TY - THES A1 - Ehlke, Moritz T1 - 3D Reconstruction of Anatomical Structures from 2D X-ray Images Y1 - 2020 UR - https://depositonce.tu-berlin.de/handle/11303/12753 U6 - https://doi.org/https://doi.org/10.14279/depositonce-11553 ER - TY - JOUR A1 - Ziesche, Ralf F. A1 - Arlt, Tobias A1 - Finegan, Donal P. A1 - Heenan, Thomas M.M. A1 - Tengattini, Alessandro A1 - Baum, Daniel A1 - Kardjilov, Nikolay A1 - Markötter, Henning A1 - Manke, Ingo A1 - Kockelmann, Winfried A1 - Brett, Dan J.L. A1 - Shearing, Paul R. T1 - 4D imaging of lithium-batteries using correlative neutron and X-ray tomography with a virtual unrolling technique JF - Nature Communications N2 - The temporally and spatially resolved tracking of lithium intercalation and electrode degradation processes are crucial for detecting and understanding performance losses during the operation of lithium-batteries. Here, high-throughput X-ray computed tomography has enabled the identification of mechanical degradation processes in a commercial Li/MnO2 primary battery and the indirect tracking of lithium diffusion; furthermore, complementary neutron computed tomography has identified the direct lithium diffusion process and the electrode wetting by the electrolyte. Virtual electrode unrolling techniques provide a deeper view inside the electrode layers and are used to detect minor fluctuations which are difficult to observe using conventional three dimensional rendering tools. Moreover, the ‘unrolling’ provides a platform for correlating multi-modal image data which is expected to find wider application in battery science and engineering to study diverse effects e.g. electrode degradation or lithium diffusion blocking during battery cycling. Y1 - 2020 U6 - https://doi.org/10.1038/s41467-019-13943-3 VL - 11 SP - 777 ER - TY - JOUR A1 - Willsch, Maraike A1 - Friedrich, Frank A1 - Baum, Daniel A1 - Jurisch, Ivo A1 - Ohl, Michael T1 - A comparative description of the mesosomal musculature in Sphecidae and Ampulicidae (Hymenoptera, Apoidea) using 3D techniques JF - Deutsche Entomologische Zeitschrift N2 - Conflicting hypotheses about the relationships among the major lineages of aculeate Hymenoptera clearly show the necessity of detailed comparative morphological studies. Using micro-computed tomography and 3D reconstructions, the skeletal musculature of the meso- and metathorax and the first and second abdominal segment in Apoidea are described. Females of Sceliphron destillatorium, Sphex (Fernaldina) lucae (both Sphecidae), and Ampulex compressa (Ampulicidae) were examined. The morphological terminology provided by the Hymenoptera Anatomy Ontology is used. Up to 42 muscles were found. The three species differ in certain numerical and structural aspects. Ampulicidae differs significantly from Sphecidae in the metathorax and the anterior abdomen. The metapleural apodeme and paracoxal ridge are weakly developed in Ampulicidae, which affect some muscular structures. Furthermore, the muscles that insert on the coxae and trochanters are broader and longer in Ampulicidae. A conspicuous characteristic of Sphecidae is the absence of the metaphragma. Overall, we identified four hitherto unrecognized muscles. Our work suggests additional investigations on structures discussed in this paper. Y1 - 2020 U6 - https://doi.org/10.3897/dez.67.49493 VL - 67 IS - 1 SP - 51 EP - 67 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Lindner, Niels A1 - Roth, Sarah T1 - A Concurrent Approach to the Periodic Event Scheduling Problem JF - Journal of Rail Transport Planning & Management N2 - We introduce a concurrent solver for the periodic event scheduling problem (PESP). It combines mixed integer programming techniques, the modulo network simplex method, satisfiability approaches, and a new heuristic based on maximum cuts. Running these components in parallel speeds up the overall solution process. This enables us to significantly improve the current upper and lower bounds for all benchmark instances of the library PESPlib. Y1 - 2020 U6 - https://doi.org/10.1016/j.jrtpm.2019.100175 SN - 2210-9706 IS - 15 SP - 100175 ER - TY - GEN A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas 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 Maroti and Kroon 2005, 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 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. T3 - ZIB-Report - 19-61 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75501 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - A Discrete-Continuous Algorithm for Free Flight Planning N2 - We propose a hybrid discrete-continuous algorithm for flight planning in free flight airspaces. In a first step, our DisCOptER method discrete-continuous optimization for enhanced resolution) computes a globally optimal approximate flight path on a discretization of the problem using the A* method. This route initializes a Newton method that converges rapidly to the smooth optimum in a second step. The correctness, accuracy, and complexity of the method are goverened by the choice of the crossover point that determines the coarseness of the discretization. We analyze the optimal choice of the crossover point and demonstrate the asymtotic superority of DisCOptER over a purely discrete approach. T3 - ZIB-Report - 20-33 KW - shortest path KW - flight planning KW - free flight KW - discrete-continuous algorithm KW - optimal control KW - discrete optimization Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81343 SN - 1438-0064 ER - TY - CHAP A1 - Yokoyama, Ryohei A1 - Kamada, Hiroki A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - A Hierarchical Optimization Approach to Robust Design of Energy Supply Systems Based on a Mixed-Integer Linear Model T2 - Conference N2 - In designing energy supply systems, designers should heighten the robustness in performance criteria against the uncertainty in energy demands. In this paper, a robust optimal design method using a hierarchi- cal mixed-integer linear programming (MILP) method is proposed to maximize the robustness of energy sup- ply systems under uncertain energy demands based on a mixed-integer linear model. A robust optimal design problem is formulated as a three-level min-max-min MILP one by expressing uncertain energy demands by intervals, evaluating the robustness in a performance criterion based on the minimax regret cri- terion, and considering relationships among integer design variables, uncertain energy demands, and inte- ger and continuous operation variables. This problem is solved by evaluating upper and lower bounds for the minimum of the maximum regret of the performance criterion repeatedly outside, and evaluating lower and upper bounds for the maximum regret repeatedly inside. Since these different types of optimization problems are difficult to solve even using commercial MILP solvers, they are solved by applying a hierarchi- cal MILP method developed for ordinary optimal design problems with its modifications. In a case study, the proposed approach is applied to the robust optimal design of a cogeneration system. Through the study, its validity and effectiveness are ascertained, and some features of the obtained robust designs are clarified. Y1 - 2020 SP - 601 EP - 613 ER - TY - JOUR A1 - Le Duc, Huy A1 - Conrad, Tim T1 - A light-weight and highly flexible software system for analyzing large bio-medical datasets JF - Future Generation Computer Systems Y1 - 2020 ER - TY - GEN A1 - Most, Dieter A1 - Giannelos, Spyros A1 - Yueksel-Erguen, Inci A1 - Beulertz, Daniel A1 - Haus, Utz-Uwe A1 - Charousset-Brignol, Sandrine A1 - Frangioni, Antonio T1 - A Novel Modular Optimization Framework for Modelling Investment and Operation of Energy Systems at European Level N2 - Project plan4res (www.plan4res.eu) involves the development of a modular framework for the modeling and analysis of energy system strategies at the European level. It will include models describing the investment and operation decisions for a wide variety of technologies related to electricity and non-electricity energy sectors across generation, consumption, transmission and distribution. The modularity of the framework allows for detailed modelling of major areas of energy systems that can help stakeholders from different backgrounds to focus on specific topics related to the energy landscape in Europe and to receive relevant outputs and insights tailored to their needs. The current paper presents a qualitative description of key concepts and methods of the novel modular optimization framework and provides insights into the corresponding energy landscape. T3 - ZIB-Report - 20-08 KW - energy systems analysis and optimization KW - simulation and planning under uncertainty KW - renewables integration KW - sector coupling KW - climate change impact Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78079 SN - 1438-0064 ER - TY - JOUR A1 - Sun, Yahui A1 - Rehfeldt, Daniel A1 - Brazil, Marcus A1 - Thomas, Doreen A1 - Halgamuge, Saman T1 - A Physarum-Inspired Algorithm for Minimum-Cost Relay Node Placement in Wireless Sensor Networks JF - IEEE/ACM Transactions on Networking Y1 - 2020 U6 - https://doi.org/10.1109/TNET.2020.2971770 ER - TY - JOUR A1 - Tesch, Alexander T1 - A Polyhedral Study of Event-Based Models for the Resource-Constrained Project Scheduling Problem JF - Journal of Scheduling N2 - We consider event-based Mixed-Integer Programming (MIP) models for the Resource-Constrained Project Scheduling Problem (RCPSP) that represent an alternative to the common time-indexed model (DDT) of Pritsker et al. (1969) for the case where the underlying time horizon is large or job processing times are subject to huge variations. In contrast to the time-indexed model, the size of event-based models does not depend on the time horizon. For two event-based formulations OOE and SEE of Koné et al. (2011) we present new valid inequalities that dominate the original formulation. Additionally, we introduce a new event-based model: the Interval Event-Based Model (IEE). We deduce linear transformations between all three models that yield the strict domination order IEE > SEE > OOE for their linear programming (LP) relaxations, meaning that IEE has the strongest linear relaxation among the event-based models. We further show that the popular DDT formulation can be retrieved from IEE by certain polyhedral operations, thus giving a unifying view on a complete branch of MIP formulations for the RCPSP. In addition, we analyze the computational performance of all presented models on test instances of the PSPLIB (Kolisch and Sprecher 1997). Y1 - 2020 ER - TY - GEN A1 - Bittracher, Andreas A1 - Schütte, Christof T1 - A probabilistic algorithm for aggregating vastly undersampled large Markov chains N2 - Model reduction of large Markov chains is an essential step in a wide array of techniques for understanding complex systems and for efficiently learning structures from high-dimensional data. We present a novel aggregation algorithm for compressing such chains that exploits a specific low-rank structure in the transition matrix which, e.g., is present in metastable systems, among others. It