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International Symposium on Empirical Software engineering and Measurement, ESEM

作者： Jose Fortuna Abrantes Guilherme Horta Travassos COPPE/Systems Engineering and Computer Science Program Federal University of Rio de Janeiro Rio de Janeiro Brazil

Objective: to investigate studies about software processes looking for practices which can be used to obtain agility in software processes. Method: A systematic review including seven search engines was executed in Feb/2010. To apply the defined criteria to select papers and extract information regarding working practices bringing agility to software processes. Results: from 6696 retrieved papers, 441 were selected to support the identification of 236 occurrences of 51 distinct practices associated with the concept of agility. Their descriptions were deeply analyzed and consolidated. After discarding those which appeared in the technical literature in a small amount of papers, 17 agile practices were identified. Conclusion: although further studies are necessary to evaluate the efficacy of these 17 agile practices, 12 of them have been more commonly approached in the software projects and could be primarily considered: test driven development, continuous integration, pair programming, planning game, onsite customer, collective code ownership, small releases, metaphor, refactoring, sustainable pace, simple design and coding standards.

关键词： Software Software engineering Context programming profession Business Encoding

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Hardware Particle Swarm Optimization with passive congregation for embedded applications

Hardware Particle Swarm Optimization with passive congregati...

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Southern Conference on programmable Logic

作者： Muñoz, Daniel M. Llanos, Carlos H. Coelho, Leandro Dos S. Ayala-Rincón, Mauricio Department of Mechanical Engineering Automation and Control Group/GRACO University of Brasilia Brasilia D.F. Brazil Industrial and Systems Engineering Graduate Program Pontifical Catholic University of Parana Curitiba Parana Brazil Department of Computer Science and Mathematics University of Brasilia Brasilia D.F. Brazil

ISBN: (纸本)9781424488483

Achieving high performance optimization algorithms for embedded applications can be very challenging, particularly when several requirements such as high accuracy computations, short elapsed time, area cost, low power consumption and portability must be accomplished. This paper proposes a hardware implementation of the Particle Swarm Optimization algorithm with passive congregation (HPPSOpc), which was developed using several floating-point arithmetic libraries. The passive congregation is a biological behavior which allows the swarm to preserve its integrity, balancing between global and local search. The HPPSOpc architecture was implemented on a Virtex5 FPGA device and validated using two multimodal benchmark problems. Synthesis, simulation and execution time results demonstrates that the passive congregation approach is a low cost solution for solving embedded optimization problems with a high performance. © 2011 IEEE.

关键词： Digital arithmetic

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High Level Rule Modeling Language for Airline Crew Pairing

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AIP Conference Proceedings 2011年第1期1389卷 798-801页

作者： Erdal Mutlu Ş. İlker Birbil Kerem Bülbül Hüsnü Yenigün aSabanci University Computer Science & Engineering Program Orhanli‐Tuzla 34956 Istanbul Turkey bSabanci University Manufacturing Systems & Industrial Eng. Program Orhanli‐Tuzla 34956 Istanbul Turkey

The crew pairing problem is an airline optimization problem where a set of least costly pairings (consecutive flights to be flown by a single crew) that covers every flight in a given flight network is sought. A pairing is defined by using a very complex set of feasibility rules imposed by international and national regulatory agencies, and also by the airline itself. The cost of a pairing is also defined by using complicated rules. When an optimization engine generates a sequence of flights from a given flight network, it has to check all these feasibility rules to ensure whether the sequence forms a valid pairing. Likewise, the engine needs to calculate the cost of the pairing by using certain rules. However, the rules used for checking the feasibility and calculating the costs are usually not static. Furthermore, the airline companies carry out what‐if‐type analyses through testing several alternate scenarios in each planning period. Therefore, embedding the implementation of feasibility checking and cost calculation rules into the source code of the optimization engine is not a practical approach. In this work, a high level language called ARUS is introduced for describing the feasibility and cost calculation rules. A compiler for ARUS is also implemented in this work to generate a dynamic link library to be used by crew pairing optimization engines.

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Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: A preliminary study 11

Ranking docked models of protein-protein complexes using pre...

