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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

JOURNAL OF CHEMINFORMATICS 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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On abstraction of probabilistic systems

On abstraction of probabilistic systems

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International Autumn School on Stochastic Model Checking : Rigorous Dependability Analysis Using Model Checking Techniques for Stochastic Systems, ROCKS 2012

作者： Dehnert, Christian Gebler, Daniel Volpato, Michele Jansen, David N. Software Modeling and Verification Group RWTH Aachen University Ahornstraße 55 Aachen52056 Germany Department of Computer Science VU University Amsterdam De Boelelaan 1081a Amsterdam1081 HV Netherlands Institute for Computing and Information Sciences Radboud University Heyendaalseweg 135 Nijmegen6500 GL Netherlands

ISBN: (纸本)9783662454886

Probabilistic model checking extends traditional model checking by incorporating quantitative information about the probability of system transitions. However, probabilistic models that describe interesting behavior are often too complex for straightforward analysis. Abstraction is one way to deal with this complexity: instead of analyzing the ("concrete") model, a simpler ("abstract") model that preserves the relevant properties is built and analyzed. This paper surveys various abstraction techniques proposed in the past decade. For each abstraction technique we identify in what sense properties are preserved or provide alternatively suitable boundaries. © 2014, Springer-Verlag Berlin Heidelberg.

关键词： Model checking

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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Power-optimized stiffness and nonlinear position control of an actuator with Variable Torsion Stiffness

Power-optimized stiffness and nonlinear position control of ...

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2013 IEEE/ASME International Conference on Advanced Intelligent Mechatronics: Mechatronics for Human Wellbeing, AIM 2013

作者： Beckerle, P. Wojtusch, J. Schuy, J. Strah, B. Rinderknecht, S. Stryk, O.V. Institute for Mechatronic Systems Department of Mechanical Engineering Technische Universität Darmstadt Darmstadt Germany Simulation Systems Optimization and Robotics Group Department of Computer Science Technische Universität Darmstadt Darmstadt Germany

ISBN: (纸本)9781467353199

Introducing compliant actuation to robotic joints is an approach to ensure safety in closer human-machine interaction. Further, the possibility to adjust stiffness can be benificial considering energy storage and the power consumption required to track certain trajectories. The subject of this paper is the stiffness and position control of the Variable Torsion Stiffness (VTS) actuator for application in compliant robotic joints. For the realization of a variable rotational stiffness, the active length of a torsional elastic element in serial configuration between drive and link is adjusted in VTS. After the deduction of an extended drive train model, this paper gives an advanced power analysis clarifying power-optimal settings from previous basic models and identifying additional settings that allow for a more versatile operation. Based on these results that can be generalized to other variable elastic actuator concepts, an optimized strategy for setting stiffness is determined considering the whole system dynamics including natural frequencies as well as antiresonance effects. For position control of VTS in a prototypical implementation, a nonlinear position controller is designed by means of feedback linearization. Although the system is modified significantly by changing drive train stiffness, the stiffness adaptation of the controller ensures the required tracking performance. © 2013 IEEE.

关键词： Stiffness

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Design and dynamics model of a lightweight series elastic tendon-driven robot arm

Design and dynamics model of a lightweight series elastic te...

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IEEE International Conference on Robotics and Automation (ICRA)

作者： Thomas Lens Oskar von Stryk Simulation Optimization and Robotics Group Department of Computer Science Technische Universität Darmstadt Germany

ISBN: (纸本)9781467356404

This paper presents the design of a lightweight robot arm intended for safe physical human-robot interaction. The robot arm design combines tendon actuation with elasticity in the tendons to achieve a significant reduction in mass and passive compliant behavior. The use of elastic tendons in all joints in order to gain maximum safety and performance properties, however, results in a significant increase of the model complexity with oscillatory behavior and kinematic coupling of the joint equilibrium positions. Therefore, special effort needs to be made to model the robot arm dynamics, which is an essential basis for model-based algorithms utilizing and fully exploiting the particular properties of the robot arm. This paper therefore derives the full dynamics model of the robot arm with focus on the nonlinear elastic tendon actuators, the kinematic tendon coupling, and modeling complexity reduction by reflecting all model parameters to the joint space. The resulting model is validated by comparing the identified simulation model with experimental data of an application-related pick-and-place trajectory and a trajectory with undamped oscillating motions of the robot arm.