enables the recovery of the aggregates from a vastly undersampled transition matrix which in practical applications may gain a speedup of several orders of mag- nitude over methods that require the full transition matrix. Moreover, we show that the new technique is robust under perturbation of the transition matrix. The practical applicability of the new method is demonstrated by identifying a reduced model for the large-scale traffic flow patterns from real-world taxi trip data. T3 - ZIB-Report - 20-21 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78688 UR - https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/7587 SN - 1438-0064 ER - TY - JOUR A1 - Koch, Thorsten A1 - Chen, Ying A1 - Lim, Kian Guan A1 - Xu, Xiaofei A1 - Zakiyeva, Nazgul T1 - A review study of functional autoregressive models with application to energy forecasting JF - WIREs Computational Statistics Y1 - 2020 U6 - https://doi.org/10.1002/wics.1525 N1 - https://ink.library.smu.edu.sg/cgi/viewcontent.cgi?article=7693&context=lkcsb_research ER - TY - JOUR A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - A Riesz-projection-based method for nonlinear eigenvalue problems JF - J. Comput. Phys. Y1 - 2020 U6 - https://doi.org/10.1016/j.jcp.2020.109678 VL - 419 SP - 109678 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Schuster, Ingmar A1 - Sullivan, T. J. T1 - A rigorous theory of conditional mean embeddings JF - SIAM Journal on Mathematics of Data Science Y1 - 2020 U6 - https://doi.org/10.1137/19M1305069 VL - 2 IS - 3 SP - 583 EP - 606 ER - TY - GEN A1 - Grimm, Boris A1 - Borndörfer, Ralf A1 - Olthoff, Mats T1 - A Solution Approach to the Vehicle Routing Problem with Perishable Goods 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. T3 - ZIB-Report - 20-03 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77020 SN - 1438-0064 ER - TY - JOUR A1 - Udvary, Daniel A1 - Harth, Philipp A1 - Macke, Jakob H. A1 - Hege, Hans-Christian A1 - de Kock, Christiaan P. J. A1 - Sakmann, Bert A1 - Oberlaender, Marcel T1 - A Theory for the Emergence of Neocortical Network Architecture JF - BioRxiv Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1101/2020.11.13.381087 ER - TY - GEN A1 - Bittracher, Andreas A1 - Schütte, Christof ED - Junge, Oliver ED - Schütze, O. ED - Froyland, Gary ED - Ober-Blobaum, S. ED - Padberg-Gehle, E. T1 - A weak characterization of slow variables in stochastic dynamical systems T2 - Advances in Dynamics, Optimization and Computation. Series: Studies in Systems, Decision and Control. A volume dedicated to Michael Dellnitz on the occasion of his 60th birthday Y1 - 2020 SN - 978-3-030-51264-4 U6 - https://doi.org/10.1007/978-3-030-51264-4_6 VL - 304 SP - 132 EP - 150 PB - Springer International ER - TY - CHAP A1 - Sofranac, Boro A1 - Gleixner, Ambros A1 - Pokutta, Sebastian T1 - Accelerating Domain Propagation: an Efficient GPU-Parallel Algorithm over Sparse Matrices T2 - 2020 IEEE/ACM 10th Workshop on Irregular Applications: Architectures and Algorithms (IA3) N2 - Fast domain propagation of linear constraints has become a crucial component of today's best algorithms and solvers for mixed integer programming and pseudo-boolean optimization to achieve peak solving performance. Irregularities in the form of dynamic algorithmic behaviour, dependency structures, and sparsity patterns in the input data make efficient implementations of domain propagation on GPUs and, more generally, on parallel architectures challenging. This is one of the main reasons why domain propagation in state-of-the-art solvers is single thread only. In this paper, we present a new algorithm for domain propagation which (a) avoids these problems and allows for an efficient implementation on GPUs, and is (b) capable of running propagation rounds entirely on the GPU, without any need for synchronization or communication with the CPU. We present extensive computational results which demonstrate the effectiveness of our approach and show that ample speedups are possible on practically relevant problems: on state-of-the-art GPUs, our geometric mean speed-up for reasonably-large instances is around 10x to 20x and can be as high as 195x on favorably-large instances. Y1 - 2020 U6 - https://doi.org/10.1109/IA351965.2020.00007 N1 - URL of the Slides: https://app.box.com/s/qy0pjmhtbm7shk2ypxjxlh2sj4nudvyu N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2020/09/20/gpu-prob.html SP - 1 EP - 11 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Fackeldey, Konstantin A1 - Wagner, Gerhard A1 - Arthanari, Haribabu T1 - Accounting of Receptor Flexibility in Ultra-Large Virtual Screens with VirtualFlow Using a Grey Wolf Optimization Method JF - Supercomputing Frontiers and Innovations N2 - Structure-based virtual screening approaches have the ability to dramatically reduce the time and costs associated to the discovery of new drug candidates. Studies have shown that the true hit rate of virtual screenings improves with the scale of the screened ligand libraries. Therefore, we have recently developed an open source drug discovery platform (VirtualFlow), which is able to routinely carry out ultra-large virtual screenings. One of the primary challenges of molecular docking is the circumstance when the protein is highly dynamic or when the structure of the protein cannot be captured by a static pose. To accommodate protein dynamics, we report the extension of VirtualFlow to allow the docking of ligands using a grey wolf optimization algorithm using the docking program GWOVina, which substantially improves the quality and efficiency of flexible receptor docking compared to AutoDock Vina. We demonstrate the linear scaling behavior of VirtualFlow utilizing GWOVina up to 128 000 CPUs. The newly supported docking method will be valuable for drug discovery projects in which protein dynamics and flexibility play a significant role. Y1 - 2020 U6 - https://doi.org/10.14529/jsfi200301 VL - 7 IS - 3 SP - 4 EP - 12 ER - TY - JOUR A1 - Bonnet, Luc A1 - Akian, Jean-Luc A1 - Savin, Éric A1 - Sullivan, T. J. T1 - Adaptive reconstruction of imperfectly-observed monotone functions, with applications to uncertainty quantification JF - Algorithms N2 - Motivated by the desire to numerically calculate rigorous upper and lower bounds on deviation probabilities over large classes of probability distributions, we present an adaptive algorithm for the reconstruction of increasing real-valued functions. While this problem is similar to the classical statistical problem of isotonic regression, the optimisation setting alters several characteristics of the problem and opens natural algorithmic possibilities. We present our algorithm, establish sufficient conditions for convergence of the reconstruction to the ground truth, and apply the method to synthetic test cases and a real-world example of uncertainty quantification for aerodynamic design. Y1 - 2020 U6 - https://doi.org/10.3390/a13080196 VL - 13 IS - 8 SP - 196 ER - TY - CHAP A1 - Lemke, Mathias A1 - Stein, Lewin T1 - Adjoint-Based Identification of Sound Sources for Sound Reinforcement and Source Localization T2 - Notes on Numerical Fluid Mechanics and Multidisciplinary Design N2 - The identification of sound sources is a common problem in acoustics. Different parameters are sought, among these are signal and position of the sources. We present an adjoint-based approach for sound source identification, which employs computational aeroacoustic techniques. Two different applications are presented as a proof-of-concept: optimization of a sound reinforcement setup and the localization of (moving) sound sources. Y1 - 2020 SN - 978-3-030-52429-6 U6 - https://doi.org/https://doi.org/10.1007/978-3-030-52429-6_17 VL - 145 SP - 263 EP - 278 PB - Springer, Cham ER - TY - JOUR A1 - Rössig, Ansgar A1 - Petkovic, Milena T1 - Advances in Verification of ReLU Neural Networks JF - Journal of Global Optimization N2 - We consider the problem of verifying linear properties of neural networks. Despite their success in many classification and prediction tasks, neural networks may return unexpected results for certain inputs. This is highly problematic with respect to the application of neural networks for safety-critical tasks, e.g. in autonomous driving. We provide an overview of algorithmic approaches that aim to provide formal guarantees on the behavior of neural networks. Moreover, we present new theoretical results with respect to the approximation of ReLU neural networks. On the other hand, we implement a solver for verification of ReLU neural networks which combines mixed integer programming (MIP) with specialized branching and approximation techniques. To evaluate its performance, we conduct an extensive computational study. For that we use test instances based on the ACAS Xu System and the MNIST handwritten digit data set. Our solver is publicly available and able to solve the verification problem for instances which do not have independent bounds for each input neuron. Y1 - 2020 U6 - https://doi.org/10.1007/s10898-020-00949-1 PB - Springer ER - TY - JOUR A1 - Anzt, H. A1 - Bach, F. A1 - Druskat, S. A1 - Löffler, F. A1 - Loewe, A. A1 - Renard, B. Y. A1 - Seemann, G. A1 - Struck, A. A1 - Achhammer, E. A1 - Appell, F. A1 - Bader, M. A1 - Brusch, L. A1 - Busse, C. A1 - Chourdakis, G. A1 - Dabrowski, P. W. A1 - Ebert, P. A1 - Flemisch, B. A1 - Friedl, S. A1 - Fritzsch, B. A1 - Funk, M. D. A1 - Gast, V. A1 - Goth, F. A1 - Grad, J.-N. A1 - Hermann, Sibylle A1 - Hohmann, F. A1 - Janosch, S. A1 - Kutra, D. A1 - Linxweiler, J. A1 - Muth, T. A1 - Peters-Kottig, Wolfgang A1 - Rack, F. A1 - Raters, F. H. C. A1 - Rave, S. A1 - Reina, G. A1 - Reißig, M. A1 - Ropinski, T. A1 - Schaarschmidt, J. A1 - Seibold, H. A1 - Thiele, J. P. A1 - Uekermann, B. A1 - Unger, S. A1 - Weeber, R. T1 - An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action [version 1; peer review: 1 approved, 1 approved with reservations] JF - F1000Research N2 - Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin. KW - Sustainable Software Development KW - Research Software Y1 - 2020 U6 - https://doi.org/10.12688/f1000research.23224.1 IS - 9:295 ER - TY - CHAP A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Shinano, Yuji T1 - An exact high performance solver for Steiner tree problems in graphs and related problems T2 - Modeling, Simulation and Optimization of Complex Processes HPSC 2018 Y1 - 2020 PB - Springer ER - TY - JOUR A1 - Gamrath, Gerald A1 - Berthold, Timo A1 - Salvagnin, Domenico T1 - An exploratory computational analysis of dual degeneracy in mixed-integer programming JF - EURO Journal on Computational Optimization N2 - Dual degeneracy, i.e., the presence of multiple optimal bases to a linear programming (LP) problem, heavily affects the solution process of mixed integer programming (MIP) solvers. Different optimal bases lead to different cuts being generated, different branching decisions being taken and different solutions being found by primal heuristics. Nevertheless, only a few methods have been published that either avoid or exploit dual degeneracy. The aim of the present paper is to conduct a thorough computational study