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2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011

作者： Xue, Li C. Jordan, Rafael A. El-Manzalawy, Yasser Dobbs, Drena Honavar, Vasant Bioinformatics and Computational Biology Program Iowa State University Ames IA 50011 United States Department of Genetics Development and Cell Biology Iowa State University Ames 50011 United States Department of Computer Science Iowa State University Ames IA 50011 United States Department of Computer Science Pontificia Universidad Javeriana Cali Colombia Department of Systems and Computer Engineering AI-Azhar University Cairo Egypt

ISBN: (纸本)9781450307963

Computational protein-protein docking is a valuable tool for determining the conformation of complexes formed by interacting proteins. Selecting near-native conformations from the large number of possible models generated by docking software presents a significant challenge in practice. We introduce a novel method for ranking docked conformations based on the degree of overlap between the interface residues of a docked conformation formed by a pair of proteins with the set of predicted interface residues between them. Our approach relies on a method, called PS-HomPPI, for reliably predicting proteinprotein interface residues by taking into account information derived from both interacting proteins. PS-HomPPI infers the residues of a query protein that are likely to interact with a partner protein based on known interface residues of the homo-interologs of the query-partner protein pair, i.e., pairs of interacting proteins that are homologous to the query protein and partner protein. Our results on Docking Benchmark 3.0 show that the quality of the ranking of docked conformations using our method is consistently superior to that produced using ClusPro cluster-size-based and energy-based criteria for 61 out of the 64 docking complexes for which PS-HomPPI produces interface predictions. An implementation of our method for ranking docked models is freely available at: http://***/DockRank/. Copyright © 2011 ACM.

关键词： Proteins

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Opposition-based shuffled PSO with passive congregation applied to FM matching synthesis

Opposition-based shuffled PSO with passive congregation appl...

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IEEE Congress on Evolutionary Computation

作者： Munoz, Daniel M. Llanos, Carlos H. Dos S. Coelho, Leandro Ayala-Rincon, Mauricio Department of Mechanical Engineering Automation and Control Group/GRACO University of Brasilia Brasilia D.F. Brazil Industrial and Systems Engineering Graduate Program LAS/PPGEPS Pontifical Catholic University of Parana Curitiba Parana Brazil Department of Computer Science and Mathematics University of Brasilia Brasilia D.F. Brazil

ISBN: (纸本)9781424478347

Synthesis of musical instruments or human voice is a time consuming process which requires theoretical and experimental knowledge about the synthesis engine. Commonly, performers need to deal with synthesizer interfaces and a process of trial and error for creating musical sounds similar to a target sound. This drawback can be overcome by adjusting automatically the synthesizer parameters using optimization algorithms. In this paper a hybrid particle swarm optimization (PSO) algorithm is proposed to solve the frequency modulation (FM) matching synthesis problem. The proposed algorithm takes advantage of a shuffle process for exchanging information between particles and applies the selective passive congregation and the opposition-based learning approaches to preserve swarm diversity. Both approaches for injecting diversity are based on simple operators, preserving the easy implementation philosophy of the particle swarm optimization. The proposed hybrid particle swarm optimization algorithm was validated for a three-nested FM synthesizer, which represents a 6-dimensional multimodal optimization problem with strong epistasis. Simulation results revealed that the proposed algorithm presented promising results in terms of quality of solutions. © 2011 IEEE.

关键词： Global optimization

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Dynamic process adaptation: A context-aware approach

Dynamic process adaptation: A context-aware approach

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International Conference on computer Supported Cooperative Work in Design

作者： Vanessa Tavares Nunes Cláudia M. Lima Werner Flávia Maria Santoro COPPE PESC-Systems Engineering and Computer Science Program UFRJ Rio de Janeiro Brazil NP2Tec and Postgraduate Information Systems Program UNIRIO Rio de Janeiro Brazil

Dynamism of day-to-day activities in organizations is inextricably linked and there is a variety of information, insight and reasoning being processed between people and systems, in carrying out a business process. We argue that flexibility in processes could be managed in real time, using context information collected in the work environment. This paper proposes a context management architecture approach that aims to improve and automate dynamic process adaptation. We explain how process adaptation may occur in real time and discuss a scenario for this proposal.

关键词： Context Adaptation models Organizations Cognition Context modeling Uncertainty

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Synthesis and Second-Order Nonlinear Optical Properties of New Coumaromethacrylate-Methylmethacrylate Copolymers

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MRS Online Proceedings Library 2011年第1期173卷 601-606页

作者： R. A. Henry J. M. Hoover A. Knoesen S. T. Kowel G. A. Lindsay M. A. Mortazavi Research Department Chemistry Division China Lake USA Department of Electrical Engineering and Computer Science Organized Research Program on Polymeric Ultrathin Film Systems University of California Davis USA

The synthesis and second-order nonlinear optical (NLO) properties of a new family of optically nonlinear coumarin dye-containing polymers is reported. Polymerizable coumaromethacrylate (CMA) monomers having various alkyl spacers (C2 to C5) between the polymerizable group and the chromophore were prepared and copolymerized with methylmethacrylate (MMA) and other vinyl monomers. The CMA copolymers had high chromophoric content (up to 18 × 1020) and glass transitions as high as 132°C. Spin cast films were prepared on BK7 substrates and oriented by corona-onset poling at elevated temperatures (COPET). The poled CMA copolymer films were characterized for spectroscopic absorption and second harmonic properties. A comparison of the nonlinear optical properties of poled CMA-MMA copolymers to poled guest-host systems is made. Relative to guest/host systems, CMA-MMA copolymer films exhibit larger and much more stable second-order nonlinear optical properties.

