TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakayama, Yuki A1 - Wakui, Tetsuya T1 - Model reduction by time aggregation for optimal design of energy supply systems by an MILP hierarchical branch and bound method JF - Energy N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of en- ergy supply systems in consideration of multi-period operation. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been pro- posed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accor- dance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Thus, it may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies. Y1 - 2019 VL - 181 SP - 782 EP - 792 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Takeuchi, Kotaro A1 - Wakui, Tetsuya T1 - Operation-based time-period clustering for optimal design of energy supply systems by a hierarchical MILP method JF - THE 32ND INTERNATIONAL CONFERENCE ON EFFICIENCY, COST, OPTIMIZATION, SIMULATION AND ENVIRONMENTAL IMPACT OF ENERGY SYSTEMS(ECOS 2019) N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, a method of clustering periods has been proposed based on the optimal operational strategies of the systems to avoid a large decrease in the lower bound for the optimal value of the objective function by model reduction. This method has been realized only by solving the relaxed optimal design problem at the upper level in advance. The method can decrease the number of operation variables and constraints at the upper level, and thus can decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the proposed clustering method is effective to enhance the computation efficiency in comparison with the conventional one which clusters periods regularly in time series. Y1 - 2019 SP - 527 EP - 539 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Evaluation of Design Alternatives for a Gas Turbine Cogeneration Plant Based on Multiobjective K-Best Solutions JF - International Conference on Power Engineering-2019 N2 - To realize the best performance in energy supply, it is an important task to determine types, capacities, and numbers of energy conversion equipment appropriately. It is also necessary to take account of seasonal and hourly variations in energy demands and corresponding operational strategies of equipment. The mixed-integer linear programming (MILP) method has been utilized widely to derive the optimal solution for such a design problem. From the design viewpoint, it is important to generate not only the optimal solution but also suboptimal ones which follow the optimal one without omission, what are called K-best solutions. In this paper, an MILP method utilizing the hierarchical relationship between design and operation variables is applied along with some strategies to efficiently drive K-best solutions of a multiobjective optimal design problem of a gas turbine cogeneration system for district energy supply. The annual total cost and primary energy consumption are adopted as the objective functions to be minimized. A case study is conducted, and K-best solutions with an allowable increase in the value of the combined objective function are derived for each value of the weight for the annual total cost. Through the study, it is clarified how the weight affects the computation time, the number of the K-best solutions, and the design specifications and the values of the objective functions for the K-best solutions. Y1 - 2019 SP - 1112 EP - 1117 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Wakui, Tetsuya T1 - Search for K-best solutions in optimal design of energy supply systems by an extended MILP hierarchical branch and bound method JF - Energy N2 - For the purpose of making a decision in the optimal design of an energy supply system, it is important to investigate not only the optimal solution but also suboptimal ones which follow the optimal one without any omissions, what are called K-best solutions. In this paper, a mixed-integer linear programming method utilizing the hierarchical relationship between design and operation variables proposed previ- ously is extended to search the K-best solutions very efficiently. In addition, methods for updating the incumbents are incorporated into the extended method for three options for the criterion set newly in deriving the K-best solutions. This extended method is implemented into open and commercial MILP solvers, and is applied to illustrative and practical case studies, respectively, on the optimal design of cogeneration systems. Through the studies, it turns out that the proposed method is much superior in terms of solution optimality and computation efficiency to a conventional method, and that the computation efficiency to derive one of the K-best solutions by the proposed method increases with the number of K-best solutions. In addition, features of the K-best solutions in the value of objective function are clarified. Y1 - 2019 U6 - https://doi.org/https://doi.org/10.1016/j.energy.2018.02.077 VL - 184 SP - 45 EP - 57 ER - TY - CHAP A1 - Paetsch, Olaf T1 - Possibilities and Limitations of Automatic Feature Extraction shown by the Example of Crack Detection in 3D-CT Images of Concrete Specimen T2 - iCT 2019 N2 - To assess the influence of the alkali-silica reaction (ASR) on pavement concrete 3D-CT imaging has been applied to concrete samples. Prior to imaging these samples have been drilled out of a concrete beam pre-damaged by fatigue loading. The resulting high resolution 3D-CT images consist of several gigabytes of voxels. Current desktop computers can visualize such big datasets without problems but a visual inspection or manual segmentation of features such as cracks by experts can only be carried out on a few slices. A quantitative analysis of cracks requires a segmentation of the whole specimen which could only be done by an automatic feature detection. This arises the question of the reliability of an automatic crack detection algorithm, its certainty and limitations. Does the algorithm find all cracks? Does it find too many cracks? Can parameters of that algorithm, once identified as good, be applied to other samples as well? Can ensemble computing with many crack parameters overcome the difficulties with parameter finding? By means of a crack detection algorithm based on shape recognition (template matching) these questions will be discussed. Since the author has no access to reliable ground truth data of cracks the assessment of the certainty of the automatic crack is restricted to visual inspection by experts. Therefore, an artificial dataset based on a combination of manually segmented cracks processed together with simple image processing algorithms is used to quantify the accuracy of the crack detection algorithm. Part of the evaluation of cracks in concrete samples is the knowledge of the surrounding material. The surrounding material can be used to assess the detected cracks, e.g. micro-cracks within the aggregate-matrix interface may be starting points for cracks on a macro scale. Furthermore, the knowledge of the surrounding material can help to find better parameter sets for the crack detection itself because crack characteristics may vary depending on their surrounding material. Therefore, in addition to a crack detection a complete segmentation of the sample into the components of concrete, such as aggregates, cement matrix and pores is needed. Since such a segmentation task cannot be done manually due to the amount of data, an approach utilizing convolutional neuronal networks stemming from a medical application has been applied. The learning phase requires a ground truth i.e. a segmentation of the components. This has to be created manually in a time-consuming task. However, this segmentation can be used for a quantitative evaluation of the automatic segmentation afterwards. Even though that work has been performed as a short term subtask of a bigger project funded by the German Research Foundation (DFG) this paper discusses problems which may arise in similar projects, too. [1.2MB | id=23664 ] iCT 2019 Session: Short talks Thu 13:50 Auditorium 2019-03 Möglichkeiten und Grenzen automatischer Merkmalserkennung am Beispiel von Risserkennungen in 3D-CT-Aufnahmen von Betonproben O. Paetsch11 Visualisation and Data Analysis; Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany Abstract [1MB | id=23104 ] DE DGZfP 2018 Session: Bauwesen 2018-09 Quantitative Rissanalyse im Fahrbahndeckenbeton mit der 3D-Computertomographie D. Meinel125, K. Ehrig128, F. Weise16, O. Paetsch211 1Division 8.5; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany 2Visualisation and Data Analysis; Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany concrete, ROI tomography, in-situ-CT, 3D-CT, Beton, AKR, Feuchtetransport, automatic crack detection Abstract [0.7MB | id=18980 ] DE DGZfP 2015 Session: CT Algorithmen 2016-04 3D Corrosion Detection in Time-dependent CT Images of Concrete O. Paetsch111, D. Baum15, S. Prohaska17, K. Ehrig228, D. Meinel225, G. Ebell24 1Visualisation and Data Analysis; Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division 8.5; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany CT, multi-angle radiography, defect detection, Feature Extraction, image processing, concrete, corrosion Abstract [0.5MB | id=18043 ] DIR 2015 Session: Quantitative imaging and image processing 2015-08 Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben O. Paetsch111, D. Baum15, G. Ebell24, K. Ehrig228, A. Heyn2, D. Meinel225, S. Prohaska17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany Computertomographie [0.4MB | id=17375 ] DE DGZfP 2014 Session: Bauwesen 2015-03 Examination of Damage Processes in Concrete with CT D. Meinel125, K. Ehrig128, V. L’Hostis2, B. Muzeau2, O. Paetsch311 1BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany 2Laboratoire d’Etude du Comportement des Bétons et des Argiles; Commissariat Energie Atomique (CEA)287, Gif-Sur-Yvette, France 3Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany X-ray computed tomography, concrete, corrosion, crack detection, 3D visualization Abstract [4.9MB | id=15692 ] iCT 2014 Session: Non-destructive Testing and 3D Materials Characterisation of... 2014-06 3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben O. Paetsch111, D. Baum15, D. Breßler1, K. Ehrig228, D. Meinel225, S. Prohaska1,17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany Radiographic Testing (RT), statistical analysis, 3D Computed Tomography, visualization, concrete structural damage, automated crack detection [1MB | id=15343 ] DE DGZfP 2013 Session: Computertomographie 2014-03 Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computertomographie