on the presence of dual degeneracy for the instances of well-known public MIP instance collections. How many instances are affected by dual degeneracy? How degenerate are the affected models? How does branching affect degeneracy: Does it increase or decrease by fixing variables? Can we identify different types of degenerate MIPs? As a tool to answer these questions, we introduce a new measure for dual degeneracy: the variable–constraint ratio of the optimal face. It provides an estimate for the likelihood that a basic variable can be pivoted out of the basis. Furthermore, we study how the so-called cloud intervals—the projections of the optimal face of the LP relaxations onto the individual variables—evolve during tree search and the implications for reducing the set of branching candidates. Y1 - 2020 U6 - https://doi.org/10.1007/s13675-020-00130-z IS - 8 SP - 241 EP - 246 ER - TY - GEN A1 - Maristany de las Casas, Pedro A1 - Borndörfer, Ralf A1 - Kraus, Luitgard A1 - Sedeño-Noda, Antonio T1 - An FPTAS for Dynamic Multiobjective Shortest Path Problems N2 - We propose in this paper the Dynamic Multiobjective Shortest Problem. It features multidimensional states that can depend on several variables and not only on time; this setting is motivated by flight planning and electric vehicle routing applications. We give an exact algorithm for the FIFO case and derive from it an FPTAS, which is computationally efficient. It also features the best known complexity in the static case. T3 - ZIB-Report - 20-31 KW - Multiobjective Shortest Paths KW - Time Dependent Shortest Paths KW - Multiobjective Approximation Algorithms KW - Flight Planning Problem Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-80954 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Boeszoermnyi, Andras A1 - Wang, Zi-Fu A1 - Fischer, Patrick D. A1 - Coote, Paul A1 - Das, Krishna M. Padmanabha A1 - Malets, Yehor S. A1 - Radchenko, Dmytro S. A1 - Moroz, Yurii A1 - Scott, David A. A1 - Fackeldey, Konstantin A1 - Hoffmann, Moritz A1 - Iavniuk, Iryna A1 - Wagner, Gerhard A1 - Arthanari, Haribabu T1 - An open-source drug discovery platform enables ultra-large virtual screens JF - Nature N2 - On average, an approved drug today costs $2-3 billion and takes over ten years to develop1. In part, this is due to expensive and time-consuming wet-lab experiments, poor initial hit compounds, and the high attrition rates in the (pre-)clinical phases. Structure-based virtual screening (SBVS) has the potential to mitigate these problems. With SBVS, the quality of the hits improves with the number of compounds screened2. However, despite the fact that large compound databases exist, the ability to carry out large-scale SBVSs on computer clusters in an accessible, efficient, and flexible manner has remained elusive. Here we designed VirtualFlow, a highly automated and versatile open-source platform with perfect scaling behaviour that is able to prepare and efficiently screen ultra-large ligand libraries of compounds. VirtualFlow is able to use a variety of the most powerful docking programs. Using VirtualFlow, we have prepared the largest and freely available ready-to-dock ligand library available, with over 1.4 billion commercially available molecules. To demonstrate the power of VirtualFlow, we screened over 1 billion compounds and discovered a small molecule inhibitor (iKeap1) that engages KEAP1 with nanomolar affinity (Kd = 114 nM) and disrupts the interaction between KEAP1 and the transcription factor NRF2. We also identified a set of structurally diverse molecules that bind to KEAP1 with submicromolar affinity. This illustrates the potential of VirtualFlow to access vast regions of the chemical space and identify binders with high affinity for target proteins. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1038/s41586-020-2117-z VL - 580 SP - 663 EP - 668 PB - Springer Nature ER - TY - GEN A1 - Schwartz, Stephan T1 - An Overview of Graph Covering and Partitioning N2 - While graph covering is a fundamental and well-studied problem, this field lacks a broad and unified literature review. The holistic overview of graph covering given in this article attempts to close this gap. The focus lies on a characterization and classification of the different problems discussed in the literature. In addition, notable results and common approaches are also included. Whenever appropriate, our review extends to the corresponding partioning problems. T3 - ZIB-Report - 20-24 KW - Graph Covering KW - Graph Partitioning Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79431 SN - 1438-0064 ER - TY - JOUR A1 - Fröhler, Bernhard A1 - Elberfeld, Tim A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - De Beenhouwer, Jan A1 - Sijbers, Jan A1 - Kastner, Johann A1 - Heinzl, Christoph T1 - Analysis and comparison of algorithms for the tomographic reconstruction of curved fibres JF - Nondestructive Testing and Evaluation N2 - We present visual methods for the analysis and comparison of the results of curved fibre reconstruction algorithms, i.e., of algorithms extracting characteristics of curved fibres from X-ray computed tomography scans. In this work, we extend previous methods for the analysis and comparison of results of different fibre reconstruction algorithms or parametrisations to the analysis of curved fibres. We propose fibre dissimilarity measures for such curved fibres and apply these to compare multiple results to a specified reference. We further propose visualisation methods to analyse differences between multiple results quantitatively and qualitatively. In two case studies, we show that the presented methods provide valuable insights for advancing and parametrising fibre reconstruction algorithms, and support in improving their results in characterising curved fibres. Y1 - 2020 U6 - https://doi.org/10.1080/10589759.2020.1774583 VL - 35 IS - 3 SP - 328 EP - 341 ER - TY - GEN A1 - Sahu, Manish A1 - Szengel, Angelika A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Analyzing laparoscopic cholecystectomy with deep learning: automatic detection of surgical tools and phases T2 - 28th International Congress of the European Association for Endoscopic Surgery (EAES) N2 - Motivation: The ever-rising volume of patients, high maintenance cost of operating rooms and time consuming analysis of surgical skills are fundamental problems that hamper the practical training of the next generation of surgeons. The hospitals prefer to keep the surgeons busy in real operations over training young surgeons for obvious economic reasons. One fundamental need in surgical training is the reduction of the time needed by the senior surgeon to review the endoscopic procedures performed by the young surgeon while minimizing the subjective bias in evaluation. The unprecedented performance of deep learning ushers the new age of data-driven automatic analysis of surgical skills. Method: Deep learning is capable of efficiently analyzing thousands of hours of laparoscopic video footage to provide an objective assessment of surgical skills. However, the traditional end-to-end setting of deep learning (video in, skill assessment out) is not explainable. Our strategy is to utilize the surgical process modeling framework to divide the surgical process into understandable components. This provides the opportunity to employ deep learning for superior yet automatic detection and evaluation of several aspects of laparoscopic cholecystectomy such as surgical tool and phase detection. We employ ZIBNet for the detection of surgical tool presence. ZIBNet employs pre-processing based on tool usage imbalance, a transfer learned 50-layer residual network (ResNet-50) and temporal smoothing. To encode the temporal evolution of tool usage (over the entire video sequence) that relates to the surgical phases, Long Short Term Memory (LSTM) units are employed with long-term dependency. Dataset: We used CHOLEC 80 dataset that consists of 80 videos of laparoscopic cholecystectomy performed by 13 surgeons, divided equally for training and testing. In these videos, up to three different tools (among 7 types of tools) can be present in a frame. Results: The mean average precision of the detection of all tools is 93.5 ranging between 86.8 and 99.3, a significant improvement (p <0.01) over the previous state-of-the-art. We observed that less frequent tools like Scissors, Irrigator, Specimen Bag etc. are more related to phase transitions. The overall precision (recall) of the detection of all surgical phases is 79.6 (81.3). Conclusion: While this is not the end goal for surgical skill analysis, the development of such a technological platform is essential toward a data-driven objective understanding of surgical skills. In future, we plan to investigate surgeon-in-the-loop analysis and feedback for surgical skill analysis. Y1 - 2020 UR - https://academy.eaes.eu/eaes/2020/28th/298882/manish.sahu.analyzing.laparoscopic.cholecystectomy.with.deep.learning.html?f=listing%3D0%2Abrowseby%3D8%2Asortby%3D2 ER - TY - JOUR A1 - Duarte, Belmiro A1 - Sagnol, Guillaume T1 - Approximate and exact optimal designs for 2^k factorial experiments for generalized linear models via second order cone programming JF - Statistical Papers N2 - Model-based optimal designs of experiments (M-bODE) for nonlinear models are typically hard to compute. The literature on the computation of M-bODE for nonlinear models when the covariates are categorical variables, i.e. factorial experiments, is scarce. We propose second order cone programming (SOCP) and Mixed Integer Second Order Programming (MISOCP) formulations to find, respectively, approximate and exact A- and D-optimal designs for 2𝑘 factorial experiments for Generalized Linear Models (GLMs). First, locally optimal (approximate and exact) designs for GLMs are addressed using the formulation of Sagnol (J Stat Plan Inference 141(5):1684–1708, 2011). Next, we consider the scenario where the parameters are uncertain, and new formulations are proposed to find Bayesian optimal designs using the A- and log det D-optimality criteria. A quasi Monte-Carlo sampling procedure based on the Hammersley sequence is used for computing the expectation in the parametric region of interest. We demonstrate the application of the algorithm with the logistic, probit and complementary log–log models and consider full and fractional factorial designs. Y1 - 2020 U6 - https://doi.org/10.1007/s00362-018-01075-7 VL - 61 SP - 2737 EP - 2767 ER - TY - THES A1 - Kruber, Nico T1 - Approximate Distributed Set Reconciliation with Defined Accuracy Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:11-110-18452/22105-6 UR - https://doi.org/10.18452/21294 ER - TY - JOUR A1 - Pimentel, Pedro A1 - Szengel, Angelika A1 - Ehlke, Moritz A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Estacio, Laura A1 - Doenitz, Christian A1 - Ramm, Heiko ED - Li, Jianning ED - Egger, Jan T1 - Automated Virtual Reconstruction of Large Skull Defects using Statistical Shape Models and Generative Adversarial Networks BT - First Challenge, AutoImplant 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 8, 2020, Proceedings JF - Towards the Automatization of Cranial Implant Design in Cranioplasty N2 - We present an automated method for extrapolating missing regions in label data of the skull in an anatomically plausible manner. The ultimate goal is to design patient-speci� c cranial implants for correcting large, arbitrarily shaped defects of the skull that can, for example, result from trauma of the head. Our approach utilizes a 3D statistical shape model (SSM) of the skull and a 2D generative adversarial network (GAN) that is trained in an unsupervised fashion from samples of healthy patients alone. By � tting the SSM to given input labels containing the skull defect, a First approximation of the healthy state of the patient is obtained. The GAN is then applied to further correct and smooth the output of the SSM in an anatomically plausible manner. Finally, the defect region is extracted using morphological operations and subtraction between the extrapolated healthy state of the patient and the defective input labels. The method is trained and evaluated based on data from the MICCAI 2020 AutoImplant challenge. It produces state-of-the art results on regularly shaped cut-outs that were present in the training and testing data of the challenge. Furthermore, due to unsupervised nature of the approach, the method generalizes well to previously unseen defects of varying shapes that were only present in the hidden test dataset. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-64327-0_3 N1 - Best Paper Award VL - 12439 SP - 16 EP - 27 PB - Springer International Publishing ET - 1 ER - TY - CHAP A1 - Breuer, Thomas A1 - Bussieck, Michael A1 - Cao, Karl-Kien A1 - Fiand, Fred A1 - Gils, Hans-Christian A1 - Gleixner, Ambros A1 - Khabi, Dmitry A1 - Kempke, Nils A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Wetzel, Manuel T1 - BEAM-ME: Accelerating Linear Energy Systems Models by a Massively Parallel Interior Point Method T2 - NIC Symposium 2020 Y1 - 2020 VL - 50 SP - 345 EP - 352 ER - TY - CHAP A1 - Hanik, Martin A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - Bi-invariant Two-Sample Tests in Lie Groups for Shape Analysis T2 - Shape in Medical Imaging N2 - We propose generalizations of the T²-statistics of Hotelling and the Bhattacharayya distance for data taking values in Lie groups. A key feature of the derived measures is that they are compatible with the group structure even for manifolds that do not admit any bi-invariant metric. This property, e.g., assures analysis that does not depend on the reference shape, thus, preventing bias due to arbitrary choices thereof. Furthermore, the generalizations agree with the common definitions for the special case of flat vector spaces guaranteeing consistency. Employing a permutation test setup, we further obtain nonparametric, two-sample testing procedures that themselves are bi-invariant and consistent. We validate our method in group tests revealing significant differences in hippocampal shape between individuals with mild cognitive impairment and normal controls. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-61056-2_4 SP - 44 EP - 54 PB - Springer International Publishing CY - Cham ER - TY - CHAP A1 - Combettes, Cyrille W. A1 - Pokutta, Sebastian T1 - Boosting Frank-Wolfe by Chasing Gradients T2 - Proceedings of ICML Y1 - 2020 N1 - Additional Note: github code: https://github.com/cyrillewcombettes/boostfw N1 - URL of the Code: https://colab.research.google.com/drive/1TSOVjDFF1X2ADBo_adHLsUVrblSutRKw N1 - URL of the Slides: https://app.box.com/s/wwj247r5d456q0778p9b9y1jm6txuifb N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2020/03/16/boostFW.html N1 - https://www.youtube.com/watch?v=BfyV0C5FRbE ER - TY - JOUR A1 - Gotzes, Uwe A1 - Hoppmann-Baum, Kai T1 - Bounding the final rank during a round robin tournament with integer programming JF - Operational Research N2 - This article is mainly motivated by the urge to answer two kinds of questions regarding the Bundesliga, which is Germany’s primary football (soccer) division having the highest average stadium attendance worldwide: “At any point in the season, what is the lowest final rank a certain team can achieve?” and “At any point in the season, what is the highest final rank a certain team can achieve?”. Although we focus on the Bundesliga in particular, the integer programming formulations we introduce to answer these questions can easily be adapted to a variety of other league systems and tournaments. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/s12351-020-00546-w VL - 1866-1505 ER - TY - JOUR A1 - Koch, Thorsten A1 - Schmidt, Martin A1 - Hiller, Benjamin A1 - Pfetsch, Marc A1 - Geißler, Björn A1 - Henrion, René A1 - Joormann, Imke A1 - Martin, Alexander A1 - Morsi, Antonio A1 - Römisch, Werner A1 - Schewe, Lars A1 - Schultz, Rüdiger T1 - Capacity Evaluation for Large-Scale Gas Networks JF - German Success Stories in Industrial Mathematics Y1 - 2020 SN - 978-3-030-81454-0 U6 - https://doi.org/10.1007/978-3-030-81455-7 VL - 35 SP - 23 EP - 28 ER - TY - JOUR A1 - Brüning, Jan A1 - Hildebrandt, Thomas A1 - Heppt, Werner A1 - Schmidt, Nora A1 - Lamecker, Hans A1 - Szengel, Angelika A1 - Amiridze, Natalja A1 - Ramm, Heiko A1 - Bindernagel, Matthias A1 - Zachow, Stefan A1 - Goubergrits, Leonid T1 - Characterization of the Airflow within an Average Geometry of the Healthy Human Nasal Cavity JF - Scientific Reports N2 - This study’s objective was the generation of a standardized geometry of the healthy nasal cavity. An average geometry of the healthy nasal cavity was generated using a statistical shape model based on 25 symptom-free subjects. Airflow within the average geometry and these geometries was calculated using fluid simulations. Integral measures of the nasal resistance, wall shear stresses (WSS) and velocities were calculated as well as cross-sectional areas (CSA). Furthermore, individual WSS and static pressure distributions were mapped onto the average geometry. The average geometry featured an overall more regular shape that resulted in less resistance, reduced wall shear stresses and velocities compared to the median of the 25 geometries. Spatial distributions of WSS and pressure of average geometry agreed well compared to the average distributions of all individual geometries. The minimal CSA of the average geometry was larger than the median of all individual geometries (83.4 vs. 74.7 mm²). The airflow observed within the average geometry of the healthy nasal cavity did not equal the average airflow of the individual geometries. While differences observed for integral measures were notable, the calculated values for the average geometry lay within the distributions of the individual parameters. Spatially resolved parameters differed less prominently. Y1 - 2020 UR - https://rdcu.be/b2irD U6 - https://doi.org/10.1038/s41598-020-60755-3 VL - 3755 IS - 10 ER - TY - JOUR A1 - Chaumel, Júlia A1 - Schotte, Merlind A1 - Bizzarro, Joseph J. A1 - Zaslansky, Paul A1 - Fratzl, Peter A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage JF - Bone N2 - In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone. Y1 - 2020 U6 - https://doi.org/10.1016/j.bone.2020.115264 VL - 134 SP - 115264 ER - TY - GEN A1 - Chaumel, Júlia A1 - Schotte, Merlind A1 - Bizzarro, Joseph J. A1 - Zaslansky, Paul A1 - Fratzl, Peter A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage N2 - In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone. T3 - ZIB-Report - 20-04 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77087 SN - 1438-0064 ER - TY - JOUR A1 - Stoop, Ralph L. A1 - Straube, Arthur A1 - Johansen, Tom H. A1 - Tierno, Pietro T1 - Collective directional locking of colloidal monolayers on a periodic substrate JF - Phys. Rev. Lett. N2 - We investigate the directional locking effects that arise when a monolayer of paramagnetic colloidal particles is driven across a triangular lattice of magnetic bubbles. We use an external rotating magnetic field to generate a two-dimensional traveling wave ratchet forcing the transport of particles along a direction that intersects two crystallographic axes of the lattice. We find that, while single particles show no preferred direction, collective effects induce transversal current and directional locking at high density via a spontaneous symmetry breaking. The colloidal current may be polarized via an additional bias field that makes one transport direction energetically preferred. Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevLett.124.058002 VL - 124 SP - 058002 ER - TY - JOUR A1 - Juds, Carmen A1 - Schmidt, Johannes A1 - Weller, Michael A1 - Lange, Thorid A1 - Conrad, Tim A1 - Boerner, Hans T1 - Combining Phage Display and Next-generation Sequencing for Materials Sciences: A Case Study on Probing Polypropylene Surfaces JF - Journal of the American Chemical Society N2 - Phage display biopanning with Illumina next-generation sequencing (NGS) is applied to reveal insights into peptide-based adhesion domains for polypropylene (PP). One biopanning round followed by NGS selects robust PP-binding peptides that are not evident by Sanger sequencing. NGS provides a significant statistical base that enables motif analysis, statistics on positional residue depletion/enrichment, and data analysis to suppress false-positive sequences from amplification bias. The selected sequences are employed as water-based primers for PP?metal adhesion to condition PP surfaces and increase adhesive strength by 100\% relative to nonprimed PP. Y1 - 2020 U6 - https://doi.org/10.1021/jacs.0c03482 VL - 142 IS - 24 SP - 10624 EP - 10628 ER - TY - JOUR A1 - Sunkara, Vikram A1 - Heinz, Gitta A. A1 - Heinrich, Frederik F. A1 - Durek, Pawel A1 - Mobasheri, Ali A1 - Mashreghi, Mir-Farzin A1 - Lang, Annemarie T1 - Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint JF - bioarxiv (Accepted in Osteoarthr. Cartil.) Y1 - 2020 U6 - https://doi.org/10.1101/2020.06.13.148056 ER - TY - JOUR A1 - Christgau, Steffen A1 - Schnor, Bettina T1 - Comparing MPI Passive Target Synchronization on a Non-Cache-Coherent Shared-Memory Processor JF - Mitteilungen - Gesellschaft für Informatik e. V., Parallel-Algorithmen und Rechnerstrukturen, ISSN 0177-0454, 28. PARS-Workshop Y1 - 2020 IS - 35 SP - 121 EP - 132 ER - TY - GEN A1 - Berthold, Timo A1 - Witzig, Jakob T1 - Conflict Analysis for MINLP N2 - The generalization of MIP techniques to deal with nonlinear, potentially non-convex, constraints have been a fruitful direction of research for computational MINLP in the last decade. In this paper, we follow that path in order to extend another essential subroutine of modern MIP solvers towards the case of nonlinear optimization: the analysis of infeasible subproblems for learning additional valid constraints. To this end, we derive two different strategies, geared towards two different solution approaches. These are using local dual proofs of infeasibility for LP-based branch-and-bound and the creation of nonlinear dual proofs for NLP-based branch-and-bound, respectively. We discuss implementation details of both approaches and present an extensive computational study, showing that