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Online correction of orientation estimates using spatial memory in a neuromorphic head direction system

Online correction of orientation estimates using spatial mem...

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IEEE International Symposium on Circuits and systems (ISCAS)

作者： Tarek M. Massoud Timothy K. Horiuchi Electrical and Computer Engineering Department Institute of Systems Research University of Maryland College Park MD USA Electrical and Computer Engineering Department Institute of Systems Research Neuroscience and Cognitive Science Program University of Maryland College Park MD USA

Many animals are known to maintain an internal estimate of their orientation in the environment. In the absence of external sensory cues, this estimate inevitably exhibits drift. When sensory information is available, associations between sensory landmarks and the internal estimate can be used to correct for drift. In this paper we present a neuromorphic system to model such associations between sensory landmarks in the environment (as provided by sonar) and the activity of a hardware-based head direction cell system (HDS) that continuously integrates angular velocity signals to maintain an estimate of the orientation. These associations are shown to correct for drift errors that are encountered in the HDS.

关键词： High definition video Robot sensing systems Neurons Navigation Sonar detection Neuromorphics

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Improving protein-RNA interface prediction by combining sequence homology based method with a naive bayes classifier: Preliminary results 11

Improving protein-RNA interface prediction by combining sequ...

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2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011

作者： Xue, Li C. Walia, Rasna EL-Manzalawy, Yasser Dobbs, Drena Honavar, Vasant Bioinformatics and Computational Biology Program Iowa State University Ames IA 50011 United States Department of Genetics Development and Cell Biology Iowa State University Ames IA 50011 United States Department of Computer Science Iowa State University Ames IA 50011 United States Department of Systems and Computer Engineering Al-Azhar University Cairo Egypt

ISBN: (纸本)9781450307963

Protein-RNA interactions play important roles in cellular processes like protein synthesis, RNA processing, and gene expression regulation. Reliable identification of the interfaces involved in RNA-protein interactions is essential for comprehending the mechanisms and the functional implications of these interactions and provides a valuable guide for rational drug discovery and design. Because the determination of 3D structures of protein-RNA complexes has various technical limitations and is typically costly, reliable in silico interface prediction methods that require only the sequence information are urgently needed. We present HomPRIP, a homologous sequence based method for predicting protein-RNA interfaces, based on our conservation analysis of protein-RNA interfaces. We test Hom-PRIP on a benchmark dataset of 199 proteins and compare it with the state-of-the-art protein-RNA interface prediction methods. Our results show that HomPRIP can reliably identify protein-RNA interface residues in 71% of test proteins with at least one putative sequence homolog passing the similarity thresholds of HomPRIP. Moreover, to facilitate predictions for proteins with no identified homologs, we develop HomPRIP-NB, a method combining the HomPRIP predictor and a Naive Bayes (NB) classifier trained using evolutionary information derived from alignments against the NCBI nr database. Our results suggest that HomPRIP-NB significantly outperforms the state-of-the-art machine learning methods for predicting protein-RNA interface residues. Copyright © 2011 ACM.

关键词： Proteins

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Porantim-Opt: Optimizing the Combined Selection of Model-Based Testing Techniques

Porantim-Opt: Optimizing the Combined Selection of Model-Bas...

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IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW

作者： Arilo Claudio Dias Neto Rosiane de Freitas Rodrigues Guilherme Horta Travassos Computer Science Department Federal University of Amazonas Manaus Brazil Systems Engineering and Computer Science Program-COPPE Federal University of Rio de Janeiro Rio de Janeiro Rio de Janeiro Brazil

The combination of testing techniques is considered an effective strategy to evaluate a software product. However, the selection of which techniques to combine in a software project has been an interesting challenge in the Software engineering field. This paper presents a proposal extending an approach developed to support the combined selection of model-based testing (MBT) techniques, named Porantim, applying Multiobjective Combinatorial Optimization strategy by determining the smallest dominating set in a bipartite and weighted graph. Thus, a local search strategy algorithm is proposed generating solutions aiming at maximizing the coverage of software project characteristics and skills required by the testing team to use the techniques and minimizing the eventual effort to construct models used for test cases generation. A preliminary evaluation analyzes this new approach when compared to the Porantim's original version, and the results indicate improvements in the MBT techniques selection.

关键词： Software Testing Analytical models Software engineering Optimization programming Search problems

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