TY - THES A1 - Mexi, Gioni T1 - New Ideas for the Feasibility Pump: Using Multiple Reference Vectors Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-83724 ER - TY - THES A1 - Kunt, Tim T1 - The n-Queens Problem in Higher Dimensions N2 - How many mutually non-attacking queens can be placed on a d-dimensional chessboard of size n? The n-queens problem in higher dimensions is a generalization of the well-known n-queens problem. We provide a comprehensive overview of theoretical results, bounds, solution methods, and the interconnectivity of the problem within topics of discrete optimization and combinatorics. We present an integer programming formulation of the n-queens problem in higher dimensions and several strengthenings through additional valid inequalities. Compared to recent benchmarks, we achieve a speedup in computational time between 15-70x over all instances of the integer programs. Our computational results prove optimality of certificates for several large instances. Breaking additional, previously unsolved instances with the proposed methods is likely possible. On the primal side, we further discuss heuristic approaches to constructing solutions that turn out to be optimal when compared to the IP. We conclude with preliminary results on the number and density of the solutions. T3 - ZIB-Report - 24-05 KW - Integer Programming KW - Maximum Independent Set KW - n-Queens Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-96468 ER - TY - JOUR A1 - Tawfik, Christine A1 - Gendron, Bernard A1 - Limbourg, Sabine T1 - An iterative two-stage heuristic algorithm for a bilevel service network design and pricing model JF - European Journal of Operational Research N2 - Building upon earlier research, we revisit a bilevel formulation of service design and pricing for freight networks, with the aim of investigating its algorithmic aspects. The model adds substantial computational challenges to the existing literature, as it deals with general integer network design variables. An iterative heuristic algorithm is introduced, based on the concepts of inverse optimization and neighbourhood search. The procedure alternates between two versions of restricted formulations of the model while inducing promising changes into the service assignments. The approach has proven a high performance for all of the considered real-world instances. Its efficiency rests on its ability to deliver results within a close proximity to those obtained by the exact solver in terms of quality, yet within a significantly smaller amount of time, and to land feasible solutions for the large-sized instances that could not be previously solved. In line with the sustainable transport goals, a deeper observation of the transport management side highlights the strategy of the algorithm favouring freight consolidation and achieving high load factors. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.ejor.2021.07.052 PB - Elsevier CY - European Journal of Operational Research ER - TY - THES A1 - Rössig, Ansgar T1 - Verification of Neural Networks KW - Neural Network Verification Y1 - 2019 ER - TY - CHAP A1 - Péron, Martin A1 - Bartlett, Peter L. A1 - Becker, Kai-Helge A1 - Helmstedt, Kate A1 - Chadès, Iadine T1 - Two Approximate Dynamic Programming Algorithms for Managing Complete SIS Networks T2 - COMPASS '18 Proceedings of the 1st ACM SIGCAS Conference on Computing and Sustainable Societies N2 - Inspired by the problem of best managing the invasive mosquito Aedes albopictus across the 17 Torres Straits islands of Australia, we aim at solving a Markov decision process on large Susceptible-Infected-Susceptible (SIS) networks that are highly connected. While dynamic programming approaches can solve sequential decision-making problems on sparsely connected networks, these approaches are intractable for highly connected networks. Inspired by our case study, we focus on problems where the probability of nodes changing state is low and propose two approximate dynamic programming approaches. The first approach is a modified version of value iteration where only those future states that are similar to the current state are accounted for. The second approach models the state space as continuous instead of binary, with an on-line algorithm that takes advantage of Bellman's adapted equation. We evaluate the resulting policies through simulations and provide a