O. Paetsch111, K. Ehrig228, D. Meinel225, D. Baum15, S. Prohaska1,1,17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany Radiographic Testing (RT), visualization, crack detection, Visualisierung, computer tomography, template matching, Hessian eigenvalues, ZIBAmira, automated crack detection, percolation [0.9MB | id=14269 ] DE DGZfP 2012 Session: Computertomographie 2013-05 Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography O. Paetsch111, D. Baum15, K. Ehrig228, D. Meinel225, S. Prohaska1,1,17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany computed tomography, template matching, Hessian eigenvalues, crack statistics, visualization, crack surface, ZIBAmira [0.6MB | id=13736 ] iCT 2012 Session: Poster - Analysis and Algorithms 2012-12 3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira D. Streicher112, O. Paetsch211, R. Seiler2, S. Prohaska27, M. Krause360 [Profile of Krause] , C. Boller178 1Saarland University74, Saarbrücken, Germany 2Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 3BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany [0.4MB | id=12284 ] DE DGZfP 2011 Session: Bauwesen 2012-05 Comparison of Crack Detection Methods for Analyzing Damage Processes in Concrete with Computed Tomography K. Ehrig128, J. Goebbels153, D. Meinel125, O. Paetsch211, S. Prohaska27, V. Zobel2 1Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany 2Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany [0.7MB | id=11150 ] DIR 2011 Session: Poster 2011-11 Actual Cooperations 10th International Workshop NDT in Progress 2019 2019 Oct 7-9 11th International Symposium on NDT in Aerospace 2019 2019 Nov 13-15 3rd Singapore International NDT Conference & Exhibition, SINCE 2019 2019 Dec 4-5 10th Conference on Industrial Computed Tomography (iCT) 2020 2020 Feb 4-7 34th European Conference on Acoustic Emission Testing (EWGAE 2020) 2020 Sep 9-11 Contribute Papers and Proceedings to NDT.net Share... Home Exhibition Archive Forum Jobs Members Events Directory NDT A-Z Advertise Privacy Policy Contact About © NDT.net - Where expertise comes together. The Largest Open Access Portal of Nondestructive Testing (NDT)- since 1996 Y1 - 2019 ER - TY - THES A1 - Franz, Henriette T1 - Connected Subgraphs with Budget Constraints: Formulations and Algorithms Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-87792 ER - TY - GEN T1 - Annual Report 2018 T3 - Jahresbericht - 2018 KW - Jahresbericht Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74971 SN - 0934-5892 VL - 2018 ER - TY - JOUR A1 - Jin, Liangbing A1 - Le, Thi Thai A1 - Fukumoto, Yasuhide T1 - Frictional effect on stability of discontinuity interface in tangential velocity of a shallow-water flow JF - Physics Letters A N2 - We examine a frictional effect on the linear stability of an interface of discontinuity in tangential velocity. The fluid is moving with uniform velocity U in a region but is at rest in the other, and the bottom surface is assumed to exert drag force, quadratic in velocity, on the thin fluid layer. In the absence of the drag, the instability of the Kelvin-Helmholtz type is suppressed for U>√8 c, with c being the propagating speed of the gravity wave. We find by asymptotic analyses for both small and large values of the drag strength that the drag, regardless of its strength, makes the flow unstable for the whole range of the Froude number U/c. Y1 - 2019 U6 - https://doi.org/10.1016/j.physleta.2019.125839 VL - 383 IS - 26 SP - 125839 ER - TY - JOUR A1 - Le, Thi Thai T1 - Kelvin-Helmholtz instability in a shallow-water flow with a finite width JF - Journal of Mathematical Physics N2 - We examine an effect of side walls on the linear stability of an interface of tangential-velocity discontinuity in shallow-water flow. The flow is pure horizontal in the plane xy, and the fluid is bounded in a finite width 2d in the y− direction. In region 0 < y < d, the fluid is moving with uniform velocity U but is at rest for −d < y < 0. Without side walls, the flow is unstable for a velocity difference U<√8c U < √8 c, with c being the velocity of gravity waves. In this work, we show that if the velocity difference U is smaller than 2c, the interface is always destabilized, also known as the flow is unstable. The unstable region of an infinite width model is shrunken by the effects of side walls in the case of narrow width, while there is no range for the Froude number for stabilization in the case of large width. These results play an important role in predicting the wave propagations and have a wide application in the fields of industry. As a result of the interaction of waves and the mean flow boundary, the flow is unstable, which is caused by a decrease in the kinetic energy of disturbance. Y1 - 2019 U6 - https://doi.org/10.1063/1.5126321 VL - 60 IS - 1 SP - 123101 PB - AIP Publishing ER - TY - JOUR A1 - Schienle, Adam A1 - Maristany de las Casas, Pedro A1 - Blanco, Marco T1 - A Priori Search Space Pruning in the Flight Planning Problem N2 - We study the Flight Planning Problem for a single aircraft, where we look for a minimum cost path in the airway network, a directed graph. Arc evaluation, such as weather computation, is computationally expensive due to non-linear functions, but required for exactness. We propose several pruning methods to thin out the search space for Dijkstra's algorithm before the query commences. We do so by using innate problem characteristics such as an aircraft's tank capacity, lower and upper bounds on the total costs, and in particular, we present a method to reduce the search space even in the presence of regional crossing costs. We test all pruning methods on real-world instances, and show that incorporating crossing costs into the pruning process can reduce the number of nodes by 90\% in our setting. T3 - ZIB-Report - 20-32 Y1 - 2019 U6 - https://doi.org/https://doi.org/10.4230/OASIcs.ATMOS.2019.8 SN - 1438-0064 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakayama, Yuki A1 - Wakui, Tetsuya T1 - Model reduction by time aggregation for optimal design of energy supply systems by an MILP hierarchical branch and bound method JF - Energy N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems in consideration of multi-period operation. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accordance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Thus, it may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies. Y1 - 2019 U6 - https://doi.org/https://doi.org/10.1016/j.energy.2019.04.066 VL - 181 SP - 782 EP - 792 ER - TY - JOUR A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Koch, Thorsten A1 - Miltenberger, Matthias A1 - Kniasew, Dimitri A1 - Schlögel, Dominik A1 - Martin, Alexander A1 - Weninger, Dieter T1 - Tackling Industrial-Scale Supply Chain Problems by Mixed-Integer Programming JF - Journal of Computational Mathematics N2 - The modeling flexibility and the optimality guarantees provided by mixed-integer programming greatly aid the design of robust and future-proof decision support systems. The complexity of industrial-scale supply chain optimization, however, often poses limits to the application of general mixed-integer programming solvers. In this paper we describe algorithmic innovations that help to ensure that MIP solver performance matches the complexity of the large supply chain problems and tight time limits encountered in practice. Our computational evaluation is based on a diverse set, modeling real-world scenarios supplied by our industry partner SAP. Y1 - 2019 U6 - https://doi.org/10.4208/jcm.1905-m2019-0055 VL - 37 SP - 866 EP - 888 ER - TY - JOUR A1 - Temp, Julia A1 - Labuz, Dominika A1 - Negrete, Roger A1 - Sunkara, Vikram A1 - Machelska, Halina T1 - Pain and knee damage in male and female mice in the medial meniscal transection-induced osteoarthritis JF - Osteoarthritis and Cartilage Y1 - 2019 U6 - https://doi.org/10.1016/j.joca.2019.11.003 ER - TY - JOUR A1 - Sunkara, Vikram T1 - On the Properties of the Reaction Counts Chemical Master Equation JF - Entropy N2 - The reaction counts chemical master equation (CME) is a high-dimensional variant of the classical population counts CME. In the reaction counts CME setting, we count the reactions which have fired over time rather than monitoring the population state over time. Since a reaction either fires or not, the reaction counts CME transitions are only forward stepping. Typically there are more reactions in a system than species, this results in the reaction counts CME being higher in dimension, but simpler in dynamics. In this work, we revisit the reaction counts CME framework and its key theoretical results. Then we will extend the theory by exploiting the reactions counts’ forward stepping feature, by decomposing the state space into independent continuous-time Markov chains (CTMC). We extend the reaction counts CME theory to derive analytical forms and estimates for the CTMC decomposition of the CME. This new theory gives new insights into solving hitting times-, rare events-, and a priori domain construction problems. Y1 - 2019 U6 - https://doi.org/10.3390/e21060607 VL - 21 IS - 6 SP - 607 ER - TY - JOUR A1 - Haase, Tobias A1 - Sunkara, Vikram A1 - Kohl, Benjamin A1 - Meier, Carola A1 - Bußmann, Patricia A1 - Becker, Jessica A1 - Jagielski, Michal A1 - von Kleist, Max A1 - Ertel, Wolfgang T1 - Discerning the spatio-temporal disease patterns of surgically induced OA mouse models JF - PLOS One N2 - Osteoarthritis (OA) is the most common cause of disability in ageing societies, with no effective therapies available to date. Two preclinical models are widely used to validate novel OA interventions (MCL-MM and DMM). Our aim is to discern disease dynamics in these models to provide a clear timeline in which various pathological changes occur. OA was surgically induced in mice by destabilisation of the medial meniscus. Analysis of OA progression revealed that the intensity and duration of chondrocyte loss and cartilage lesion formation were significantly different in MCL-MM vs DMM. Firstly, apoptosis was seen prior to week two and was narrowly restricted to the weight bearing area. Four weeks post injury the magnitude of apoptosis led to a 40–60% reduction of chondrocytes in the non-calcified zone. Secondly, the progression of cell loss preceded the structural changes of the cartilage spatio-temporally. Lastly, while proteoglycan loss was similar in both models, collagen type II degradation only occurred more prominently in MCL-MM. Dynamics of chondrocyte loss and lesion formation in preclinical models has important implications for validating new therapeutic strategies. Our work could be helpful in assessing the feasibility and expected response of the DMM- and the MCL-MM models to chondrocyte mediated therapies. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0213734 VL - 14 IS - 4 PB - PLOS One ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Binkowski, Felix A1 - Burger, Sven ED - Kaltenbacher, Manfred T1 - Spectral resonance expansion by Riesz projections T2 - 14 th International Conference on Mathematical and Numerical Aspects of Wave Propagation Book of Abstracts Y1 - 2019 U6 - https://doi.org/10.34726/waves2019 SP - 234 ER - TY - CHAP A1 - Höhne, Theresa A1 - Schnauber, Peter A1 - Rodt, Sven A1 - Reitzenstein, Stephan A1 - Burger, Sven ED - Novotny, Lukas ED - Quidant, Romain T1 - Numerical Investigation of Integrated Single-Photon Emitters in Low-Index-Contrast Waveguides T2 - Nanophotonics: Foundations & Applications, CSF Conference Book of Abstracts Y1 - 2019 SP - B11 ER - TY - JOUR A1 - Klus, Stefan A1 - Husic, Brooke E. A1 - Mollenhauer, Mattes A1 - Noe, Frank T1 - Kernel methods for detecting coherent structures in dynamical data JF - Chaos: An Interdisciplinary Journal of Nonlinear Science Y1 - 2019 U6 - https://doi.org/10.1063/1.5100267 VL - 29 IS - 12 ER - TY - THES A1 - Kostré, Margarita T1 - Hybrid Models and Simulations of Reaction-Diffusion Processes N2 - In this thesis,we are interested in multiscale models for particle-based reaction diffusion (PBRD) simulations,where we focus on coupling particle-based simulations to macroscopic chemical reservoirs. These reservoirs are given by a mean concentration of chemical species that can vary in time and space. We model these reservoirs as reaction-diffusion partial differential equations (PDEs). The goal of this work is to achieve a mathematically consistent coupling between the PBRD simulations and the reaction-diffusion PDEs. Y1 - 2019 ER - TY - CHAP A1 - Höhne, Theresa A1 - Schnauber, Peter A1 - Rodt, Sven A1 - Reitzenstein, Stephan A1 - Burger, Sven ED - Reitzenstein, Stephan ED - Heindel, Tobias T1 - Numerical Studies of Integrated Single-Photon Emitters in Low-Index-Contrast Waveguides T2 - 7th International Workshop on Engineering of Quantum Emitter Properties (EQEP) Y1 - 2019 SP - 49 ER - TY - THES A1 - Basaleh, Rascha T1 - Prediction and Analysis of Drugs Inducing Liver Injury (DILI) using ProTox-II Computational-Tool Y1 - 2019 ER - TY - CHAP A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Höhne, Theresa A1 - Zschiedrich, Lin ED - Reitzenstein, Stephan ED - Heindel, Tobias T1 - Numerical methods for simulation and optimization of the extraction efficiency from quantum-dot based single-photon emitters T2 - 7th International Workshop on Engineering of Quantum Emitter Properties (EQEP) Y1 - 2019 SP - 20 ER - TY - THES A1 - Boz, Seyma T1 - Classification of the toxicity profile of the withdrawn drugs using computational prediction platform ProTox-II Y1 - 2019 ER - TY - THES A1 - Wachsmann, Ole T1 - Computational Models for the prediction of drug-induced Nephrotoxicity Y1 - 2019 ER - TY - THES A1 - Hoffmann, Lara T1 - Automating PCCA+ applied to Eye-Tracking Data Y1 - 2019 ER - TY - CHAP A1 - Binkowski, Felix A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven ED - Matijević, Milica ED - Krstić, Marko ED - Beličev, Petra T1 - Numerical optimization of resonant nanophotonic devices T2 - The Seventh International School and Conference on Photonics (PHOTONICA Belgrade) Y1 - 2019 SN - 978-86-7306-153-5 SP - 10 ER - TY - THES A1 - Zumbansen, Max T1 - Parameter estimation of multivalent processes on ITC datasets Y1 - 2019 ER - TY - THES A1 - Donati, Luca T1 - Reweighting methods for Molecular Dynamics N2 - The dynamical response of molecular systems, when the potential energy function is perturbed at a microscopic level, is difficult to predict without a numerical or laboratory experiment. This is due to the non-linearity and high-dimensionality of molecular systems. An efficient investigation of such a behaviour is necessary to better understand the nature of molecules and to improve the predictability of Molecular Dynamics simulations. In this thesis we propose a reweighting scheme for Markov State Models (MSMs), based on the Girsanov theorem, that permits to reduce the computational cost of the analysis when the potential energy function of a molecule is perturbed. The method has been successfully extended and implemented with metadynamics, in order to build the MSM of a molecular system in a significantly shorter computational time compared to a standard unbiased MD simulation. We also propose a new method to discretize the infinitesimal generator into a rate matrix, that could be used to efficiently study Hamiltonian perturbations as well. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-refubium-24541-6 PB - Freie Universität Berlin ER - TY - THES A1 - Reidelbach, Marco T1 - Optimal Network Generation for the Simulation of Proton Transfer Processes Y1 - 2019 ER - TY - CHAP A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Santiago, Xavier Garcia A1 - Betz, Fridtjof A1 - Burger, Sven ED - Saastamoinen, Kimmo T1 - Spectral Expansion of the Scattering Response of Resonant Nanostructures T2 - EOS Topical Meeting on Diffractive Optics Y1 - 2019 SN - 978-952-68553-8-7 SP - 1 ER - TY - THES A1 - Omari, Mohamed T1 - A Mathematical Model of Bovine Metabolism and Reproduction: Application to Feeding Strategies, Drug Administration and Experimental Design Y1 - 2019 ER - TY - CHAP A1 - Zschiedrich, Lin A1 - Binkowski, Felix A1 - Burger, Sven ED - Asquini, Rita T1 - Light-matter Interaction in Optical Resonators: Spectral Expansion by Riesz Projection T2 - Photonics & Electromagnetics Research Symposium Abstracts (PIERS Rome) Y1 - 2019 SP - 1067 ER - TY - CHAP A1 - Kewes, Günter A1 - Binkowski, Felix A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Stete, Felix A1 - Koopman, Wouter A1 - Bargheer, Matias A1 - Benson, Oliver ED - Asquini, Rita T1 - Line Broadening Mechanisms in Hybrid Plasmonic Systems for Strong Coupling T2 - Photonics & Electromagnetics Research Symposium Abstracts (PIERS Rome) Y1 - 2019 SP - 704 ER - TY - CHAP A1 - Burger, Sven A1 - Binkowski, Felix A1 - Zschiedrich, Lin ED - Asquini, Rita T1 - Finite Element Simulations of Optical Resonances in Dispersive Nanoresonators T2 - Photonics & Electromagnetics Research Symposium Abstracts (PIERS Rome) Y1 - 2019 SP - 699 ER - TY - CHAP A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Burger, Sven ED - Asquini, Rita T1 - Computing Optical Resonances in Plasmonic Systems Using a Contour Integral Method T2 - Photonics & Electromagnetics Research Symposium Abstracts (PIERS Rome) Y1 - 2019 SP - 1068 ER - TY - CHAP A1 - Becker, Christiane A1 - Manley, Phillip A1 - Jäger, Klaus A1 - Eisenhauer, David A1 - Sutter, Johannes A1 - Albrecht, Steve A1 - Zheng, Kaibo A1 - Pullerits, Tonu A1 - Burger, Sven ED - Zhoudi, Said ED - Topa, Antonio T1 - Nanophotonic enhanced perovskite-silicon solar cell devices T2 - The 10th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2019) Y1 - 2019 SN - 2429-1390 SP - 858 ER - TY - CHAP A1 - Manley, Phillip A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane ED - Zhoudi, Said ED - Topa, Antonio T1 - Nanophotonic Enhancement of Light Out-Coupling for Deep-UV LEDs T2 - The 10th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2019) Y1 - 2019 SN - 2429-1390 SP - 745 ER - TY - CHAP A1 - Burger, Sven A1 - Binkowski, Felix A1 - Zschiedrich, Lin ED - Zhoudi, Said ED - Topa, Antonio T1 - Computing resonances in nano-photonic devices using Riesz-projection-based methods T2 - The 10th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2019) Y1 - 2019 SN - 2429-1390 SP - 92 ER - TY - GEN ED - Ernst, Oliver ED - Nobile, Fabio ED - Schillings, Claudia ED - Sullivan, T. J. T1 - Uncertainty Quantification, 11-15 March 2019 T2 - Oberwolfach Reports Y1 - 2019 U6 - https://doi.org/10.4171/OWR/2019/12 VL - 16 IS - 1 SP - 695 EP - 772 ER - TY - JOUR A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Ma, Xiaolin A1 - Broberg, Eeva K. A1 - Penttinen, P. A1 - Reiche, J. A1 - Biere, Barbara A1 - Schweiger, Brunhilde A1 - Rath, Barbara A1 - Hoppe, Christian T1 - Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care JF - Clinical Microbiology and Infection Y1 - 2019 U6 - https://doi.org/10.1016/j.cmi.2018.05.023 SN - 1469-0691 VL - 25 IS - 3 SP - 380.e9 EP - 380.e16 ER - TY - CHAP A1 - Iravani, Sahar A1 - Conrad, Tim ED - Holzinger, A. ED - Kieseberg, P. ED - Tjoa, A. ED - Weippl, E. T1 - Deep Learning for Proteomics Data for Feature Selection and Classification T2 - Machine Learning and Knowledge Extraction. CD-MAKE 2019 Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-29726-8_19 VL - 11713 PB - Springer, Cham ER - TY - JOUR A1 - Koltai, Péter A1 - Lie, Han Cheng A1 - Plonka, Martin T1 - Fréchet differentiable drift dependence of Perron–Frobenius and Koopman operators for non-deterministic dynamics JF - Nonlinearity N2 - We prove the Fréchet differentiability with respect to the drift of Perron–Frobenius and Koopman operators associated to time-inhomogeneous ordinary stochastic differential equations. This result relies on a similar differentiability result for pathwise expectations of path functionals of the solution of the stochastic differential equation, which we establish using Girsanov's formula. We demonstrate the significance of our result in the context of dynamical systems and operator theory, by proving continuously differentiable drift dependence of the simple eigen- and singular values and the corresponding eigen- and singular functions of the stochastic Perron–Frobenius and Koopman operators. Y1 - 2019 U6 - https://doi.org/10.1088/1361-6544/ab1f2a VL - 32 IS - 11 SP - 4232 EP - 4257 ER - TY - THES A1 - Meitzner, Felix T1 - Influence of Ordinary Differential Equations on Neural Networks N2 - In this thesis, I want to analyze how neural networks trained to resemble a given function based on particular values react to additional knowledge about the function in terms of a differential equation that the function satisfies. In the first chapter, I will recall the definition of initial value problems and discuss the existence and uniqueness of their solutions, as well as touch on a method to numerically approximate them. Furthermore, I will give a mathematical introduction to neural networks. Then, I will consider a system of two first-order differential equations and test how their solution will be approximated by a neural net. In the next step, I want to see how added noise to the training data and the influence of the differential equation on the loss functional of the neural net will affect the error of the predicted solution against the exact data. Furthermore, I will test if this influence can help reduce the amount of necessary data points in order to reach similar degrees of accuracy. Y1 - 2019 ER - TY - THES A1 - Ribera Borrell, Enric T1 - From ergodic infinite-time to finite-time transition path theory Y1 - 2019 ER - TY - THES A1 - Gaedke-Merzhäuser, Lisa T1 - Adaptive Multigrid Solvers for Space-Time Discretisations Y1 - 2019 ER - TY - THES A1 - Bender, Wilhelm T1 - On a Novel Approach for Global Optimization of Non-Convex Problems N2 - In this work new approaches for global optimization are developed. We move from theoretical connections in complexity theory to very practical results in protein-ligand docking. In regard to the efficiency of the suggested optimizer, continuity methods are motivated, that yield an improved optimization method. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77074 ER - TY - THES A1 - Wegscheider, Fabian T1 - Exploiting Symmetry in Mixed-Integer Nonlinear Programming Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77055 ER - TY - CHAP A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Olthoff, Mats T1 - A Solution Approach to the Vehicle Routing Problem with Perishable Goods T2 - Operations Research 2019 Proceedings N2 - This paper focuses on a special case of vehicle routing problem where perishable goods are considered. Deliveries have to be performed until a due date date, which may vary for different products. Storing products is prohibited. Since late deliveries have a direct impact on the revenues for these products, a precise demand prediction is important. In our practical case the product demands and vehicle driving times for the product delivery are dependent on weather conditions, i.e., temperatures, wind, and precipitation. In this paper the definition and a solution approach to the Vehicle Routing Problem with Perishable Goods is presented. The approach includes a procedure how historical weather data is used to predict demands and driving times. Its run time and solution quality is evaluated on different data sets given by the MOPTA Competition 2018. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77020 ER - TY - CHAP A1 - Weinhold, Carsten A1 - Lackorzynski, Adam A1 - Bierbaum, Jan A1 - Küttler, Martin A1 - Planeta, Maksym A1 - Weisbach, Hannes A1 - Hille, Matthias A1 - Härtig, Hermann A1 - Margolin, Alexander A1 - Sharf, Dror A1 - Levy, Ely A1 - Gak, Pavel A1 - Barak, Amnon A1 - Gholami, Masoud A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander A1 - Lieber, Matthias A1 - Nagel, Wolfgang T1 - FFMK: A Fast and Fault-Tolerant Microkernel-Based System for Exascale Computing T2 - Software for Exascale Computing - SPPEXA 2016-2019 Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-47956-5_16 SP - 483 EP - 516 PB - Springer ER - TY - GEN A1 - Serrano, Felipe A1 - Muñoz, Gonzalo T1 - Maximal Quadratic-Free Sets N2 - The intersection cut paradigm is a powerful framework that facilitates the generation of valid linear inequalities, or cutting planes, for a potentially complex set S. The key ingredients in this construction are a simplicial conic relaxation of S and an S-free set: a convex zone whose interior does not intersect S. Ideally, such S-free set would be maximal inclusion-wise, as it would generate a deeper cutting plane. However, maximality can be a challenging goal in general. In this work, we show how to construct maximal S-free sets when S is defined as a general quadratic inequality. Our maximal S-free sets are such that efficient separation of a vertex in LP-based approaches to quadratically constrained problems is guaranteed. To the best of our knowledge, this work is the first to provide maximal quadratic-free sets. T3 - ZIB-Report - 19-56 KW - MINLP KW - Quadratic Optimization KW - Cutting planes Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-76922 SN - 1438-0064 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - Compression Challenges in Large Scale Partial Differential Equation Solvers JF - Algorithms N2 - Solvers for partial differential equations (PDEs) are one of the cornerstones of computational science. For large problems, they involve huge amounts of data that need to be stored and transmitted on all levels of the memory hierarchy. Often, bandwidth is the limiting factor due to the relatively small arithmetic intensity, and increasingly due to the growing disparity between computing power and bandwidth. Consequently, data compression techniques have been investigated and tailored towards the specific requirements of PDE solvers over the recent decades. This paper surveys data compression challenges and discusses examples of corresponding solution approaches for PDE problems, covering all levels of the memory hierarchy from mass storage up to the main memory. We illustrate concepts for particular methods, with examples, and give references to alternatives. Y1 - 2019 U6 - https://doi.org/10.3390/a12090197 VL - 12 IS - 9 SP - 197 ER - TY - JOUR A1 - Straube, Arthur A1 - Pagès, Josep M. A1 - Tierno, Pietro A1 - Ignés-Mullol, Jordi A1 - Sagués, Francesc T1 - Collective dynamics and conformal ordering in electrophoretically driven nematic colloids JF - Phys. Rev. Research N2 - We present a theoretical framework to understand the collective dynamics of an ensemble of electrophoretically driven colloidal particles that are forced to assemble around a single topological defect in a nematic liquid crystal by an alternating current electric field. Our generic model combines phoretic propulsion with electrostatic interactions and liquid-crystal-mediated hydrodynamics, which are effectively cast into a long-range interparticle repulsion, while nematic elasticity plays a subdominant role. Simulations based on this model fully capture the collective organization process observed in the experiments and other striking effects as the emergence of conformal ordering and a nearly frequency-independent repulsive interaction above 10Hz. Our results demonstrate the importance of hydrodynamic interactions on the assembly of driven microscale matter in anisotropic media. Y1 - 2019 U6 - https://doi.org/10.1103/PhysRevResearch.1.022008 VL - 1 SP - 022008 ER - TY - JOUR A1 - Abbott, Joshua L. A1 - Straube, Arthur A1 - Aarts, Dirk G. A. L. A1 - Dullens, Roel P. A. T1 - Transport of a colloidal particle driven across a temporally oscillating optical potential energy landscape JF - New J. Phys. N2 - A colloidal particle is driven across a temporally oscillating one-dimensional optical potential energy landscape and its particle motion is analysed. Different modes of dynamic mode locking are observed and are confirmed with the use of phase portraits. The effect of the oscillation frequency on the mode locked step width is addressed and the results are discussed in light of a high-frequency theory and compared to simulations. Furthermore, the influence of the coupling between the particle and the optical landscape on mode locking is probed by increasing the maximum depth of the optical landscape. Stronger coupling is seen to increase the width of mode locked steps. Finally, transport across the temporally oscillating landscape is studied by measuring the effective diffusion coefficient of a mobile particle, which is seen to be highly sensitive to the driving velocity and mode locking. Y1 - 2019 U6 - https://doi.org/10.1088/1367-2630/ab3765 VL - 21 SP - 083027 ER - TY - CHAP A1 - Mayer, Florian A1 - Knaust, Marius A1 - Philippsen, Michael T1 - OpenMP on FPGAs—A Survey T2 - OpenMP: Conquering the Full Hardware Spectrum N2 - Due to the ubiquity of OpenMP and the rise of FPGA-based accelerators in the HPC world, several research groups have attempted to bring the two together by building OpenMP-to-FPGA compilers. This paper is a survey of the current state of the art (with a focus on the OpenMP target pragma). It first introduces and explains a design space for the compilers. Design space dimensions include how FPGA infrastructure is generated, how work is distributed, and where/how target outlining is done. A table concisely condenses the available information on the surveyed projects which are also summarized and compared. The paper concludes with possible future research directions. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-28596-8_7 SP - 94 EP - 108 ER - TY - CHAP A1 - Knaust, Marius A1 - Mayer, Florian A1 - Steinke, Thomas T1 - OpenMP to FPGA Offloading Prototype Using OpenCL SDK T2 - 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) N2 - Field-programmable gate arrays (FPGAs) are of great interest for future high-performance computing and data analytics systems, since they are capable of efficient, highly-parallel data processing. Even though high-level synthesis became more popular in the last years, the effort of porting existing scientific software onto FPGAs is still considerable. We propose to use OpenMP target offloading as a solution, which we implement in a first prototype, making use of the preexisting OpenCL SDK of the FPGA vendor. Early results demonstrate the feasibility of this approach and also reveal that further optimizations will be necessary such that code can be written in an FPGA-agnostic way. Y1 - 2019 U6 - https://doi.org/10.1109/IPDPSW.2019.00072 SP - 387 EP - 390 ER - TY - CHAP A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Tu, Dan A1 - Wright, Stephen T1 - Blended Conditional Gradients: the unconditioning of conditional gradients T2 - Proceedings of ICML Y1 - 2019 N1 - Additional Note: https://arxiv.org/abs/1805.07311 N1 - URL of the Code: https://github.com/pokutta/bcg N1 - URL of the PDF: http://proceedings.mlr.press/v97/braun19a/braun19a.pdf N1 - URL of the Poster: https://app.box.com/s/nmmm671jd72i397nysa8emfnzh1hn6hf N1 - URL of the Slides: https://app.box.com/s/xbx3z7ws6dxvl3rzgj4jp6forigycooe N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/02/18/bcg-abstract.html ER - TY - CHAP A1 - Diakonikolas, Jelena A1 - Carderera, Alejandro A1 - Pokutta, Sebastian T1 - Breaking the Curse of Dimensionality (Locally) to Accelerate Conditional Gradients T2 - OPTML Workshop Paper Y1 - 2019 N1 - URL of the Code: https://colab.research.google.com/drive/1ejjfCan7xnEhWWJXCIzb03CwQRG9iW_O N1 - URL of the PDF: https://opt-ml.org/papers/2019/paper_26.pdf N1 - URL of the Poster: https://app.box.com/s/d7p038u7df422q4jsccbmj15mngqv2ws N1 - URL of the Slides: https://app.box.com/s/gphkhapso7d1vrfnzqykkb3vx0agxh8w N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/07/04/LaCG-abstract.html ER - TY - CHAP A1 - Combettes, Cyrille W. A1 - Pokutta, Sebastian T1 - Blended Matching Pursuit T2 - Proceedings of NeurIPS Y1 - 2019 N1 - URL of the Code: https://colab.research.google.com/drive/17XYIxnCcJjKswba9mAaXFWnNGVZdsaXQ N1 - URL of the PDF: https://papers.nips.cc/paper/8478-blended-matching-pursuit N1 - URL of the