalo Dept Media Study Buffalo NY USA Indiana Univ Henry Radford Hope Sch Fine Arts Bloomington IN USA Indiana Univ Knowledge Acquisit & Project Lab Bloomington IN USA

Ygdrasil is a programming framework for creating networked, multi-user virtual worlds, especially interactive artistic worlds. It provides a shared scene graph, a plug-in system for adding new behaviors, and a high-level script interface for composing these worlds. We describe the architecture of Ygdrasil, and its use in creating two applications that were demonstrated at the iGrid 2002 workshop. (C) 2003 Elsevier science B.V. All rights reserved.

关键词： virtual reality shared virtual environments computer art

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Ygdrasil - a framework for composing shared virtual worlds

Ygdrasil - a framework for composing shared virtual worlds

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3rd Biennial international Grid application-Driven Testbed Conference (iGrid 2002)

关键词： virtual reality shared virtual environments computer art

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3rd international Conference on Machines, Computations, and Universality, MCU 2001

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3rd international Conference on Machines, Computations and Universality, MCU 2001

ISBN: (纸本)3540421211

The proceedings contain 22 papers. The special focus in this conference is on Machines, Computations, and Universality. The topics include: Three small universal turing machines;computation in gene networks;power, puzzles and properties of entanglement;combinatorial and computational problems on finite sets of words;universality results;a simple universal logic element and cellular automata for reversible computing;decidable and undecidable cases;two normal forms for rewriting P systems;on the transition graphs of turing machines;JC-nets;nonterminal complexity of programmed grammars;on the number of non-terminal symbols in graph-controlled, programmed and matrix grammars;a direct construction of a universal extended h system;speeding-up cellular automata by alternations;efficient universal pushdown cellular automata and their application to complexity;firing squad synchronization problem on bidimensional cellular automata with communication constraints;universality and efficiency;on the computational power of a continuous-space optical model of computation and on a P-optimal proof system for the set of all satisfiable boolean formulas SAT.

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Machines, Computations, and Universality - Third international Conference, MCU 2001, Proceedings

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3rd international Conference on Machines, Computations, and Universality, MCU 2001

ISBN: (纸本)3540421211

The proceedings contain 22 papers. The topics discussed include: combinatorial and computational problems on finite sets of words;a simple universal logic element and cellular automata for reversible computing;some applications of the decidability of DPDA's equivalence;the equivalence problem for computational models: decidable and undecidable cases;on the transition graphs of Turing machines;nonterminal complexity of programmed grammars;on the number of non-terminal symbols in graph-controlled, programmed and matrix grammars;speeding-up cellular automata by alternations;efficient universal pushdown cellular automata and their application to complexity;firing squad synchronization problem on bidimensional cellular automata with communication constraints;on the computational power of a continuous-space optical model of computation;and on a P-optimal proof system for the set of all satisfiable Boolean formulas (SAT).

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Image labeling and grouping by minimizing linear functionals over cones 3rd

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3rd international workshop on Energy Minimization Methods in computer Vision and Pattern Recognition

作者： Schellewald, C Keuchel, J Schnörr, C Univ Mannheim Dept Math & Comp Sci Comp Vis Graph & Pattern Recognit Grp D-68131 Mannheim Germany

ISBN: (纸本)3540425233

We consider energy minimization problems related to image labeling, partitioning, and grouping, which typically show up at mid-level stages of computer vision systems. A common feature of these problems is their intrinsic combinatorial complexity from an optimization point-of-view. Rather than trying to compute the global minimum - a goal we consider as elusive in these cases - we wish to design optimization approaches which exhibit two relevant properties: First, in each application a solution with guaranteed degree of suboptimality can be computed. Secondly, the computations are based on clearly defined algorithms which do not comprise any (hidden) tuning parameters. In this paper, we focus on the second property and introduce a novel and general optimization technique to the field of computer vision which amounts to compute a suboptimal solution by just solving a convex optimization problem. As representative examples, we consider two binary quadratic energy functionals related to image labeling and perceptual grouping. Both problems can be considered as instances of a general quadratic functional in binary variables, which is embedded into a higher-dimensional space such that suboptimal solutions can be computed as minima of linear functionals over cones in that space (semi-definite programs). Extensive numerical results reveal that, on the average, suboptimal solutions can be computed which yield a gap below 5% with respect to the global optimum in case where this is known.

关键词： computer vision

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