priority order to manage the 17 infested Torres Strait islands. Both algorithms show promise, with the continuous state approach being able to scale up to high dimensionality (50 nodes). This work provides a successful example of how AI algorithms can be designed to tackle challenging computational sustainability problems. Y1 - 2018 U6 - https://doi.org/10.1145/3209811.3209814 PB - ACM ER - TY - CHAP A1 - Diakonikolas, Jelena A1 - Carderera, Alejandro A1 - Pokutta, Sebastian T1 - Breaking the Curse of Dimensionality (Locally) to Accelerate Conditional Gradients T2 - OPTML Workshop Paper Y1 - 2019 N1 - URL of the Code: https://colab.research.google.com/drive/1ejjfCan7xnEhWWJXCIzb03CwQRG9iW_O N1 - URL of the PDF: https://opt-ml.org/papers/2019/paper_26.pdf N1 - URL of the Poster: https://app.box.com/s/d7p038u7df422q4jsccbmj15mngqv2ws N1 - URL of the Slides: https://app.box.com/s/gphkhapso7d1vrfnzqykkb3vx0agxh8w N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/07/04/LaCG-abstract.html ER - TY - CHAP A1 - Combettes, Cyrille W. A1 - Pokutta, Sebastian T1 - Blended Matching Pursuit T2 - Proceedings of NeurIPS Y1 - 2019 N1 - URL of the Code: https://colab.research.google.com/drive/17XYIxnCcJjKswba9mAaXFWnNGVZdsaXQ N1 - URL of the PDF: https://papers.nips.cc/paper/8478-blended-matching-pursuit N1 - URL of the Poster: https://app.box.com/s/j6lbh49udjd45krhxcypufxwdofw6br8 N1 - URL of the Slides: https://app.box.com/s/8lfktq6h3dqp9t2gqydu2tp8h2uxgz7m N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/05/27/bmp-abstract.html ER - TY - CHAP A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - On the Unreasonable Effectiveness of the Greedy Algorithm: Greedy Adapts to Sharpness T2 - OPTML Workshop Paper Y1 - 2019 N1 - URL of the PDF: https://opt-ml.org/papers/2019/paper_16.pdf N1 - URL of the Poster: https://app.box.com/s/24vbh1s2vib11upqyepzen3lzdl13skr ER - TY - 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 - GEN T1 - Annual Report 2014 T3 - Jahresbericht - 2014 KW - Jahresbericht Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55050 SN - 0934-5892 VL - 2014 ER - TY - CHAP A1 - Baumann, Wolfgang A1 - Laubender, Guido A1 - Läuter, Matthias A1 - Reinefeld, Alexander A1 - Schimmel, Christian A1 - Steinke, Thomas A1 - Tuma, Christian A1 - Wollny, Stefan ED - Vetter, Jeffrey S. T1 - HLRN-III at Zuse Institute Berlin T2 - Contemporary High Performance Computing: From Petascale toward Exascale, Volume Two Y1 - 2015 UR - http://www.crcpress.com/product/isbn/9781498700627 SN - 9781498700627 SP - 81 EP - 114 PB - Chapman and Hall/CRC ER - TY - GEN A1 - Taentzer, Gabriele A1 - Golas, Ulrike T1 - Local Confluence Analysis for Amalgamated Graph Transformation: Long Version N2 - Amalgamated graph transformation allows to define schemes of rules coinciding in common core activities and differing over additional parallel independent activities. Consequently, a rule scheme is specified by a kernel rule and a set of extending multi-rules forming an interaction scheme. Amalgamated transformations have been increasingly used in various modeling contexts. Critical Pair Analysis (CPA) can be used to show local confluence of graph transformation systems. It is an open challenge to lift the CPA to amalgamated graph transformation systems, especially since infinite many pairs of amalgamated rules occur in general. As a first step towards an efficient local confluence analysis of amalgamated graph transformation systems, we show that the analysis of a finite set of critical pairs suffices to prove local confluence. T3 - ZIB-Report - 15-29 KW - amalgamated graph transformation KW - parallel independence KW - critical pair analysis Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54943 SN - 1438-0064 ER - TY - GEN A1 - Schäfer, Patrick T1 - Bag-Of-SFA-Symbols in Vector Space (BOSS VS) N2 - Time series classification mimics the human understanding of similarity. When it comes to larger datasets, state of the art classifiers reach their limits in terms of unreasonable training or testing times. One representative example is the 1-nearest-neighbor DTW classifier (1-NN DTW) that is commonly used as the benchmark to compare to and has several shortcomings: it has a quadratic time and it degenerates in the presence of noise. To reduce the computational complexity lower bounding techniques or recently a nearest centroid classifier have