Poster: https://app.box.com/s/j6lbh49udjd45krhxcypufxwdofw6br8 N1 - URL of the Slides: https://app.box.com/s/8lfktq6h3dqp9t2gqydu2tp8h2uxgz7m N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/05/27/bmp-abstract.html ER - TY - CHAP A1 - Kerdreux, T. A1 - d’Aspremont, A. A1 - Pokutta, Sebastian T1 - Restarting Frank-Wolfe T2 - Proceedings of AISTATS Y1 - 2019 N1 - URL of the PDF: http://proceedings.mlr.press/v89/kerdreux19a/kerdreux19a.pdf N1 - URL of the Slides: https://app.box.com/s/prd32r6xmuef2k4gah23rd0egllz9rv5 N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/05/02/restartfw-abstract.html ER - TY - CHAP A1 - Anari, N. A1 - Haghtalab, N. A1 - Naor, S. A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - Structured Robust Submodular Maximization: Offline and Online Algorithms T2 - Proceedings of AISTATS Y1 - 2019 N1 - URL of the PDF: http://proceedings.mlr.press/v89/anari19a/anari19a.pdf ER - TY - CHAP A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - On the Unreasonable Effectiveness of the Greedy Algorithm: Greedy Adapts to Sharpness T2 - OPTML Workshop Paper Y1 - 2019 N1 - URL of the PDF: https://opt-ml.org/papers/2019/paper_16.pdf N1 - URL of the Poster: https://app.box.com/s/24vbh1s2vib11upqyepzen3lzdl13skr ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Zink, Daniel T1 - Affine Reductions for LPs and SDPs JF - Mathematical Programming A Y1 - 2019 N1 - URL of the PDF: http://rdcu.be/EPf9 VL - 173 IS - 1 SP - 281 EP - 312 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Zink, Daniel T1 - Lazifying Conditional Gradient Algorithms JF - Journal of Machine Learning Research (JMLR) Y1 - 2019 N1 - URL of the PDF: http://jmlr.org/papers/v20/18-114.html N1 - URL of the Slides: https://app.box.com/s/zsp0hixjz2ha23u1vuyosijjkjdh8kj7 VL - 20 IS - 71 SP - 1 EP - 42 ER - TY - CHAP A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - A Geodesic Mixed Effects Model in Kendall's Shape Space T2 - Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA) N2 - In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and apply the approach for the estimation of group trends and statistical testing of 3D shapes derived from an open access longitudinal imaging study on osteoarthritis. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-33226-6_22 VL - 11846 SP - 209 EP - 218 ER - TY - THES A1 - Rössig, Ansgar T1 - Verification of Neural Networks KW - Neural Network Verification Y1 - 2019 ER - TY - JOUR A1 - Schulz, Robert A1 - Yamamoto, Kenji A1 - Klossek, André A1 - Rancan, Fiorenza A1 - Vogt, Annika A1 - Schütte, Christof A1 - Rühl, Eckart A1 - Netz, Roland R. T1 - Modeling of Drug Diffusion Based on Concentration Profiles in Healthy and Damaged Human Skin JF - Biophysical Journal N2 - Based on experimental drug concentration profiles in healthy as well as tape-stripped ex vivo human skin, we model the penetration of the antiinflammatory drug dexamethasone into the skin layers by the one-dimensional generalized diffusion equation. We estimate the position-dependent free-energy and diffusivity profiles by solving the conjugated minimization problem, in which the only inputs are concentration profiles of dexamethasone in skin at three consecutive penetration times. The resulting free-energy profiles for damaged and healthy skin show only minor differences. In contrast, the drug diffusivity in the first 10 μm of the upper skin layer of damaged skin is 200-fold increased compared to healthy skin, which reflects the corrupted barrier function of tape-stripped skin. For the case of healthy skin, we examine the robustness of our method by analyzing the behavior of the extracted skin parameters when the number of input and output parameters are reduced. We also discuss techniques for the regularization of our parameter extraction method. Y1 - 2019 U6 - https://doi.org/10.1016/j.bpj.2019.07.027 VL - 117 IS - 5 SP - 998 EP - 1008 ER - TY - CHAP A1 - Benner, Peter A1 - Grundel, Sara A1 - Himpe, Christian A1 - Huck, Christoph A1 - Streubel, Tom A1 - Tischendorf, Caren T1 - Gas Network Benchmark Models T2 - Applications of Differential-Algebraic Equations: Examples and Benchmarks N2 - The simulation of gas transportation networks becomes increasingly more important as its use-cases broaden to more complex applications. Classically, the purpose of the gas network was the transportation of predominantly natural gas from a supplier to the consumer for long-term scheduled volumes. With the rise of renewable energy sources, gas-fired power plants are often chosen to compensate for the fluctuating nature of the renewables, due to their on-demand power generation capability. Such an only short-term plannable supply and demand setting requires sophisticated simulations of the gas network prior to the dispatch to ensure the supply of all customers for a range of possible scenarios and to prevent damages to the gas network. In this work we describe the modeling of gas networks and present benchmark systems to test implementations and compare new or extended models. Y1 - 2019 SN - 978-3-030-03718-5 U6 - https://doi.org/10.1007/11221_2018_5 SP - 171 EP - 197 PB - Springer International Publishing ER - TY - GEN ED - Dalitz, Wolfgang T1 - alsoMATH - A Database for Mathematical Algorithms and Software N2 - Mathematical publications are an important resource for the devel- opment of machine-based methods for mathematical knowledge man- agement. This article describes the publication-based approach to improve the information and the access to two important classes of mathematical research, mathematical software and mathematical algo- rithms. The publication-based approach is based on analyzing links and the structure of mathematical publications. It has been used to build the swMATH service which provides comprehensive information about mathematical software and algorithms. Y1 - 2019 U6 - https://doi.org/http://cl-informatik.uibk.ac.at/cek/cicm-wip-tentative/ VL - 2019 PB - Cezary Kaliszyk ER - TY - JOUR A1 - Banyassady, Bahareh A1 - Chiu, Man-Kwun A1 - Korman, Matias A1 - Mulzer, Wolfgang A1 - van Renssen, André A1 - Roeloffzen, Marcel A1 - Seiferth, Paul A1 - Stein, Yannik A1 - Vogtenhuber, Birgit A1 - Willert, Max T1 - Routing in polygonal domains JF - Computational Geometry, Theory and Applications N2 - We consider the problem of routing a data packet through the visibility graph of a polygonal domain P with n vertices and h holes. We may preprocess P to obtain a "label" and a "routing table" for each vertex of P. Then, we must be able to route a data packet between any two vertices p and q of P, where each step must use only the label of the target node q and the routing table of the current node. For any fixed epsilon > 0, we present a routing scheme that always achieves a routing path whose length exceeds the shortest path by a factor of at most 1 + epsilon. The labels have O(log n) bits, and the routing tables are of size O(((epsilon^-1)+h)log n). The preprocessing time is O((n^2)log n). It can be improved to O(n^2) for simple polygons. Y1 - 2019 U6 - https://doi.org/10.1016/j.comgeo.2019.101593 VL - 87 PB - Elsevier ER - TY - JOUR A1 - Del Vecchio, Giovanna A1 - Labuz, Dominika A1 - Temp, Julia A1 - Seitz, Viola A1 - Kloner, Michael A1 - Negrete, Roger A1 - Rodriguez-Gaztelumendi, Antonio A1 - Weber, Marcus A1 - Machelska, Halina A1 - Stein, Christoph T1 - pKa of opioid ligands as a discriminating factor for side effects JF - Scientific Reports N2 - The non-selective activation of central and peripheral opioid receptors is a major shortcoming of currently available opioids. Targeting peripheral opioid receptors is a promising strategy to preclude side effects. Recently, we showed that fentanyl-derived μ-opioid receptor (MOR) agonists with reduced acid dissociation constants (pKa) due to introducing single fluorine atoms produced injury-restricted antinociception in rat models of inflammatory, postoperative and neuropathic pain. Here, we report that a new double-fluorinated compound (FF6) and fentanyl show similar pKa, MOR affinity and [35S]-GTPγS binding at low and physiological pH values. In vivo, FF6 produced antinociception in injured and non-injured tissue, and induced sedation and constipation. The comparison of several fentanyl derivatives revealed a correlation between pKa values and pH-dependent MOR activation, antinociception and side effects. An opioid ligand's pKa value may be used as discriminating factor to design safer analgesics. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-55886-1 VL - 9 SP - 19344 ER - TY - JOUR A1 - Dibak, Manuel A1 - Fröhner, Christoph A1 - Noé, Frank A1 - Höfling, Felix T1 - Diffusion-influenced reaction rates in the presence of pair interactions JF - The Journal of Chemical Physics N2 - The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi’s volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction–diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction–diffusion equation in the steady state and derive semi- analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion-limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions. Y1 - 2019 U6 - https://doi.org/10.1063/1.5124728 VL - 151 SP - 164105 ER - TY - JOUR A1 - Venkatareddy, Narendra Lagumaddepalli A1 - Wilke, Patrick A1 - Ernst, Natalia A1 - Horch, Justus A1 - Weber, Marcus A1 - Dallmann, Andre A1 - Börner, Hans G. T1 - Mussel-glue inspired adhesives: A study on the relevance of L-Dopa and the function of the sequence at nanomaterial-peptide interfaces JF - Advanced Materials Interfaces N2 - Mussel glue‐proteins undergo structural transitions at material interfaces to optimize adhesive surface contacts. Those intriguing structure responses are mimicked by a mussel‐glue mimetic peptide (HSY*SGWSPY*RSG (Y* = l‐Dopa)) that was previously selected by phage‐display to adhere to Al2O3 after enzymatic activation. Molecular level insights into the full‐length adhesion domain at Al2O3 surfaces are provided by a divergent‐convergent analysis, combining nuclear Overhauser enhancement based 2D NOESY and saturation transfer difference NMR analysis of submotifs along with molecular dynamics simulations of the full‐length peptide. The peptide is divided into two submotifs, each containing one Dopa “anchor” (Motif‐1 and 2). The analysis proves Motif‐1 to constitute a dynamic Al2O3 binder and adopting an “M”‐structure with multiple surface contacts. Motif‐2 binds stronger by two surface contacts, forming a compact “C”‐structure. Taking these datasets as constraints enables to predict the structure and propose a binding process model of the full‐length peptide adhering to Al2O3. Y1 - 2019 U6 - https://doi.org/10.1002/admi.201900501 VL - 6 IS - 13 SP - 1900501 ER - TY - JOUR A1 - Erlekam, Franziska A1 - Igde, Sinaida A1 - Röblitz, Susanna A1 - Hartmann, Laura A1 - Weber, Marcus T1 - Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC JF - Computation N2 - In addition to the conventional Isothermal Titration Calorimetry (ITC), kinetic ITC (kinITC) not only gains thermodynamic information, but also kinetic data from a biochemical binding process. Moreover, kinITC gives insights into reactions consisting of two separate kinetic steps, such as protein folding or sequential binding processes. The ITC method alone cannot deliver kinetic parameters, especially not for multivalent bindings. This paper describes how to solve the problem using kinITC and an invariant subspace projection. The algorithm is tested for multivalent systems with different valencies. Y1 - 2019 U6 - https://doi.org/10.3390/computation7030046 VL - 7 IS - 3 SP - 46 ER - TY - CHAP A1 - Wende, Florian T1 - C++ Data Layout Abstractions through Proxy Types T2 - 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 14th International Workshop on Automatic Performance Tunings (iWAPT) N2 - Programs that process linearly indexed fields with structured element types in a data-parallel way usually suffer from the fact that compilers fail to generate efficient code if the selected data layout appears inappropriate for the chosen target architecture. If their internal heuristics cannot proof a performance gain from a data-parallel execution, compilers may fall back to scalar code generation. Data access through proxy types together with a customized container is one means to assist the compiler in generating efficient machine code in these cases without changing the user code. We present an automated proxy-type generator (using Clang’s LibTooling) and a configurable C++ container that supports different data layouts in a transparent way. Y1 - 2019 U6 - https://doi.org/10.1109/IPDPSW.2019.00126 SP - 758 EP - 767 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Minion, Michael L. T1 - An Efficient Parallel-in-Time Method for Optimization with Parabolic PDEs JF - SIAM J. Sci. Comput. N2 - To solve optimization problems with parabolic PDE constraints, often methods working on the reduced objective functional are used. They are computationally expensive due to the necessity of solving both the state equation and a backward-in-time adjoint equation to evaluate the reduced gradient in each iteration of the optimization method. In this study, we investigate the use of the parallel-in-time method PFASST in the setting of PDE-constrained optimization. In order to develop an efficient fully time-parallel algorithm, we discuss different options for applying PFASST to adjoint gradient computation, including the possibility of doing PFASST iterations on both the state and the adjoint equations simultaneously. We also explore the additional gains in efficiency from reusing information from previous optimization iterations when solving each equation. Numerical results for both a linear and a nonlinear reaction-diffusion optimal control problem demonstrate the parallel speedup and efficiency of different approaches. Y1 - 2019 U6 - https://doi.org/10.1137/19M1239313 VL - 41 IS - 6 SP - C603 EP - C626 ER - TY - CHAP A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas ED - Cacchiani, Valentina ED - Marchetti-Spaccamela, Alberto T1 - A Cut Separation Approach for the Rolling Stock Rotation Problem with Vehicle Maintenance T2 - 19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019) N2 - For providing railway services the company's railway rolling stock is one if not the most important ingredient. It decides about the number of passenger or cargo trips the company can offer, about the quality a passenger experiences the train ride and it is often related to the image of the company itself. Thus, it is highly desired to have the available rolling stock in the best shape possible. Moreover, in many countries, as Germany where our industrial partner DB Fernverkehr AG (DBF) is located, laws enforce regular vehicle inspections to ensure the safety of the passengers. This leads to rolling stock optimization problems with complex rules for vehicle maintenance. This problem is well studied in the literature for example see [Maróti and Kroon, 2005; Gábor Maróti and Leo G. Kroon, 2007], or [Cordeau et al., 2001] for applications including vehicle maintenance. The contribution of this paper is a new algorithmic approach to solve the Rolling Stock Rotation Problem for the ICE high speed train fleet of DBF with included vehicle maintenance. It is based on a relaxation of a mixed integer linear programming model with an iterative cut generation to enforce the feasibility of a solution of the relaxation in the solution space of the original problem. The resulting mixed integer linear programming model is based on a hypergraph approach presented in [Ralf Borndörfer et al., 2015]. The new approach is tested on real world instances modeling different scenarios for the ICE high speed train network in Germany and compared to the approaches of [Reuther, 2017] that are in operation at DB Fernverkehr AG. The approach shows a significant reduction of the run time to produce solutions with comparable or even better objective function values. Y1 - 2019 UR - https://drops.dagstuhl.de/opus/volltexte/2019/11413/ U6 - https://doi.org/10.4230/OASIcs.ATMOS.2019.1 VL - 75 SP - 1:1 EP - 1:12 PB - Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - GEN A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms N2 - Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies. T3 - ZIB-Report - 19-60 KW - quantitative photoacoustic imaging KW - blood oxygen saturation KW - inverse problem KW - model-based inversion KW - Monte Carlo KW - spectral unmixing Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75416 SN - 1438-0064 ER - TY - GEN A1 - Lindow, Norbert A1 - Brünig, Florian A1 - Dercksen, Vincent J. A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Redemann, Stefanie A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen T1 - Semi-automatic Stitching of Serial Section Image Stacks with Filamentous Structures N2 - In this paper, we present a software-assisted workflow for the alignment and matching of filamentous structures across a stack of 3D serial image sections. This is achieved by a combination of automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. This is supported by a quality assessment that visualizes regions that have been already inspected and, thus, allows a trade-off between quality and manual labor. The software tool was developed in collaboration with biologists who investigate microtubule-based spindles during cell division. To quantitatively understand the structural organization of such spindles, a 3D reconstruction of the numerous microtubules is essential. Each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The sections then need to be stitched, i.e. non-rigidly aligned; and the microtubules need to be traced in each section and connected across section boundaries. Experiments led to the conclusion that automatic methods for stitching alone provide only an incomplete solution to practical analysis needs. Automatic methods may fail due to large physical distortions, a low signal-to-noise ratio of the images, or other unexpected experimental difficulties. In such situations, semi-automatic validation and correction is required to rescue as much information as possible to derive biologically meaningful results despite of some errors related to data collection. Since the correct stitching is visually not obvious due to the number of microtubules (up to 30k) and their dense spatial arrangement, these are difficult tasks. Furthermore, a naive inspection of each microtubule is too time consuming. In addition, interactive visualization is hampered by the size of the image data (up to 100 GB). Based on the requirements of our collaborators, we present a practical solution for the semi-automatic stitching of serial section image stacks with filamentous structures. T3 - ZIB-Report - 19-30 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73739 SN - 1438-0064 ER - TY - CHAP A1 - Hartung, Marc A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Pinpoint Data Races via Testing and Classification T2 - 2019 IEEE International Symposium on Software Reliability Engineering Workshops (ISSREW); 3rd International Workshop on Software Faults (IWSF 2019) Y1 - 2019 U6 - https://doi.org/10.1109/ISSREW.2019.00100 SP - 386 EP - 393 ER - TY - CHAP A1 - Gholami, Masoud A1 - Schintke, Florian T1 - Multilevel Checkpoint/Restart for Large Computational Jobs on Distributed Computing Resources T2 - 2019 IEEE 38th Symposium on Reliable Distributed Systems (SRDS) Y1 - 2019 U6 - https://doi.org/10.1109/SRDS47363.2019.00025 SP - 143 EP - 152 ER - TY - GEN A1 - Becker, Kai-Helge A1 - Hiller, Benjamin T1 - Improved optimization models for potential-driven network flow problems via ASTS orientations N2 - The class of potential-driven network flow problems provides important models for a range of infrastructure networks that lead to hard-to-solve MINLPs in real-world applications. On large-scale meshed networks the relaxations usually employed are rather weak due to cycles in the network. To address this situation, we introduce the concept of ASTS orientations, a generalization of bipolar orientations, as a combinatorial relaxation of feasible solutions of potential-driven flow problems, study their structure, and show how they can be used to strengthen existing relaxations and thus provide improved optimization models. Our computational results indicate that ASTS orientations can be used to derive much stronger bounds on the flow variables than existing bound tightening methods and to yield significant performance improvements for an existing state-of-the-art MILP model for large-scale gas networks. T3 - ZIB-Report - 19-58 KW - potential-driven network flows KW - mixed-integer nonlinear programming KW - ASTS orientations KW - bipolar orientations Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75347 SN - 1438-0064 ER - TY - GEN A1 - Witzig, Jakob A1 - Berthold, Timo T1 - Conflict-Free Learning for Mixed Integer Programming N2 - Conflict learning plays an important role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. A major step for MIP conflict learning is to aggregate the LP relaxation of an infeasible subproblem to a single globally valid constraint, the dual proof, that proves infeasibility within the local bounds. Among others, one way of learning is to add these constraints to the problem formulation for the remainder of the search. We suggest to not restrict this procedure to infeasible