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Large scale chemical patent mining with UIMA and UNICORE

Journal of Cheminformatics 2012年第1期4卷 1-2页

作者： Alexander Klenner Marc Zimmermann Sandra Bergmann Mathilde Romberg Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) Sankt Augustin 53754 Germany Forschungszentrum Juelich GmbH Juelich 52425 Germany

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A new optimization phase for scientific workflow management systems

A new optimization phase for scientific workflow management ...

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IEEE International Conference on e-Science and Grid computing

作者： Sonja Holl Olav Zimmermann Martin Hofmann-Apitius Juelich Supercomputing Centre (JSC) Juelich Germany Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Sankt Augustin Germany

scientific workflows have emerged as an important tool for combining computational power with data analysis for all scientific domains in e-science. They help scientists to design and execute complex in silico experiments. However, with increasing complexity it becomes more and more infeasible to optimize scientific workflows by trial and error. To address this issue, this paper describes the design of a new optimization phase integrated in the established scientific workflow life cycle. We have also developed a flexible optimization application programming interface (API) and have integrated it into a scientific workflow management system. A sample plugin for parameter optimization based on genetic algorithms illustrates, how the API enables rapid implementation of concrete workflow optimization methods. Finally, a use case taken from the area of structural bioinformatics validates how the optimization approach facilitates setup, execution and monitoring of workflow parameter optimization in high performance computing e-science environments.

关键词： Optimization methods Planning Abstracts Engines Data analysis Genetic algorithms

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Improving Distantly Supervised Extraction of Drug-Drug and Protein-Protein Interactions 12

Improving Distantly Supervised Extraction of Drug-Drug and P...

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Conference of The European Chapter of The Association for Computational Linguistics

作者： Tamara Bobic Roman Klinger Philippe Thomas Martin Hofmann-Apitius Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven 53754 Sankt Augustin Germany Bonn-Aachen Center for Information Technology Dahlmannstrasse 2 53113 Bonn Germany Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven 53754 Sankt Augustin Germany Computer Science Institut Humboldt-Universitaet Unter den Linden 6 10099 Berlin Germany

ISBN: (纸本)9781622764907

Relation extraction is frequently and successfully addressed by machine learning methods. The downside of this approach is the need for annotated training data, typically generated in tedious manual, cost intensive work. Distantly supervised approaches make use of weakly annotated data, like automatically annotated corpora. Recent work in the biomedical domain has applied distant supervision for protein-protein interaction (PPI) with reasonable results making use of the IntAct database. Such data is typically noisy and heuristics to filter the data are commonly applied. We propose a constraint to increase the quality of data used for training based on the assumption that no self-interaction of real-world objects are described in sentences. In addition, we make use of the University of Kansas Proteomics Service (KUPS) database. These two steps show an increase of 7 percentage points (pp) for the PPI corpus AIMed. We demonstrate the broad applicability of our approach by using the same workflow for the analysis of drug-drug interactions, utilizing relationships available from the drug database DrugBank. We achieve 37.31 % in F_1 measure without manually annotated training data on an independent test set.

关键词： Protein-Protein Interaction Training data pulse position indicator Drug Interactions Heuristics Manual handling Database

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Scalable parallel AMG on ccNUMA machines with OpenMP

Scalable parallel AMG on ccNUMA machines with OpenMP

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作者： Förster, Malte Kraus, Jiri Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven 53754 Sankt Augustin Germany

In many numerical simulation codes the backbone of the application covers the solution of linear systems of equations. Often, being created via a discretization of differential equations, the corresponding matrices are very sparse. One popular way to solve these sparse linear systems are multigrid methods-in particular AMG- because of their numerical scalability. But looking at modern multi-core architectures, also the parallel scalability has to be taken into account. With the memory bandwidth usually being the bottleneck of sparse matrix operations these linear solvers can't always benefit from increasing numbers of cores. To exploit the available aggregated memory bandwidth on larger scale NUMA machines evenly distributed data is often more an issue than load balancing. Additionally, using a threading model like OpenMP, one has to ensure the data locality manually by explicit placement of memory pages. On non uniform data it is always a tradeoff between these three principles, while the ideal strategy is strongly machine- and application dependent. In this paper we want to present some benchmarks of an AMG implementation based on a new performance library. Main focus is on the comparability to state-of-the-art solver packages regarding sequential performance as well as parallel scalability on common NUMA machines. To maximize throughput on standard model problems, several thread and memory configurations have been evaluated. We will show that even on large scale multi-core architectures easy parallel programming models, like OpenMP, can achieve a competitive performance compared to more complex programming models. © Springer-Verlag 2011.