been introduced. Still, execution times to classify moderately sized datasets on a single core are in the order of hours. We present our Bag-Of-SFA-Symbols in Vector Space (BOSS VS) classifier that is robust and accurate due to invariance to noise, phase shifts, offsets, amplitudes and occlusions. We show that it is as accurate while being multiple orders of magnitude faster than state of the art classifiers. Using the BOSS VS allows for mining massive time series datasets and real-time analytics. T3 - ZIB-Report - 15-30 KW - Time Series KW - Classification KW - Data Mining Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54984 SN - 1438-0064 ER - TY - CHAP A1 - Taentzer, Gabriele A1 - Golas, Ulrike ED - Parisi-Presicce, F. ED - Westfechtel, B. T1 - Towards Local Confluence Analysis for Amalgamated Graph Transformation T2 - Graph Transformations. Proceedings of ICGT 2015 N2 - Amalgamated graph transformation allows to define schemes of rules coinciding in common core activities and differing over additional parallel independent activities. Consequently, a rule scheme is specified by a kernel rule and a set of extending multi-rules forming an interaction scheme. Amalgamated transformations have been increasingly used in various modeling contexts. Critical Pair Analysis (CPA) can be used to show local confluence of graph transformation systems. It is an open challenge to lift the CPA to amalgamated graph transformation systems, especially since infinite many pairs of amalgamated rules occur in general. As a first step towards an efficient local confluence analysis of amalgamated graph transformation systems, we show that the analysis of a finite set of critical pairs suffices to prove local confluence. Y1 - 2015 U6 - https://doi.org/10.1007/978-3-319-21145-9_5 VL - 9151 SP - 69 EP - 86 PB - Springer ER - TY - THES A1 - Kulagina, Svetlana T1 - Distributed Multi-Stage Time Series Similarity Search Y1 - 2014 ER - TY - GEN A1 - Costa, Marta A1 - Ostrovsky, Aaron D. A1 - Manton, James D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases T2 - bioRxiv preprint Y1 - 2015 U6 - https://doi.org/10.1101/006346 ER - TY - CHAP A1 - Wende, Florian A1 - Steinke, Thomas T1 - Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU T2 - Proceeding SC '13 Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis Article No. 83 ACM New York, NY, USA, 2013 Y1 - 2013 U6 - https://doi.org/http://dx.doi.org/10.1145/2503210.2503254 ER - TY - JOUR A1 - Schäfer, Patrick T1 - The BOSS is concerned with time series classification in the presence of noise JF - Data Mining and Knowledge Discovery Y1 - 2014 U6 - https://doi.org/10.1007/s10618-014-0377-7 VL - 29 IS - 6 SP - 1505 EP - 1530 PB - Springer ER - TY - GEN ED - McIntosh-Smith, Simon ED - Gillan, Charles ED - Sanna, Nico ED - Scott, Stan ED - Steinke, Thomas T1 - Special issue of the Journal of Parallel and Distributed Computing (JDPC) on novel architectures for high-performance computing T2 - Journal of Parallel and Distributed Computing Y1 - 2013 U6 - https://doi.org/10.1016/j.jpdc.2013.08.013 SN - 0743-7315 VL - 73 IS - 11 SP - 1415 EP - 1416 ER - TY - GEN A1 - Benkrid, Khaled A1 - El-Araby, Esam A1 - Huang, Miaoqing A1 - Sano, Kentaro A1 - Steinke, Thomas T1 - High-Performance Reconfigurable Computing - editorial for Special Issue of the International Journal of Reconfigurable Computing T2 - International Journal of Reconfigurable Computing Y1 - 2012 U6 - https://doi.org/10.1155/2012/104963 VL - 2012 SP - 1 EP - 2 ER - TY - JOUR A1 - Tuma, Christian A1 - Laino, Teodoro A1 - Martin, Elyette A1 - Stolz, Steffen A1 - Curioni, Alessandro T1 - Modeling the Impact of Solid Surfaces in Thermal Degradation Processes JF - ChemPhysChem Y1 - 2013 U6 - https://doi.org/10.1002/cphc.201200921 VL - 14 SP - 88 EP - 91 ER - TY - JOUR A1 - Aboulhassan, Amal A1 - Baum, Daniel A1 - Wodo, Olga A1 - Ganapathysubramanian, Baskar A1 - Amassian, Aram A1 - Hadwiger, Markus T1 - A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials JF - Computer Graphics Forum N2 - The current characterization methods of the Bulk Heterojunction (BHJ) - the main material of the new Organic Photovoltaic solar cells - are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual charac- terization and exploration of local structure-performance correlations. We propose a new formula that correlates the structural features to the