subproblems, but to also use global proof constraints from subproblems that are not (yet) infeasible, but can be expected to be pruned soon. As a special case, we also consider learning from integer feasible LP solutions. First experiments of this conflict-free learning strategy show promising results on the MIPLIB2017 benchmark set. T3 - ZIB-Report - 19-59 KW - mixed integer programming KW - conflict analysis KW - dual proof analysis KW - no-good learning KW - solution learning Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75338 SN - 1438-0064 ER - TY - GEN A1 - Gleixner, Ambros A1 - Steffy, Daniel T1 - Linear Programming using Limited-Precision Oracles N2 - Since the elimination algorithm of Fourier and Motzkin, many different methods have been developed for solving linear programs. When analyzing the time complexity of LP algorithms, it is typically either assumed that calculations are performed exactly and bounds are derived on the number of elementary arithmetic operations necessary, or the cost of all arithmetic operations is considered through a bit-complexity analysis. Yet in practice, implementations typically use limited-precision arithmetic. In this paper we introduce the idea of a limited-precision LP oracle and study how such an oracle could be used within a larger framework to compute exact precision solutions to LPs. Under mild assumptions, it is shown that a polynomial number of calls to such an oracle and a polynomial number of bit operations, is sufficient to compute an exact solution to an LP. This work provides a foundation for understanding and analyzing the behavior of the methods that are currently most effective in practice for solving LPs exactly. T3 - ZIB-Report - 19-57 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75316 SN - 1438-0064 ER - TY - GEN A1 - Müller, Benjamin A1 - Muñoz, Gonzalo A1 - Gasse, Maxime A1 - Gleixner, Ambros A1 - Lodi, Andrea A1 - Serrano, Felipe T1 - On Generalized Surrogate Duality in Mixed-Integer Nonlinear Programming N2 - The most important ingredient for solving mixed-integer nonlinear programs (MINLPs) to global epsilon-optimality with spatial branch and bound is a tight, computationally tractable relaxation. Due to both theoretical and practical considerations, relaxations of MINLPs are usually required to be convex. Nonetheless, current optimization solver can often successfully handle a moderate presence of nonconvexities, which opens the door for the use of potentially tighter nonconvex relaxations. In this work, we exploit this fact and make use of a nonconvex relaxation obtained via aggregation of constraints: a surrogate relaxation. These relaxations were actively studied for linear integer programs in the 70s and 80s, but they have been scarcely considered since. We revisit these relaxations in an MINLP setting and show the computational benefits and challenges they can have. Additionally, we study a generalization of such relaxation that allows for multiple aggregations simultaneously and present the first algorithm that is capable of computing the best set of aggregations. We propose a multitude of computational enhancements for improving its practical performance and evaluate the algorithm’s ability to generate strong dual bounds through extensive computational experiments. T3 - ZIB-Report - 19-55 KW - surrogate relaxation KW - MINLP KW - nonconvex optimization Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75179 SN - 1438-0064 ER - TY - CHAP A1 - Hartung, Marc T1 - ZIB_Glucose: Luby Blocked Restarts and Dynamic Vivification T2 - Proceedings of SAT Race 2019 : Solver and Benchmark Descriptions Y1 - 2019 SP - 43 EP - 44 ER - TY - CHAP A1 - Clausecker, Robert A1 - Reinefeld, Alexander T1 - Zero-Aware Pattern Databases with 1-Bit Compression for Sliding Tile Puzzles T2 - Proceedings of the Twelfth International Symposium on Combinatorial Search (SoCS 2019) Y1 - 2019 UR - https://aaai.org/ocs/index.php/SOCS/SOCS19/paper/view/18326 SP - 35 EP - 43 ER - TY - CHAP A1 - Beulertz, Daniel A1 - Charousset-Brignol, Sandrine A1 - Most, Dieter A1 - Giannelos, Spyros A1 - Yueksel-Erguen, Inci T1 - Development of a Modular Framework for Future Energy System Analysis T2 - 54th International Universities Power Engineering Conference (UPEC) N2 - This paper gives an overview of the modeling framework that is being developed within the Horizon2020 project plan4res. In the context of energy transition, integration of high shares of renewable energies will play a vital role for achieving the proposed climate targets. This brings new challenges to modeling tools, including data construction, implementation and solution techniques. In order to address these challenges, plan4res aims to create a well-structured and highly modular framework that will provide insights into the needs of future energy systems. An overview of the central modeling aspects is given in this paper. Finally, three case studies are presented that show the adequacy and relevance of the proposed optimization framework. Y1 - 2019 U6 - https://doi.org/10.1109/UPEC.2019.8893472 ER - TY - CHAP A1 - Lindner, Niels A1 - Liebchen, Christian ED - Cacchiani, Valentina ED - Marchetti-Spaccamela, Alberto T1 - New Perspectives on PESP: T-Partitions and Separators T2 - 19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019) N2 - In the planning process of public transportation companies, designing the timetable is among the core planning steps. In particular in the case of periodic (or cyclic) services, the Periodic Event Scheduling Problem (PESP) is well-established to compute high-quality periodic timetables. We are considering algorithms for computing good solutions for the very basic PESP with no additional extra features as add-ons. The first of these algorithms generalizes several primal heuristics that had been proposed in the past, such as single-node cuts and the modulo network simplex algorithm. We consider partitions of the graph, and identify so-called delay cuts as a structure that allows to generalize several previous heuristics. In particular, when no more improving delay cut can be found, we already know that the other heuristics could not improve either. The second of these algorithms turns a strategy, that had been discussed in the past, upside-down: Instead of gluing together the network line-by-line in a bottom-up way, we develop a divide-and-conquer-like top-down approach to separate the initial problem into two easier subproblems such that the information loss along their cutset edges is as small as possible. We are aware that there may be PESP instances that do not fit well the separator setting. Yet, on the RxLy-instances of PESPlib in our experimental computations, we come up with good primal solutions and dual bounds. In particular, on the largest instance (R4L4), this new separator approach, which applies a state-of-the-art solver as subroutine, is able to come up with better dual bounds than purely applying this state-of-the-art solver in the very same time. Y1 - 2019 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2019.2 VL - 75 SP - 2:1 EP - 2:18 PB - Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - CHAP A1 - Euler, Ricardo A1 - Borndörfer, Ralf T1 - A Graph- and Monoid-based Framework for Price-Sensitive Routing in Local Public Transportation Networks T2 - 19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019) N2 - We present a novel framework to mathematically describe the fare systems of local public transit companies. The model allows the computation of a provably cheapest itinerary even if prices depend on a number of parameters and non-linear conditions. Our approach is based on a ticket graph model to represent tickets and their relation to each other. Transitions between tickets are modeled via transition functions over partially ordered monoids and a set of symbols representing special properties of fares (e.g. surcharges). Shortest path algorithms rely on the subpath optimality property. This property is usually lost when dealing with complicated fare systems. We restore it by relaxing domination rules for tickets depending on the structure of the ticket graph. An exemplary model for the fare system of Mitteldeutsche Verkehrsbetriebe (MDV) is provided. By integrating our framework in the multi-criteria RAPTOR algorithm we provide a price-sensitive algorithm for the earliest arrival problem and assess its performance on data obtained from MDV. We discuss three preprocessing techniques that improve run times enough to make the algorithm applicable for real-time queries. Y1 - 2019 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2019.12 VL - 75 SP - 12:1 EP - 12:15 ER - TY - JOUR A1 - Oltmanns, Elias A1 - Hasler, Tim A1 - Peters-Kottig, Wolfgang A1 - Kuper, Heinz-Günter T1 - Different Preservation Levels: The Case of Scholarly Digital Editions JF - Data Science Journal N2 - Ensuring the long-term availability of research data forms an integral part of data management services. Where OAIS compliant digital preservation has been established in recent years, in almost all cases the services aim at the preservation of file-based objects. In the Digital Humanities, research data is often represented in highly structured aggregations, such as Scholarly Digital Editions. Naturally, scholars would like their editions to remain functionally complete as long as possible. Besides standard components like webservers, the presentation typically relies on project specific code interacting with client software like webbrowsers. Especially the latter being subject to rapid change over time invariably makes such environments awkward to maintain once funding has ended. Pragmatic approaches have to be found in order to balance the curation effort and the maintainability of access to research data over time. A sketch of four potential service levels aiming at the long-term availability of research data in the humanities is outlined: (1) Continuous Maintenance, (2) Application Conservation, (3) Application Data Preservation, and (4) Bitstream Preservation. The first being too costly and the last hardly satisfactory in general, we suggest that the implementation of services by an infrastructure provider should concentrate on service levels 2 and 3. We explain their strengths and limitations considering the example of two Scholarly Digital Editions. KW - Digital Preservation Y1 - 2019 U6 - https://doi.org/10.5334/dsj-2019-051 VL - 18 IS - 1(51) ER - TY - GEN A1 - Omari, Mohamed A1 - Plöntzke, Julia A1 - Röblitz, Susanna T1 - A pharmacokinetic-pharmacodynamic model for single dose administration of Dexamethasone in dairy cows N2 - We present a mechanistic pharmacokinetic-pharmacodynamic model to