both techniques can significantly enhance performance when solving MINLPs to global optimality. T3 - ZIB-Report - 20-20 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78964 SN - 1438-0064 ER - TY - JOUR A1 - Witzig, Jakob A1 - Gleixner, Ambros T1 - Conflict-Driven Heuristics for Mixed Integer Programming JF - INFORMS Journal on Computing N2 - Two essential ingredients of modern mixed-integer programming (MIP) solvers are diving heuristics that simulate a partial depth-first search in a branch-and-bound search tree and conflict analysis of infeasible subproblems to learn valid constraints. So far, these techniques have mostly been studied independently: primal heuristics under the aspect of finding high-quality feasible solutions early during the solving process and conflict analysis for fathoming nodes of the search tree and improving the dual bound. Here, we combine both concepts in two different ways. First, we develop a diving heuristic that targets the generation of valid conflict constraints from the Farkas dual. We show that in the primal this is equivalent to the optimistic strategy of diving towards the best bound with respect to the objective function. Secondly, we use information derived from conflict analysis to enhance the search of a diving heuristic akin to classical coefficient diving. The computational performance of both methods is evaluated using an implementation in the source-open MIP solver SCIP. Experiments are carried out on publicly available test sets including Miplib 2010 and Cor@l. Y1 - 2020 U6 - https://doi.org/10.1287/ijoc.2020.0973 VL - 33 IS - 2 SP - 706 EP - 720 ER - TY - CHAP A1 - Witzig, Jakob A1 - Berthold, Timo T1 - Conflict-Free Learning for Mixed Integer Programming T2 - Integration of AI and OR Techniques in Constraint Programming. CPAIOR 2020 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. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-58942-4_34 IS - 12296 SP - 521 EP - 530 PB - Springer, Cham. ER - TY - JOUR A1 - Kersting, Hans A1 - Sullivan, T. J. A1 - Hennig, Philipp T1 - Convergence rates of Gaussian ODE filters JF - Statistics and Computing Y1 - 2020 U6 - https://doi.org/10.1007/s11222-020-09972-4 VL - 30 SP - 1791 EP - 1816 PB - Springer CY - Statistics and Computing ER - TY - CHAP A1 - Hartung, Marc A1 - Kaiser, Benjamin T1 - Crafted Benchmarks with Artificial Community Structure and Known Complexity T2 - Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions Y1 - 2020 UR - http://hdl.handle.net/10138/318450 SP - 89 EP - 90 ER - TY - CHAP A1 - Hartung, Marc T1 - CTSat: C++ Template Abstractions for Dynamic Interchangeable SAT Solver Features T2 - Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions Y1 - 2020 UR - http://hdl.handle.net/10138/318450 SP - 32 EP - 33 ER - TY - JOUR A1 - Klus, Stefan A1 - Nüske, Feliks A1 - Peitz, Sebastian A1 - Niemann, Jan-Hendrik A1 - Clementi, Cecilia A1 - Schütte, Christof T1 - Data-driven approximation of the Koopman generator: Model reduction, system identification, and control JF - Physica D: Nonlinear Phenomena Y1 - 2020 U6 - https://doi.org/10.1016/j.physd.2020.132416 VL - 406 ER - TY - JOUR A1 - Chen, Ying A1 - Xu, Xiuqin A1 - Koch, Thorsten T1 - Day-ahead high-resolution forecasting of natural gas demand and supply in Germany with a hybrid model JF - Applied Energy N2 - As the natural gas market is moving towards short-term planning, accurate and robust short-term forecasts of the demand and supply of natural gas is of fundamental importance for a stable energy supply, a natural gas control schedule, and transport operation on a daily basis. We propose a hybrid forecast model, Functional AutoRegressive and Convolutional Neural Network model, based on state-of-the-art statistical modeling and artificial neural networks. We conduct short-term forecasting of the hourly natural gas flows of 92 distribution nodes in the German high-pressure gas pipeline network, showing that the proposed model provides nice and stable accuracy for different types of nodes. It outperforms all the alternative models, with an improved relative accuracy up to twofold for plant nodes and up to fourfold for municipal nodes. For the border nodes with rather flat gas flows, it has an accuracy that is comparable to the best performing alternative model. KW - Natural gas flow forecasting KW - Neural network KW - Hybrid model KW - Functional autoregressive Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1016/j.apenergy.2019.114486 VL - 262 IS - 114486 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Spiegel, Christoph A1 - Zimmer, Max T1 - Deep Neural Network Training with Frank-Wolfe N2 - This paper studies the empirical efficacy and benefits of using projection-free first-order methods in the form of Conditional Gradients, a.k.a. Frank-Wolfe methods, for training Neural Networks with constrained parameters. We draw comparisons both to current state-of-the-art stochastic Gradient Descent methods as well as across different variants of stochastic Conditional Gradients. In particular, we show the general feasibility of training Neural Networks whose parameters are constrained by a convex feasible region using Frank-Wolfe algorithms and compare different stochastic variants. We then show that, by choosing an appropriate region, one can achieve performance exceeding that of unconstrained stochastic Gradient Descent and matching state-of-the-art results relying on L2-regularization. Lastly, we also demonstrate that, besides impacting performance, the particular choice of constraints can have a drastic impact on the learned representations. Y1 - 2020 ER - TY - JOUR A1 - Jäger, Klaus A1 - Tillmann, Peter A1 - Becker, Christiane T1 - Detailed illumination model for bifacial solar cells JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.383570 VL - 28 SP - 4751 ER - TY - CHAP A1 - Lindner, Niels A1 - Liebchen, Christian ED - Huisman, Dennis ED - Zaroliagis, Christos D. T1 - Determining all integer vertices of the PESP polytope by flipping arcs T2 - 20th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2020) N2 - We investigate polyhedral aspects of the Periodic Event Scheduling Problem (PESP), the mathematical basis for periodic timetabling problems in public transport. Flipping the orientation of arcs, we obtain a new class of valid inequalities, the flip inequalities, comprising both the known cycle and change-cycle inequalities. For a point of the LP relaxation, a violated flip inequality can be found in pseudo-polynomial time, and even in linear time for a spanning tree solution. Our main result is that the integer vertices of the polytope described by the flip inequalities are exactly the vertices of the PESP polytope, i.e., the convex hull of all feasible periodic slacks with corresponding modulo parameters. Moreover, we show that this flip polytope equals the PESP polytope in some special cases. On the computational side, we devise several heuristic approaches concerning the separation of cutting planes from flip inequalities. We finally present better dual bounds for the smallest and largest instance of the benchmarking library PESPlib. Y1 - 2020 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2020.5 VL - 85 SP - 5:1 EP - 5:18 PB - Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - GEN A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Determining all integer vertices of the PESP polytope by flipping arcs N2 - We investigate polyhedral aspects of the Periodic Event Scheduling Problem (PESP), the mathematical basis for periodic timetabling problems in public transport. Flipping the orientation of arcs, we obtain a new class of valid inequalities, the flip inequalities, comprising both the known cycle and change-cycle inequalities. For a point of the LP relaxation, a violated flip inequality can be found in pseudo-polynomial time, and even in linear time for a spanning tree solution. Our main result is that the integer vertices of the polytope described by the flip inequalities are exactly the vertices of the PESP polytope, i.e., the convex hull of all feasible periodic slacks with corresponding modulo parameters. Moreover, we show that this flip polytope equals the PESP polytope in some special cases. On the computational side, we devise several heuristic approaches concerning the separation of cutting planes from flip inequalities. These produce better dual bounds for the smallest and largest instance of the benchmarking library PESPlib. T3 - ZIB-Report - 20-19 KW - Periodic Event Scheduling Problem KW - Periodic Timetabling KW - Mixed Integer Programming Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78793 SN - 1438-0064 ER - TY - CHAP A1 - Rodt, Sven A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Heindel, Tobias A1 - Bounouar, Samir A1 - Kantner, Markus A1 - Koprucki, Thomas A1 - Bandelow, Uwe A1 - Burger, Sven A1 - Reitzenstein, Stephan ED - Kneissl, Michael ED - Knorr, Andreas ED - Reitzenstein, Stephan ED - Hoffmann, Axel T1 - Deterministic Quantum Devices for Optical Quantum Communication T2 - Semiconductor Nanophotonics Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-35656-9_8 VL - 194 SP - 285 EP - 359 PB - Springer CY - Cham ER - TY - JOUR A1 - Rams, Mona A1 - Conrad, Tim T1 - Dictionary Learning for transcriptomics data reveals type-specific gene modules in a multi-class setting JF - it - Information Technology Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1515/itit-2019-0048 SN - 2196-7032 VL - 62 IS - 3-4 PB - De Gruyter CY - Oldenbourg ER - TY - JOUR A1 - Weber, Marcus A1 - Weitere Autoren, ED - Reichardt, Christine T1 - DIN SPEC 2343: Übertragung von sprachbasierten Daten zwischen Künstlichen Intelligenzen - Festlegung von Parametern und Formaten JF - Beuth Verlag N2 - Dieses Dokument legt Parameter und Formate für die Übertragung sprachbasierter Daten zwischen verschiedenen KI-Ökosystemen fest. Y1 - 2020 ER - TY - JOUR A1 - Mrowiński, Paweł A1 - Schnauber, Peter A1 - Kaganskiy, Arsenty A1 - Schall, Johannes A1 - Burger, Sven A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Directional single-photon emission from deterministic quantum dot waveguide structures JF - Phys. Status Solidi RRL Y1 - 2020 U6 - https://doi.org/10.1002/pssr.202000115 VL - 14 SP - 2000115 ER - TY - JOUR A1 - Stein, Lewin A1 - Straube, Florian A1 - Weinzierl, Stefan A1 - Lemke, Mathias T1 - Directional sound source modeling using the adjoint Euler equations in a finite-difference time-domain approach JF - Acoustical Society of America N2 - An adjoint-based approach for synthesizing complex sound sources by discrete, grid-based monopoles in finite-difference time-domain simulations is presented. Previously [Stein et al., 2019a, J. Acoust. Soc. Am. 146(3), 1774–1785] demonstrated that the approach allows to consider unsteady and non-uniform ambient conditions such as wind flow and thermal gradient in contrast to standard methods of numerical sound field simulation. In this work, it is proven that not only ideal monopoles but also realistic sound sources with complex directivity characteristics can be synthesized. In detail, an oscillating circular piston and a real 2-way near-field monitor are modeled. The required number of monopoles in terms of the SPL deviation between the directivity of the original and the synthesized source is analyzed. Since the computational effort is independent of the number of monopoles used for the synthesis, also more complex sources can be reproduced by increasing the number of monopoles utilized. In contrast to classical least-square problem solvers, this does not increase the computational effort, which makes the method attractive for predicting the effect of sound reinforcement systems with highly directional sources under difficult acoustic boundary conditions. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1121/10.0002425 VL - 148 IS - 5 SP - 3075 EP - 3085 PB - The Journal of the Acoustical Society of America ER - TY - JOUR A1 - Kieninger, Stefanie A1 - Donati, Luca A1 - Keller, Bettina G. T1 - Dynamical reweighting methods for Markov models JF - Current Opinion in Structural Biology N2 - Conformational dynamics is essential to biomolecular processes. Markov State Models (MSMs) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations is still at an early stage of development. Several dynamical reweighing approaches have been proposed, which can be classified as approaches based on (i) Kramers rate theory, (ii) rescaling of the probability density flux, (iii) reweighting by formulating a likelihood function, (iv) path reweighting. We present the state-of-the-art and discuss the methodological differences of these methods, their limitations and recent applications. Y1 - 2020 U6 - https://doi.org/10.1016/j.sbi.2019.12.018 VL - 61 SP - 124 EP - 131 ER - TY - JOUR A1 - Scholtz, Gerhard A1 - Knötel, David A1 - Baum, Daniel T1 - D’Arcy W. Thompson’s Cartesian transformations: a critical evaluation JF - Zoomorphology N2 - The images of D’Arcy Wentworth Thompson’s book “On Growth and Form” got an iconic status and became influential for biometrics and other mathematical approaches to organismic form. In particular, this is true for those of the chapter on the theory of transformation, which even has an impact on art and humanities. Based on his approach, Thompson formulated far-reaching conclusions with a partly anti-Darwinian stance. Here, we use the example of Thompson’s transformation of crab carapaces to test to what degree the transformation of grids, landmarks, and shapes result in congruent images. For comparison, we applied the same series of tests to digitized carapaces of real crabs. Both approaches show similar results. Only the simple transformations show a reasonable form of congruence. In particular, the transformations to majoid spider crabs reveal a complicated transformation of grids with partly crossing lines. By contrast, the carapace of the lithodid species is relatively easily created despite the fact that it is no brachyuran, but evolved a spider crab-like shape convergently from a hermit crab ancestor. Y1 - 2020 U6 - https://doi.org/10.1007/s00435-020-00494-1 VL - 139 SP - 293 EP - 308 ER - TY - JOUR A1 - Chewle, Surahit A1 - Emmerling, Franziska A1 - Weber, Marcus T1 - Effect of choice of solvent on crystallization pathway of Paracetamol: An experimental and theoretical case study JF - Crystals N2 - The choice of solvents influences crystalline solid formed during the crystallization of active pharmaceutical ingredients (API). The underlying effects are not always well understood because of the complexity of the systems. Theoretical models are often insufficient to describe this phenomenon. In this study, the crystallization behavior of the model drug paracetamol in different solvents was studied based on experimental and molecular dynamics data. The crystallization process was followed in situ using time-resolved Raman spectroscopy. Molecular dynamics with simulated annealing algorithm was used for an atomistic understanding of the underlying processes. The experimental and theoretical data indicate that paracetamol molecules adopt a particular geometry in a given solvent predefining the crystallization of certain polymorphs. Y1 - 2020 U6 - https://doi.org/10.3390/cryst10121107 VL - 10 IS - 12 SP - 1107 ER - TY - JOUR A1 - Kramer, Tobias A1 - Rodríguez, Mirta T1 - Effect of disorder and polarization sequences on two-dimensional spectra of light harvesting complexes JF - Photosynthesis Research N2 - Two-dimensional electronic spectra (2DES) provide unique ways to track the energy transfer dynamics in light-harvesting complexes. The interpretation of the peaks and structures found in experimentally recorded 2DES is often not straightforward, since several processes are imaged simultaneously. The choice of specific pulse polarization sequences helps to disentangle the sometimes convoluted spectra, but brings along other disturbances. We show by detailed theoretical calculations how 2DES of the Fenna-Matthews-Olson complex are affected by rotational and conformational disorder of the chromophores. Y1 - 2020 U6 - https://doi.org/10.1007/s11120-019-00699-6 VL - 144 SP - 147 EP - 154 ER - TY - CHAP A1 - Yokoyama, Ryohei A1 - Takeuchi, Kotaro A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Effect of Model Reduction by Time Aggregation in Multiobjective Optimal Design of Energy Supply Systems by a Hierarchical MILP Method T2 - Conference N2 - The mixed-integer linear programming (MILP) method has been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems effi- ciently. As one of the strategies to enhance the computation efficiency furthermore, a method of reducing model by time aggregation has been proposed to search design candidates accurately and efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method and model reduction by time aggregation are applied to the multiobjective optimal design. In applying the model reduc- tion, the methods of clustering periods by the order of time series, based on an operational strategy, and by the k-medoids method are applied. As a case study, the multiobjective optimal design of a gas turbine cogeneration system with a practical configuration is investigated by adopting the annual total cost and pri- mary energy consumption as the objective functions to be minimized simultaneously, and the clustering methods are compared with one another in terms of the computation efficiency. It turns out that the model reduction by any clustering method is effective to enhance the computation efficiency when importance is given to minimizing the first objective function. It also turns out that the model reduction only by the k- medoids method is effective very limitedly when importance is given to minimizing the second objective function. Y1 - 2020 SP - 627 EP - 639 ER - TY - JOUR A1 - Farchmin, Nando A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Wurm, Matthias A1 - Bodermann, Bernd A1 - Bär, Markus A1 - Heidenreich, Sebastian T1 - Efficient Bayesian inversion for shape reconstruction of lithography masks JF - J. Micro/Nanolith. MEMS MOEMS Y1 - 2020 U6 - https://doi.org/10.1117/1.JMM.19.2.024001 VL - 19 SP - 024001 ER - TY - GEN A1 - Becker, Kai-Helge A1 - Hiller, Benjamin T1 - Efficient Enumeration of Acyclic Graph Orientations with Sources or Sinks Revisited N2 - In a recent paper, Conte et al. [CGMR2017] presented an algorithm for enumerating all acyclic orientations of a graph G=(V,E) with a single source (and related orientations) with delay O(|V||E|). In this paper we revisit the problem by going back to an early paper by de Fraysseix et al. [FMR1995], who proposed an algorithm for enumerating all bipolar orientations of a graph based on a recursion formula. We first formalize de Fraysseix et al.'s algorithm for bipolar orientations and determine that its delay is also O(|V||E|). We then apply their recursion formula to the case of Conte et al.'s enumeration problem and show that this yields a more efficient enumeration algorithm with delay O(\sqrt(|V|)|E|). Finally, a way to further streamline the algorithm that leads to a particularly simple implementation is suggested. T3 - ZIB-Report - 20-05 KW - acyclic orientations KW - enumeration algorithm KW - multiple sources and sinks KW - bipolar orientations Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77684 SN - 1438-0064 ER - TY - CHAP A1 - Sahu, Manish A1 - Strömsdörfer, Ronja A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Endo-Sim2Real: Consistency learning-based domain adaptation for instrument segmentation T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI), Part III N2 - Surgical tool segmentation in endoscopic videos is an important component of computer assisted interventions systems. Recent success of image-based solutions using fully-supervised deep learning approaches can be attributed to the collection of big labeled datasets. However, the annotation of a big dataset of real videos can be prohibitively expensive and time consuming. Computer simulations could alleviate the manual labeling problem, however, models trained on simulated data do not generalize to real data. This work proposes a consistency-based framework for joint learning of simulated and real (unlabeled) endoscopic data to bridge this performance generalization issue. Empirical results on two data sets (15 videos of the Cholec80 and EndoVis'15 dataset) highlight the effectiveness of the proposed Endo-Sim2Real method for instrument segmentation. We compare the segmentation of the proposed approach with state-of-the-art solutions and show that our method improves segmentation both in terms of quality and quantity. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/978-3-030-59716-0_75 VL - 12263 PB - Springer Nature ER - TY - GEN A1 - Hendel, Gregor A1 - Anderson, Daniel A1 - Le Bodic, Pierre A1 - Pfetsch, Marc T1 - Estimating the Size of Branch-And-Bound Trees N2 - This paper investigates the estimation of the size of Branch-and-Bound (B&B) trees for solving mixed-integer programs. We first prove that the size of the B&B tree cannot be approximated within a factor of~2 for general binary programs, unless P equals NP. Second, we review measures of the progress of the B&B search, such as the gap, and propose a new measure, which we call leaf frequency. We study two simple ways to transform these progress measures into B&B tree size estimates, either as a direct projection, or via double-exponential smoothing, a standard time-series forecasting technique. We then combine different progress measures and their trends into nontrivial estimates using Machine Learning techniques, which yields more precise estimates than any individual measure. The best method we have identified uses all individual measures as features of a random forest model. In a large computational study, we train and validate all methods on the publicly available MIPLIB and Coral general purpose benchmark sets. On average, the best method estimates B&B tree sizes within a factor of 3 on the set of unseen test instances even during the early stage of the search, and improves in accuracy as the search progresses. It also achieves a factor 2 over the entire search on each out of six additional sets of homogeneous instances we have tested. All techniques are available in version 7 of the branch-and-cut framework SCIP. T3 - ZIB-Report - 20-02 KW - mixed integer programming KW - machine learning KW - branch and bound KW - forecasting Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78144 SN - 1438-0064 ER - TY - JOUR A1 - Helfmann, Luzie A1 - Ribera Borrell, Enric A1 - Schütte, Christof A1 - Koltai, Peter T1 - Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics JF - Journal of Nonlinear Science Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/s00332-020-09652-7 VL - 30 SP - 3321 EP - 3366 ER - TY - JOUR A1 - Pflüger, Mika A1 - Kline, R. Joseph A1 - Fernández Herrero, Analia A1 - Hammerschmidt, Martin A1 - Soltwisch, Victor A1 - Krumrey, Michael T1 - Extracting dimensional parameters of gratings produced with self-aligned multiple patterning using grazing-incidence small-angle x-ray scattering JF - J. Micro Nanolithogr. MEMS MOEMS Y1 - 2020 U6 - https://doi.org/10.1117/1.JMM.19.1.014001 VL - 19 SP - 014001 ER - TY - GEN A1 - Pflüger, Mika A1 - Kline, R Joseph A1 - Fernández Herrero, Analía A1 - Hammerschmidt, Martin A1 - Soltwisch, Victor A1 - Krumrey, Michael T1 - Extracting dimensional parameters of gratings produced with self-aligned multiple patterning using grazing-incidence small-angle x-ray scattering [Source Code] Y1 - 2020 U6 - https://doi.org/10.24433/CO.0953516.v2 ER - TY - JOUR A1 - Pakhomov, Anton A1 - Löchner, Franz A1 - Zschiedrich, Lin A1 - Saravi, Sina A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Pertsch, Thomas A1 - Setzpfand, Frank T1 - Far-field polarization signatures of surface optical nonlinearity in noncentrosymmetric semiconductors JF - Sci. Rep. Y1 - 2020 U6 - https://doi.org/10.1038/s41598-020-67186-0 VL - 10 SP - 10545 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Döpking, Sandra A1 - Burger, Sven A1 - Matera, Sebastian T1 - Field Heterogeneities and Their Impact on Photocatalysis: Combining Optical and Kinetic Monte Carlo Simulations on the Nanoscale JF - J. Phys. Chem. C Y1 - 2020 U6 - https://doi.org/10.1021/acs.jpcc.9b11469 VL - 124 SP - 3177 ER - TY - JOUR A1 - Höfling, Felix A1 - Dietrich, Siegfried T1 - Finite-size corrections for the static structure factor of a liquid slab with open boundaries JF - The Journal of Chemical Physics N2 - The presence of a confining boundary can modify the local structure of a liquid markedly. In addition, small samples of finite size are known to exhibit systematic deviations of thermodynamic quantities relative to their bulk values. Here, we consider the static structure factor of a liquid sample in slab geometry with open boundaries at the surfaces, which can be thought of as virtually cutting out the sample from a macroscopically large, homogeneous fluid. This situation is a relevant limit for the interpretation of grazing-incidence diffraction experiments at liquid interfaces and films. We derive an exact, closed expression for the slab structure factor, with the bulk structure factor as the only input. This shows that such free boundary conditions cause significant differences between the two structure factors, in particular, at small wavenumbers. An asymptotic analysis of this result yields the scaling exponent and an accurate, useful approximation of these finite-size corrections. Furthermore, the open boundaries permit the interpretation of the slab as an open system, supporting particle exchange with a reservoir. We relate the slab structure factor to the particle number fluctuations and discuss conditions under which the subvolume of the slab represents a grand canonical ensemble with chemical potential μ and temperature T. Thus, the open slab serves as a test-bed for the small-system thermodynamics in a μT reservoir. We provide a microscopically justified and exact result for the size dependence of the isothermal compressibility. Our findings are corroborated by simulation data for Lennard-Jones liquids at two representative temperatures. Y1 - 2020 U6 - https://doi.org/10.1063/5.0017923 VL - 153 SP - 054119 ER - TY - CHAP A1 - Gleixner, Ambros A1 - Kempke, Nils-Christian A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Uslu, Svenja T1 - First Experiments with Structure-Aware Presolving for a Parallel Interior-Point Method T2 - Operations Research Proceedings 2019 N2 - In linear optimization, matrix structure can often be exploited algorithmically. However, beneficial presolving reductions sometimes destroy the special structure of a given problem. In this article, we discuss structure-aware implementations of presolving as part of a parallel interior-point method to solve linear programs with block-diagonal structure, including both linking variables and linking constraints. While presolving reductions are often mathematically simple, their implementation in a high-performance computing environment is a complex endeavor. We report results on impact, performance, and scalability of the resulting presolving routines on real-world energy system models with up to 700 million nonzero entries in the constraint matrix. KW - block structure KW - energy system models KW - interior-point method KW - high performance computing KW - linear programming KW - parallelization KW - presolving KW - preprocessing Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-48439-2_13 SP - 105 EP - 111 PB - Springer International Publishing ET - 1 ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - Flat optics in high numerical aperture broadband imaging systems JF - J. Opt. Y1 - 2020 U6 - https://doi.org/10.1088/2040-8986/ab8ea2 VL - 22 SP - 065607 ER - TY - GEN A1 - Hoppmann-Baum, Kai A1 - Hennings, Felix A1 - Zittel, Janina A1 - Gotzes, Uwe A1 - Spreckelsen, Eva-Maria A1 - Spreckelsen, Klaus A1 - Koch, Thorsten T1 - From Natural Gas towards Hydrogen - A Feasibility Study on Current Transport Network Infrastructure and its Technical Control N2 - This study examines the usability of a real-world, large-scale natural gas transport infrastructure for hydrogen transport. We investigate whether a converted network can transport the amounts of hydrogen necessary to satisfy current energy demands. After introducing an optimization model for the robust transient control of hydrogen networks, we conduct computational experiments based on real-world demand scenarios. Using a representative network, we demonstrate that replacing each turbo compressor unit by four parallel hydrogen compressors, each of them comprising multiple serial compression stages, and imposing stricter rules regarding the balancing of in- and outflow suffices to realize transport in a majority of scenarios. However, due to the reduced linepack there is an increased need for technical and non-technical measures leading to a more dynamic network control. Furthermore, the amount of energy needed for compression increases by 364% on average. T3 - ZIB-Report - 20-27 KW - Hydrogen Transport KW - Hydrogen Infrastructure KW - Network Flows KW - Mixed Integer Programming KW - Energiewende Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-79901 SN - 1438-0064 ER - TY - GEN A1 - Musiał, Anna A1 - Żołnacz, Kinga A1 - Srocka, Nicole A1 - Kravets, Oleh A1 - Große, Jan A1 - Olszewski, Jacek A1 - Poturaj, Krzysztof A1 - Wojcik, Grzegorz A1 - Mergo, Paweł A1 - Dybka, Kamil A1 - Dyrkacz, Mariusz A1 - Dlubek, Michal A1 - Lauritsen, Kristian A1 - Bülter, Andreas A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Rodt, Sven A1 - Urbanczyk, Wacław A1 - Sek, Grzegorz A1 - Reitzenstein, Stephan T1 - Front Cover: Plug&Play Fiber‐Coupled 73 kHz Single‐Photon Source Operating in the Telecom O‐Band (Adv. Quantum Technol. 6/2020) T2 - Adv. Quantum Technol. Y1 - 2020 U6 - https://doi.org/10.1002/qute.202070061 VL - 3 SP - 2070061 ER - TY - CHAP A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Gas production for 14 species on comet 67P/Churyumov-Gerasimenko from 2014-2016 T2 - Europlanet Science Congress N2 - During a two year period between 2014 and 2016 the coma of comet 67P/Churyumov-Gerasimenko (67P/C-G) has been probed by the Rosetta spacecraft. Density data for 14 gas species was recorded with the COmet Pressure Sensor (COPS) and the Double Focusing Mass Spectrometer (DFMS) being two sensors of the ROSINA instrument. The combination with an inverse gas model yields emission rates on each of 3996 surface elements of a surface shape for the cometary nucleus. The temporal evolution of gas production, of relative abundances, and peak productions weeks after perihelion are investigated. Solar irradiation and gas production are in a complex relation revealing features differing for gas species, for mission time, and for the hemispheres of the comet. This characterization of gas composition allows one to correlate 67P/C-G to other solar and interstellar comets, their formation conditions and nucleus properties, see [Bodewits D., et al., 2020 Nature Astronomy]. Y1 - 2020 U6 - https://doi.org/10.5194/epsc2020-319 VL - 14 SP - EPSC2020-319 PB - Europlanet Science Congress ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - General design formalism for highly efficient flat optics for broadband applications JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.386573 VL - 28 SP - 6452 ER - TY - BOOK A1 - Reuter, Bernhard T1 - Generalisierte Markov-Modellierung N2 - Markov State Models (MSM) sind der Goldstandard zur Modellierung biomolekularer Dynamik, da sie die Identifizierung und Analyse metastabiler Zustände ermöglichen. Die robuste Perron-Cluster-Cluster-Analyse (PCCA+) ist ein verbreiteter Spectral-Clustering-Algorithmus, der für das Clustering hochdimensionaler MSM verwendet wird. Da die PCCA+ auf reversible Prozesse beschränkt ist, wird sie zur Generalisierten PCCA+ (G-PCCA) verallgemeinert, die geeignet ist, nichtreversible Prozesse aufzuklären. Bernhard Reuter untersucht hier mittels G-PCCA die nichtthermischen Auswirkungen von Mikrowellen auf die Proteindynamik. Dazu führt er molekulardynamische Nichtgleichgewichtssimulationen des Amyloid-β-(1–40)-Peptids durch und modelliert diese. Y1 - 2020 SN - 978-3-658-29711-4 U6 - https://doi.org/10.1007/978-3-658-29712-1 PB - Springer Spektrum, Wiesbaden ER - TY - GEN A1 - Anderson, Lovis A1 - Turner, Mark A1 - Koch, Thorsten T1 - Generative deep learning for decision making in gas networks N2 - A decision support system relies on frequent re-solving of similar problem instances. While the general structure remains the same in corresponding applications, the input parameters are updated on a regular basis. We propose a generative neural network design for learning integer decision variables of mixed-integer linear programming (MILP) formulations of these problems. We utilise a deep neural network discriminator and a MILP solver as our oracle to train our generative neural network. In this article, we present the results of our design applied to the transient gas optimisation problem. With the trained network we produce a feasible solution in 2.5s, use it as a warm-start solution, and thereby decrease global optimal solution solve time by 60.5%. T3 - ZIB-Report - 20-38 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81103 