关键词： Joints Tendons Robots Springs Actuators Pulleys Couplings

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Physicochemical signatures of nanoparticle-dependent complement activation

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Computational science and Discovery 2014年第1期7卷 015003-15002页

作者： Thomas, Dennis G. Chikkagoudar, Satish Heredia-Langner, Alejandro Tardiff, Mark F. Xu, Zhixiang Hourcade, Dennis E. Pham, Christine T. N. Lanza, Gregory M. Weinberger, Kilian Q. Baker, Nathan A. Knowledge Discovery and Informatics Pacific Northwest National Laboratory RichlandWA99352 United States Applied Statistics and Computational Modeling Group Pacific Northwest National Laboratory RichlandWA99352 United States Department of Computer Science and Engineering Washington University in St. Louis St. LouisMO63130 United States Division of Rheumatology Department of Medicine Washington University School of Medicine St. LouisMO63110 United States Division of Cardiology Department of Medicine Washington University School of Medicine St. LouisMO63110 United States

Nanoparticles are potentially powerful therapeutic tools that have the capacity to target drug payloads and imaging agents. However, some nanoparticles can activate complement, a branch of the innate immune system, and cause adverse side-effects. Recently, we employed an in vitro hemolysis assay to measure the serum complement activity of perfluorocarbon nanoparticles that differed by size, surface charge, and surface chemistry, quantifying the nanoparticle-dependent complement activity using a metric called Residual Hemolytic Activity (RHA). In the present work, we have used a decision tree learning algorithm to derive the rules for estimating nanoparticle-dependent complement response based on the data generated from the hemolytic assay studies. Our results indicate that physicochemical properties of nanoparticles, namely, size, polydispersity index, zeta potential, and mole percentage of the active surface ligand of a nanoparticle, can serve as good descriptors for prediction of nanoparticle-dependent complement activation in the decision tree modeling framework. © 2014 IOP Publishing Ltd.

关键词： Nanoparticles

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DNS and les of excited rectangular jets 8

DNS and les of excited rectangular jets

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8th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2013

作者： Tyliszczak, Artur Geurts, Bernard J. Department of Mechanical Engineering and Computer Science Institute of Thermal Machinery Czestochowa University of Technology Al. Armii Krajowej 21 Czestochowa42-200 Poland Department of Applied Mathematics Multiscale Modeling and Simulation University of Twente P.O. Box 217 AE Enschede7500 Netherlands

The paper presents results of numerical studies devoted to an active flow control method applied to jet flow and focusses on rectangular jets with aspect ratio Ar = 1, 2 and 3. Square and rectangular jets are more unstable than their circular counterparts, which is expressed by an increased intensity of mixing. It is shown that the application of a suitable excitation (forcing) at the jet nozzle can qualitatively alter the character of the flow, resulting in an increased spreading rate of passive tracer. The excitation is obtained from a superposition of axial and helical forcing terms. We study the mixing in the flow upon varying parameters such as the frequency of the excitations and possible phase shifts between components. The numerical results are obtained applying LES and DNS based on a high-order compact difference code for the incompressible flows.

关键词： Aspect ratio

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Designing multi-objective multi-armed bandits algorithms: a study

Designing multi-objective multi-armed bandits algorithms: a ...