simulate the effect of dexamethasone on the glucose metabolism in dairy cows. The coupling of the pharmacokinetic model to the pharmacodynamic model is based on mechanisms underlying homeostasis regulation by dexamethasone. In particular, the coupling takes into account the predominant role of dexamethasone in stimulating glucagon secretion, glycogenolysis and lipolysis and in impairing the sensitivity of cells to insulin. Simulating the effect of a single dose of dexamethasone on the physiological behaviour of the system shows that the adopted mechanisms are able to induce a temporary hyperglycemia and hyperinsulinemia, which captures the observed data in non-lactating cows. In lactating cows, the model simulations show that a single dose of dexamethasone reduces the lipolytic effect, owing to the reduction of glucose uptake by the mammary gland. T3 - ZIB-Report - 19-53 KW - systems biology; modelling; differential equations; metabolism; nutrition; bovine; fertility; reproduction; hormones; follicles; Dexamethasone; PK-PD Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75043 SN - 1438-0064 ER - TY - JOUR A1 - Girolami, Mark A. A1 - Ipsen, Ilse C. F. A1 - Oates, Chris A1 - Owen, Art B. A1 - Sullivan, T. J. T1 - Editorial: Special edition on probabilistic numerics JF - Statistics and Computing Y1 - 2019 U6 - https://doi.org/doi:10.1007/s11222-019-09892-y VL - 29 IS - 6 SP - 1181 EP - 1183 ER - TY - GEN A1 - Witzig, Jakob A1 - Berthold, Timo A1 - Heinz, Stefan T1 - Computational Aspects of Infeasibility Analysis in Mixed Integer Programming N2 - The analysis of infeasible subproblems plays an important role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. There are two fundamentally different concepts to generate valid global constraints from infeasible subproblems. The first is to analyze the sequence of implications, obtained by domain propagation, that led to infeasibility. The result of this analysis is one or more sets of contradicting variable bounds from which so-called conflict constraints can be generated. This concept is called conflict graph analysis and has its origin in solving satisfiability problems and is similarly used in constraint programming. The second concept is to analyze infeasible linear programming (LP) relaxations. Every ray of the dual LP provides a set of multipliers that can be used to generate a single new globally valid linear constraint. This method is called dual proof analysis. The main contribution of this paper is twofold. Firstly, we present three enhancements of dual proof analysis: presolving via variable cancellation, strengthening by applying mixed integer rounding functions, and a filtering mechanism. Further, we provide an intense computational study evaluating the impact of every presented component regarding dual proof analysis. Secondly, this paper presents the first integrated approach to use both conflict graph and dual proof analysis simultaneously within a single MIP solution process. All experiments are carried out on general MIP instances from the standard public test set MIPLIB 2017; the presented algorithms have been implemented within the non-commercial MIP solver SCIP and the commercial MIP solver FICO Xpress. T3 - ZIB-Report - 19-54 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74962 SN - 1438-0064 ER - TY - GEN T1 - Annual Report 2017 T3 - Jahresbericht - 2017 KW - Jahresbericht Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74948 SN - 0934-5892 VL - 2017 ER - TY - JOUR A1 - Nyakatura, John A1 - Baumgarten, Roxane A1 - Baum, Daniel A1 - Stark, Heiko A1 - Youlatos, Dionisios T1 - Muscle internal structure revealed by contrast-enhanced μCT and fibre recognition: The hindlimb extensors of an arboreal and a fossorial squirrel JF - Mammalian Biology N2 - In individuals of similar body mass representing closely related species with different lifestyles, muscle architectural properties can be assumed to reflect adaptation to differing, lifestyle-related functional demands. We here employ a fiber recognition algorithm on contrast-enhanced micro-computed tomography (μCT) scans of one specimen each of an arboreal (Sciurus vulgaris) and a fossorial (Spermophilus citellus) sciuromorph rodent. The automated approach accounts for potential heterogeneity of architectural properties within a muscle by analyzing all fascicles that compose a muscle. Muscle architectural properties (volume, fascicle length, and orientation, and force-generating capacity) were quantified in 14 hindlimb (hip, knee, and ankle) extensor muscles and compared between specimens. We expected the arboreal squirrel to exhibit greater force-generating capacity and a greater capacity for length change allowing more powerful hindlimb extension. Generally and mostly matching our expectations, the S. vulgaris specimen had absolutely and relatively larger extensor muscles than the S. citellus specimen which were thus metabolically more expensive and demonstrate the relatively larger investment into powerful hindlimb extension necessary in the arboreal context. We conclude that detailed quantitative data on hindlimb muscle internal structure as was gathered here for a very limited sample further lends support to the notion that muscle architecture reflects adaptation to differential functional demands in closely related species with different locomotor behaviors and lifestyles. Y1 - 2019 U6 - https://doi.org/10.1016/j.mambio.2019.10.007 VL - 99 SP - 71 EP - 80 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Improving the throughput of a scalable FLESnet using the Data-Flow Scheduler JF - CBM Progress Report 2018 Y1 - 2019 SN - 978-3-9815227-6-1 U6 - https://doi.org/10.15120/GSI-2019-01018 SP - 149 EP - 150 ER - TY - GEN A1 - Chen, Ying A1 - Koch, Thorsten A1 - Xu, Xiaofei T1 - Regularized partially functional autoregressive model with application to high-resolution natural gas forecasting in Germany N2 - We propose a partially functional autoregressive model with exogenous variables (pFAR) to describe the dynamic evolution of the serially correlated functional data. It provides a unit� ed framework to model both the temporal dependence on multiple lagged functional covariates and the causal relation with ultrahigh-dimensional exogenous scalar covariates. Estimation is conducted under a two-layer sparsity assumption, where only a few groups and elements are supposed to be active, yet without knowing their number and location in advance. We establish asymptotic properties of the estimator and investigate its unite sample performance along with simulation studies. We demonstrate the application of pFAR with the high-resolution natural gas flows in Germany, where the pFAR model provides insightful interpretation as well as good out-of-sample forecast accuracy. T3 - ZIB-Report - 19-34 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74880 SN - 1438-0064 ER - TY - GEN A1 - Christgau, Steffen A1 - Schnor, Bettina T1 - MPI Passive Target Synchronization on a Non-Cache-Coherent Shared-Memory Processor N2 - MPI passive target synchronization offers exclusive and shared locks. These are the building blocks for the implementation of applications with Readers & Writers semantic, like for example distributed hash tables. This paper discusses the implementation of MPI passive target synchronization on a non-cache-coherent multicore, the Intel Single-Chip Cloud Computer. The considered algorithms differ in their communication style (message based versus shared memory), their data structures (centralized versus distributed) and their semantics (with/without Writer preference). It is shown that shared memory approaches scale very well and deliver good performance, even in absence of cache coherence. T3 - ZIB-Report - 19-52 KW - process synchronization KW - programming models and systems for manycores KW - MPI Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74774 SN - 1438-0064 ER - TY - JOUR A1 - Heller, Eric J. A1 - Fleischmann, Ragnar A1 - Kramer, Tobias T1 - Branched Flow N2 - In many physical situations involving diverse length scales, waves or rays representing them travel through media characterized by spatially smooth, random, modest refractive index variations. "Primary" diffraction (by individual sub-wavelength features) is absent. Eventually the weak refraction leads to imperfect focal "cusps". Much later, a statistical regime characterized by momentum diffusion is manifested. An important intermediate regime is often overlooked, one that is diffusive only in an ensemble sense. Each realization of the ensemble possesses dramatic ray limit structure that guides the waves (in the same sense that ray optics is used to design lens systems). This structure is a universal phenomenon called branched flow. Many important phenomena develop in this intermediate regime. Here we give examples and some of the physics of this emerging field. Y1 - 2019 ER - TY - GEN A1 - Maher, Stephen J. A1 - Ralphs, Ted A1 - Shinano, Yuji T1 - Assessing the Effectiveness of (Parallel) Branch-and-bound Algorithms N2 - Empirical studies are fundamental in assessing the effectiveness of implementations of branch-and-bound algorithms. The complexity of such implementations makes empirical study difficult for a wide variety of reasons. Various attempts have been made to develop and codify a set of standard techniques for the assessment of optimization algorithms and their software implementations; however, most previous work has been focused on classical sequential algorithms. Since parallel computation has become increasingly mainstream, it is necessary to re-examine and modernize these practices. In this paper, we propose a framework for assessment based on the notion that resource consumption is at the heart of what we generally refer to as the “effectiveness” of an implementation. The proposed framework carefully distinguishes between an implementation’s baseline efficiency, the efficacy with which it utilizes a fixed allocation of resources, and its scalability, a measure of how the efficiency changes as resources (typically additional computing cores) are added or removed. Efficiency is typically applied to sequential implementations, whereas scalability is applied to parallel implementations. Efficiency and scalability are both important contributors in determining the overall effectiveness of a given parallel implementation, but the goal of improved efficiency is often at odds with the goal of improved scalability. Within the proposed framework, we review the challenges to effective evaluation and discuss the strengths and weaknesses of existing methods of assessment. T3 - ZIB-Report - 19-03 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74702 ER -