关键词： Matrix algebra

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Automatically selected skip edges in conditional random fields for named entity recognition

Automatically selected skip edges in conditional random fiel...

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8th International Conference on Recent Advances in Natural Language Processing, RANLP 2011

作者： Klinger, Roman Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven 53754 Sankt Augustin Germany

Incorporating distant information via manually selected skip chain templates has been shown to be beneficial for the performance of conditional random field models in contrast to a simple linear chain based structure (Sutton and McCallum, 2007;Galley, 2006;Liu et al., 2010). The set of properties to be captured by a template is typically manually chosen with respect to the application domain. In this paper, a search strategy to find meaningful skip chains independent from the application domain is proposed. From a huge set of potentially beneficial templates, some can be shown to have a positive impact on the performance. The search for a meaningful graphical structure demonstrates the usefulness of the approach with an increase of nearly 2% F1 measure on a publicly available data set (Klinger et al., 2008).

关键词： Chains

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Nonlinear metamodeling and robust optimization in automotive design

Nonlinear metamodeling and robust optimization in automotive...

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作者： Clees, Tanja Nikitin, Igor Nikitina, Lialia Thole, Clemens-August Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven 53754 Sankt Augustin Germany

ISBN: (纸本)9789898425782

We overview the methods for nonlinear metamodeling of a simulation database featuring continuous exploration of simulation results, tolerance prediction, sensitivity analysis, robust multiobjective optimization and rapid interpolation of bulky FEM data. Large scatter of simulation results, in crash-test simulations caused for example by buckling, is still a challenging issue for increasing predictability of simulation and accuracy of optimization results. For industrially relevant simulations with large scatter, novel stochastic methods are introduced and their efficiency is demonstrated for benchmark cases.

关键词： Multiobjective optimization

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Compensation of pressure peaks in PWK-type hydraulic pumps

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Key Engineering Materials 2011年 490卷 33-44页

作者： Osiecki, Leszek Patrosz, Piotr Zawistowski, Tomasz Landvogt, Bettina Piechna, Janusz Zyliñski, Bartek Gdansk University of Technology ul. Narutowicza 11/12 80-233 Gdansk Poland Space Research Center Polish Academy of Sciences ul. Bartycka 18A 00-716 Warszawa Poland Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven 53754 Sankt Augustin Germany Warsaw University of Technology Pl. Politechniki 1 00-661 Warszawa Poland Bandak Engineering Postboks 1505 Ålesund Norway

Hydraulic axial pumps equipped with cam-driven commutation unit (PWK pumps) proved their high efficiency up to 55 MPa and ability to work self-sucking, even at high speed. Displacement of PWK pump may easily be changed by moving its control cam. Full discharge from hydrostatic forces makes such control possible by direct action of a low-energy actuator like proportional electromagnet or stepping motor. That eliminates heavy and costly hydraulic servomechanism, necessary in other variable displacement machines. Such a control mechanism was positively evaluated in prototype tests in Department of Hydraulics and Pneumatics of Gdañsk University of Technology. The new commutation unit generates however harmful pressure peaks. The paper presents the compensation method for pressure peaks by use of the elastic compensation chamber. It shows also results of multidisciplinary FEA and CFD analysis necessary to properly design the compensation chamber. © 2012 Trans Tech Publications, Switzerland.

关键词： Stepping motors

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A UNICORE Plugin for HPC-Enabled scientific Workflows in Taverna 2.2

A UNICORE Plugin for HPC-Enabled Scientific Workflows in Tav...