SN - 1438-0064 ER - TY - JOUR A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - Sullivan, T. J. A1 - von Tycowicz, Christoph T1 - Geodesic Analysis in Kendall's Shape Space with Epidemiological Applications JF - Journal of Mathematical Imaging and Vision N2 - We analytically determine Jacobi fields and parallel transports and compute geodesic regression in Kendall’s shape space. Using the derived expressions, we can fully leverage the geometry via Riemannian optimization and thereby reduce the computational expense by several orders of magnitude over common, nonlinear constrained approaches. The methodology is demonstrated by performing a longitudinal statistical analysis of epidemiological shape data. As an example application we have chosen 3D shapes of knee bones, reconstructed from image data of the Osteoarthritis Initiative (OAI). Comparing subject groups with incident and developing osteoarthritis versus normal controls, we find clear differences in the temporal development of femur shapes. This paves the way for early prediction of incident knee osteoarthritis, using geometry data alone. Y1 - 2020 U6 - https://doi.org/10.1007/s10851-020-00945-w VL - 62 IS - 4 SP - 549 EP - 559 ER - TY - JOUR A1 - Melnyk, Kateryna A1 - Montavon, Grègoire A1 - Klus, Stefan A1 - Conrad, Tim T1 - Graph Kernel Koopman Embedding for Human Microbiome Analysis JF - Applied Network Science N2 - More and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, or some cancer types. Thanks to modern high-throughput omics technologies, it becomes possible to directly analyze human microbiome and its influence on the health status. Microbial communities are monitored over long periods of time and the associations between their members are explored. These relationships can be described by a time-evolving graph. In order to understand responses of the microbial community members to a distinct range of perturbations such as antibiotics exposure or diseases and general dynamical properties, the time-evolving graph of the human microbial communities has to be analyzed. This becomes especially challenging due to dozens of complex interactions among microbes and metastable dynamics. The key to solving this problem is the representation of the time-evolving graphs as fixed-length feature vectors preserving the original dynamics. We propose a method for learning the embedding of the time-evolving graph that is based on the spectral analysis of transfer operators and graph kernels. We demonstrate that our method can capture temporary changes in the time-evolving graph on both synthetic data and real-world data. Our experiments demonstrate the efficacy of the method. Furthermore, we show that our method can be applied to human microbiome data to study dynamic processes. Y1 - 2020 U6 - https://doi.org/10.1007/s41109-020-00339-2 VL - 5 IS - 96 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Handling Compute-Node Failures in FLESnet JF - CBM Progress Report 2019 Y1 - 2020 SN - 978-3-9815227-8-5 U6 - https://doi.org/10.15120/GSI-2020-00904 SP - 167 EP - 168 ER - TY - JOUR A1 - Feis, Joshua A1 - Beutel, Dominik A1 - Köpfler, Julian A1 - Santiago, Xavier Garcia A1 - Rockstuhl, Carsten A1 - Wegener, Martin A1 - Fernandez-Corbaton, Ivan T1 - Helicity-Preserving Optical Cavity Modes for Enhanced Sensing of Chiral Molecules JF - Phys. Rev. Lett. Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevLett.124.033201 VL - 124 SP - 033201 ER - TY - JOUR A1 - Lang, Annemarie A1 - Helfmeier, Sarah A1 - Stefanowski, Jonathan A1 - Kuppe, Aditi A1 - Sunkara, Vikram A1 - Pfeiffenberger, Moritz A1 - Wolter, Angelique A1 - Damerau, Alexandra A1 - Hemmati-Sadeghi, Shabnam A1 - Ringe, Jochen A1 - Haag, Rainer A1 - Hauser, Anja E. A1 - Löhning, Max A1 - Perka, Carsten A1 - Duda, Georg A1 - Hoff, Paula A1 - Schmidt-Bleek, Katharina A1 - Gaber, Timo A1 - Buttgereit, Frank T1 - HIF-stabilization prevents delayed fracture healing JF - bioarxiv Y1 - 2020 U6 - https://doi.org/10.1101/2020.07.02.182832 ER - TY - JOUR A1 - Khorashad, Larousse Khosravi A1 - Besteiro, Lucas V. A1 - Correa-Duarte, Miguel A1 - Burger, Sven A1 - Wang, Zhiming M. A1 - Govorov, Alexander O. T1 - Hot electrons generated in chiral plasmonic nanocrystals as a mechanism for surface photochemistry and chiral growth JF - J. Am. Chem. Soc. Y1 - 2020 U6 - https://doi.org/10.1021/jacs.9b11124 VL - 142 SP - 4193 ER - TY - JOUR A1 - Ray, Sourav A1 - Sunkara, Vikram A1 - Schütte, Christof A1 - Weber, Marcus T1 - How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs JF - Molecular Simulation N2 - Molecular simulations of ligand–receptor interactions are a computational challenge, especially when their association- (‘on’-rate) and dissociation- (‘off’-rate) mechanisms are working on vastly differing timescales. One way of tackling this multiscale problem is to compute the free-energy landscapes, where molecular dynamics (MD) trajectories are used to only produce certain statistical ensembles. The approach allows for deriving the transition rates between energy states as a function of the height of the activation-energy barriers. In this article, we derive the association rates of the opioids fentanyl and N-(3-fluoro-1-phenethylpiperidin-4-yl)-N-phenyl propionamide (NFEPP) in a μ-opioid receptor by combining the free-energy landscape approach with the square-root-approximation method (SQRA), which is a particularly robust version of Markov modelling. The novelty of this work is that we derive the association rates as a function of the pH level using only an ensemble of MD simulations. We also verify our MD-derived insights by reproducing the in vitro study performed by the Stein Lab. Y1 - 2020 U6 - https://doi.org/10.1080/08927022.2020.1839660 VL - 46 IS - 18 SP - 1443 EP - 1452 PB - Taylor and Francis ER - TY - GEN A1 - Ray, Sourav A1 - Sunkara, Vikram A1 - Schütte, Christof A1 - Weber, Marcus T1 - How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs N2 - Molecular simulations of ligand-receptor interactions are a computational challenge, especially when their association- (``on''-rate) and dissociation- (``off''-rate) mechanisms are working on vastly differing timescales. In addition, the timescale of the simulations themselves is, in practice, orders of magnitudes smaller than that of the mechanisms; which further adds to the complexity of observing these mechanisms, and of drawing meaningful and significant biological insights from the simulation. One way of tackling this multiscale problem is to compute the free-energy landscapes, where molecular dynamics (MD) trajectories are used to only produce certain statistical ensembles. The approach allows for deriving the transition rates between energy states as a function of the height of the activation-energy barriers. In this article, we derive the association rates of the opioids fentanyl and N-(3-fluoro-1-phenethylpiperidin-4-yl)- N-phenyl propionamide (NFEPP) in a $\mu$-opioid receptor by combining the free-energy landscape approach with the square-root-approximation method (SQRA), which is a particularly robust version of Markov modelling. The novelty of this work is that we derive the association rates as a function of the pH level using only an ensemble of MD simulations. We also verify our MD-derived insights by reproducing the in vitro study performed by the Stein Lab, who investigated the influence of pH on the inhibitory constant of fentanyl and NFEPP (Spahn et al. 2017). MD simulations are far more accessible and cost-effective than in vitro and in vivo studies. Especially in the context of the current opioid crisis, MD simulations can aid in unravelling molecular functionality and assist in clinical decision-making; the approaches presented in this paper are a pertinent step forward in this direction. T3 - ZIB-Report - 20-18 KW - Opioid, Ligand-Receptor Interaction, Binding Kinetics, Molecular Dynamics, Metadynamics, SQRA Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78437 SN - 1438-0064 ER - TY - JOUR A1 - Lindner, Niels T1 - Hypersurfaces with defect JF - Journal of Algebra N2 - A projective hypersurface X⊆P^n has defect if h^i(X) ≠ h^i(P^n) for some i∈{n,…,2n−2} in a suitable cohomology theory. This occurs for example when X⊆P^4 is not Q-factorial. We show that hypersurfaces with defect tend to be very singular: In characteristic 0, we present a lower bound on the Tjurina number, where X is allowed to have arbitrary isolated singularities. For X with mild singularities, we prove a similar result in positive characteristic. As an application, we obtain an estimate on the asymptotic density of hypersurfaces without defect over a finite field. Y1 - 2020 U6 - https://doi.org/10.1016/j.jalgebra.2020.02.022 VL - 555 SP - 1 EP - 35 ER - TY - JOUR A1 - Schotte, Merlind A1 - Chaumel, Júlia A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae JF - MethodsX N2 - A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach. Y1 - 2020 U6 - https://doi.org/10.1016/j.mex.2020.100905 VL - 7 SP - 100905 ER - TY - GEN A1 - Schotte, Merlind A1 - Chaumel, Júlia A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae N2 - A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach. T3 - ZIB-Report - 20-12 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78237 SN - 1438-0064 ER - TY - THES A1 - Baumann, Felix T1 - Impact of Contact Surfaces on the Death Estimation N2 - The determination of time of death is one of the central tasks in forensic medicine. A standard method of time of death estimation elies on matching temperature measurements of the corpse with a post-mortem cooling model. In addition to widely used empirical post-mortem models, modelling based on a precise mathematical simulation of the cooling process have been gaining popularity. The simulation based cooling models and the resulting time of death estimates dependon a large variety of parameters. These include hermal properties for different body tissue types, environmental conditions such as temperature and air flow, and the presence of clothing and coverings. In this thesis we focus on a specific arameter - the contact between corpse and underground - and investigate its influence on the time of death estimation. Resulting we aim to answer the question whether it is necessary to consider contact mechanics in the underlying mathematical cooling model. KW - time of death estimation KW - contact mechanics KW - heat equation KW - inverse problems Y1 - 2020 ER - TY - THES A1 - Löbel, Fabian T1 - Implementing the Network Simplex for Hypergraphs N2 - The well-known network simplex algorithm is a powerful tool to solve flow problems on graphs. Based on a recent dissertation by Isabel Beckenbach, we develop the necessary theory to extend the network simplex to capacitated flow problems on hypergraphs and implement this new variant. We then attempt to solve instances arising from real-life vehicle rotation planning problems. Y1 - 2020 ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Implications, conflicts, and reductions for Steiner trees T3 - ZIB-Report - 20-28 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-80039 SN - 1438-0064 ER -