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International Joint Conference on Neural Networks

作者： Madalina M. Drugan Ann Nowe Computational Modeling lab Artificial Intelligence group of Computer Science Department Vrije Universiteit Brussels Pleinlaan 2 B-1050 Brussels Belgium

ISBN: (纸本)9781467361279

We propose an algorithmic framework for multi-objective multi-armed bandits with multiple rewards. Different partial order relationships from multi-objective optimization can be considered for a set of reward vectors, such as scalarization functions and Pareto search. A scalarization function transforms the multi-objective environment into a single objective environment and are a popular choice in multi-objective reinforcement learning. Scalarization techniques can be straightforwardly implemented into the current multi-armed bandit framework, but the efficiency of these algorithms depends very much on their type, linear or non-linear (e.g. Chebyshev), and their parameters. Using Pareto dominance order relationship allows to explore the multi-objective environment directly, however this can result in large sets of Pareto optimal solutions. In this paper we propose and evaluate the performance of multi-objective MABs using three regret metric criteria. The standard UCB1 is extended to scalarized multi-objective UCB1 and we propose a Pareto UCB1 algorithm. Both algorithms are proven to have a logarithmic upper bound for their expected regret. We also introduce a variant of the scalarized multi-objective UCB1 that removes online inefficient scalarizations in order to improve the algorithm's efficiency. These algorithms are experimentally compared on multi-objective Bernoulli distributions, Pareto UCB1 being the algorithm with the best empirical performance.

关键词： study multiple rewards reward vectors algorithms algorithm efficiency Regret optimal solution Reward Environments

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Parallel Verification of UML Using DiVinE Tool

Parallel Verification of UML Using DiVinE Tool

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International Conference on computer science and Information Technology

作者： Muhammad Abdul Basit-Ur-Rahim Jamil Ahmad Fahim Arif Department of Computer Software Engineering Military College of Signals National University of Science & Technology Islamabad Pakistan Research Center for Modeling and Simulation Military College of Signals National University of Science & Technology Islamabad Pakistan

ISBN: (纸本)9781467356107

Unified modeling Language is being used for modeling of business processes, real-time systems, embedded systems and hybrid systems. In software engineering, there are different techniques for verification of such systems. Model checking is one of the techniques for the automatic verification of software models. Earlier, these model were verified by sequential model checking tools. For very large complex systems, parallel verification can save verification time. DiVinE is a model checking tool for both CPUs and GPUs clusters to perform parallel linear time logic (LTL) verification of systems. In this paper, we propose a parallel verification methodology for UML models using DiVinE tool. We explain this methodology by the case study example of fuel filling machine.

关键词： UML Verification DiVinE Parallel Verification UML Verification checking tools central processing units Parallel Lines Complex systems hybrid systems Model checking Business process management Software engineering program verification modelling languages FILLING MACHINE Case studies

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Reducing computation time in simulation-based optimization of manufacturing systems 13

Reducing computation time in simulation-based optimization o...

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simulation Winter Conference

作者： Matthias Frank Christoph Laroque Tobias Uhlig Chair of Modeling and Simulation Technical University of Dresden Dresden GERMANY Business Computing esp. CIM University of Paderborn Paderborn GERMANY Department of Computer Science Universität der Bundeswehr München Neubiberg GERMANY

ISBN: (纸本)9781479920778

The analysis of production systems using discrete, event-based simulation is wide spread and generally accepted as a decision support technology. It aims either at the comparison of competitive system designs or the identification of a best possible parameter configuration of a simulation model. Here, combinatorial techniques of simulation and optimization methods support the user in finding optimal solutions, but typically result in long computation times, which often prohibits a practical application in industry. To close this gap, this paper presents a fast converging procedure combining a Genetic Algorithm with a material flow simulation including an interactive analysis of simulation runs. An early termination of simulation runs is used for unpromising parameter configurations. The integrated implementation allows automated, distributed simulation runs for practical, complex production systems. A use-case shows the proof of concept with a reference model and demonstrates the resulting speed-up of this approach.

关键词： Computational modeling Optimization Genetic algorithms Mathematical model Solid modeling Materials Sociology

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