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IEEE World Congress on Services (SERVICES)

作者： Sonja Holl Olav Zimmermann Martin Hofmann-Apitius Juelich Supercomputing Center (JSC) Forschungszentrum Juelich GmbH Juelich Germany Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

As scientific workflows are becoming more complex and apply compute-intensive methods to increasingly large data volumes, access to HPC resources is becoming mandatory. We describe the development of a novel plug in for the Tavern a workflow system, which provides transparent and secure access to HPC/grid resources via the UNICORE grid middleware, while maintaining the ease of use that has been the main reason for the success of scientific workflow systems. A use case from the bioinformatics domain demonstrates the potential of the UNICORE plug in for Tavern a by creating a scientific workflow that executes the central parts in parallel on a cluster resource.

关键词： Middleware Servers Monitoring Databases Bioinformatics Support vector machines Computer architecture

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Achieving an improved understanding of the factors affecting an aircraft environmental control system by coupling a 1D cabin air distribution system model with a 3D passenger cabin model using Co-simulation middleware

Achieving an improved understanding of the factors affecting...

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SAE 2009 AeroTech Congress and Exhibition

作者： Kelsall, David Ludhi, Abdul Bayrasy, Pascal Wolf, Klaus Flowmaster Ltd Fraunhofer Institute for Algorithms and Scientific Computing SCAI

Aircraft Environmental Control Systems (ECS) are designed to optimize passenger comfort by providing satisfactory cabin pressurization, and temperature and humidity control whilst minimising the risks to passenger health from airborne toxins and diseases. The paper presents a case study that investigates how the cooling load discharge from an ECS system affects the flow behaviour inside a typical mid-size, wide-body aircraft passenger cabin. The investigation uses commercial off-the-shelf one dimensional (1D) Computational Fluid Dynamics (CFD) software to model the cooling pack, cabin air distribution system, and three quarters of the passenger cabin. The centre section of the cabin is modelled using a commercial off-the-shelf three dimensional (3D) CFD package, with the co-simulation middleware providing coupling adapters to ensure that two-way, bilateral exchange of boundary parameters between the 1D and the 3D CFD models gives continuity of mass and momentum transfer. The 1D and 3D CFD applications and Co-simulation middleware are supplied by 3 independent commercial organisations. The results of the case study are discussed including the co-simulated 'velocity field of the air discharge' and the 'temperature gradient inside the cabin' within the 3D CFD model as well as the flow and temperature fields within the one-dimensional ECS cooling pack model. The paper concludes by discussing how the proper implementation of the co-simulation methods developed in this case study could bring significant benefits to engineering companies using CFD tools, including improved quality of simulation results and reduced simulation run times. Copyright © 2009 SAE International.

关键词： Computational fluid dynamics

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Life science application support in an interoperable e-science environment

Life science application support in an interoperable e-scien...

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Annual IEEE Symposium on Computer-Based Medical Systems

作者： Sonja Holl Morris Riedel Bastian Demuth Mathilde Romberg Achim Streit Vinod Kasam Forschungszentrum Juelich Juelich Supercomputing Center Juelich Germany Schloss Birlinghoven Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

In the last decade, life science applications have become more and more integrated into e-Science environments, hence they are typically very demanding, both in terms of computational capabilities and data capacities. Especially the access to life science applications, embedded in such environments via Grid clients still constitutes a major hurdle for scientists that do not have an IT background. Life science applications often comprise a whole set of small programs instead of a single executable. Many of the graphical Grid clients are not perfectly suited for these types of applications, as they often assume that Grid jobs will run a single executable instead of a set of chained executions (i.e. sequences). This means that in order to execute a sequence of multiple programs on a single Grid resource, piping data from one program to the next, the user would have to run a hand-written shell script. Otherwise each program is independently scheduled as a Grid job, which causes unnecessary file transfers between the jobs, even if they are scheduled on the same resource. We present a generic solution to this problem and provide a reference implementation, which seamlessly integrates with the Grid middleware UNICORE. Our approach focuses on a comfortable user interface for the creation of such program sequences, validated in UNICORE-driven HPC-based Grids. Thus, we applied our approach in order to provide support for the usage of the AMBER package (a widely-used collection of programs for molecular dynamics simulations) within Grid workflows. We finally provide a scientific use case of our approach leveraging the interoperability of two different scientific infrastructures that represents an instance of the infrastructure interoperability reference model.

关键词： Middleware Biology computing Sequences Biological system modeling Bioinformatics scientific computing User interfaces Packaging Collaborative work Chemistry

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