performance bottlenecks. Since research into BHJ materials is highly multidisci- plinary, we enable a visual feedback strategy that allows the scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characteri- zations. We furthermore show that our approach could reduce the previous work-flow time from days to minutes. Y1 - 2015 U6 - https://doi.org/10.1111/cgf.12652 VL - 34 IS - 3 SP - 401 EP - 410 PB - Wiley ER - TY - JOUR A1 - Schäfer, Patrick T1 - Experiencing the Shotgun Distance for Time Series Analysis JF - Transactions on Machine Learning and Data Mining Y1 - 2014 SN - 1864-9734 VL - 7 IS - 1 SP - 3 EP - 25 ER - TY - GEN A1 - Aboulhassan, Amal A1 - Baum, Daniel A1 - Wodo, Olga A1 - Ganapathysubramanian, Baskar A1 - Amassian, Aram A1 - Hadwiger, Markus T1 - A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials N2 - Current characterization methods of the so-called Bulk Heterojunction (BHJ), which is the main material of Organic Photovoltaic (OPV) solar cells, are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual characterization and exploration of local structure-performance correlations. We also propose a formula that correlates the structural features with the performance bottlenecks. Since research into BHJ materials is highly multidisciplinary, our framework enables a visual feedback strategy that allows scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characterizations. Furthermore, we show that our approach could substantially reduce the turnaround time. T3 - ZIB-Report - 15-20 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54353 SN - 1438-0064 ER - TY - GEN T1 - Annual Report 2013 T3 - Jahresbericht - 2013 KW - Jahresbericht Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52848 SN - 0934-5892 VL - 2013 ER - TY - JOUR A1 - Dierkes, Thomas A1 - Ortmann, Karl Michael T1 - On the efficient utilisation of duration JF - Insurance: Mathematics and Economics N2 - In this article we present a new approach to estimate the change of the present value of a given cashflow pattern caused by an interest rate shift. Our approximation is based on analysing the evolution of the present value function through a linear differential equation. The outcome is far more accurate than the standard approach achieved by a Taylor expansion. Furthermore, we derive an approximation formula of second order that produces nearly accurate results. In particular, we prove that our method is superior to any known alternative approximation formula based on duration. In order to demonstrate the power of this improved approximation we apply it to coupon bonds, level annuities, and level perpetuities. We finally generalise the approach to a non-flat term structure. As for applications in insurance, we estimate the change of the discounted value of future liabilities due to a proportional shift in the set of capital accumulation factors. These findings are of particular importance to capital adequacy calculations with respect to interest rate stress scenarios that are part of regulatory solvency requirements. Y1 - 2015 U6 - https://doi.org/10.1016/j.insmatheco.2014.11.002 VL - 60 SP - 29 EP - 37 ER - TY - CHAP A1 - Lange, Alexander T1 - A mathematical framework for predicting lifestyles of viral pathogens T2 - Modelling Biological Evolution 2017: Developing Novel Approaches Y1 - 2017 ER - TY - JOUR A1 - Kramer, Tobias A1 - Läuter, Matthias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Seasonal changes of the volatile density in the coma and on the surface of comet 67P/Churyumov-Gerasimenko JF - Monthly Notices of the Royal Astronomical Society N2 - Starting from several monthly data sets of Rosetta’s COmetary Pressure Sensor we reconstruct the gas density in the coma around comet 67P/Churyumov-Gerasimenko. The underlying inverse gas model is constructed by fitting ten thousands of measurements to thousands of potential gas sources distributed across the entire nucleus surface. The ensuing self-consistent solution for the entire coma density and surface activity reproduces the temporal and spatial variations seen in the data for monthly periods with Pearson correlation coefficients of 0.93 and higher. For different seasonal illumination conditions before and after perihelion we observe a systematic shift of gas sources on the nucleus. Y1 - 2017 U6 - https://doi.org/10.1093/mnras/stx866 VL - 469 SP - S20 EP - S28 ER - TY - GEN A1 - Aboulhassan, Amal A1 - Sicat, Ronell A1 - Baum, Daniel A1 - Wodo, Olga A1 - Hadwiger, Markus T1 - Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies N2 - The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths. T3 - ZIB-Report - 17-16 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63239 SN - 1438-0064 ER - TY - JOUR A1 - Zander, Thomas A1 - Dreischarf, Marcel A1 - Timm, Anne-Katrin A1 - Baumann, Wolfgang A1 - Schmidt, Hendrik T1 - Impact of material and morphological parameters on the mechanical response of the lumbar spine - A finite element sensitivity study JF - Journal of Biomechanics KW - finite element modelling KW - lumbar spine KW - sensitivity analysis KW - model validation KW - coefficient of determination Y1 - 2016 U6 - https://doi.org/10.1016/j.jbiomech.2016.12.014 VL - 53 SP - 185 EP - 190 ER - TY - JOUR A1 - Ritter, Zully A1 - Belavy, Daniel A1 - Baumann, Wolfgang A1 - Felsenberg, Dieter T1 - In vivo bone remodeling rates determination and compressive stiffness variations before, during 60 days bed rest and two years follow up: a micro-FE-analysis from HR-pQCT measurements of the Berlin bed rest study-2 JF - Acta Astronautica KW - finite-element analysis KW - bone structure KW - compressive stiffness KW - bed rest KW - HR-pQCT measurement Y1 - 2017 U6 - https://doi.org/10.1016/j.actaastro.2016.12.002 VL - 132 SP - 67 EP - 77 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Quasi-invariance of countable products of Cauchy measures under non-unitary dilations JF - Electronic Communications in Probability Y1 - 2018 U6 - https://doi.org/10.1214/18-ECP113 VL - 23 IS - 8 SP - 1 EP - 6 ER - TY - CHAP A1 - Coconu, Liviu A1 - Hege, Hans-Christian T1 - devEyes: Tangible Devices on Augmented Passive Surfaces T2 - TEI '17 Proceedings of the Eleventh International Conference on Tangible, Embedded, and Embodied Interaction, Yokohama, Japan, March 20 - 23, 2017 N2 - We present a novel approach to turn smartphones/ tablets into tangible near-surface devices with augmented reality (AR) capability on virtually any passive surface, like desks, tables and wallboards. A low-cost optoelectronic add-on for the device back camera enables position tracking on an almost invisible printable fiducial marker grid. This approach is promising in terms of adoption potential because it can be used anywhere with existing devices, requires no dedicated hardware installations and is applicable to a broad range of real-world applications. Y1 - 2017 U6 - https://doi.org/10.1145/3024969.3025065 SP - 409 EP - 411 ER - TY - THES A1 - Conrad, Tim T1 - Metabolic Pathways Y1 - 2004 UR - http://publications.imp.fu-berlin.de/10/ ER - TY - JOUR A1 - Aboulhassan, Amal A1 - Sicat, Ronell A1 - Baum, Daniel A1 - Wodo, Olga A1 - Hadwiger, Markus T1 - Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies JF - Computer Graphics Forum N2 - The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths. Y1 - 2017 U6 - https://doi.org/10.1111/cgf.13191 VL - 36 IS - 3 SP - 329 EP - 339 PB - Wiley ER - TY - JOUR A1 - Gelß, Patrick A1 - Matera, Sebastian A1 - Schütte, Christof T1 - Solving the master equation without kinetic Monte Carlo: Tensor train approximations for a CO oxidation model JF - Journal of Computational Physics N2 - In multiscale modeling of heterogeneous catalytic processes, one crucial point is the solution of a Markovian master equation describing the stochastic reaction kinetics. Usually, this is too high-dimensional to be solved with standard numerical techniques and one has to rely on sampling approaches based on the kinetic Monte Carlo method. In this study we break the curse of dimensionality for the direct solution of the Markovian master equation by exploiting the Tensor Train Format for this purpose. The performance of the approach is demonstrated on a first principles based, reduced model for the CO oxidation on the RuO2(110) surface. We investigate the complexity for increasing system size and for various reaction conditions. The advantage over the stochastic simulation approach is illustrated by a problem with increased Y1 - 2016 U6 - https://doi.org/10.1016/j.jcp.2016.03.025 VL - 314 SP - 489 EP - 502 ER - TY - JOUR A1 - Orgis, Thomas A1 - Läuter, Matthias A1 - Handorf, Dörthe A1 - Dethloff, Klaus T1 - Baroclinic waves on the β plane using low-order Discontinuous Galerkin discretisation JF - Journal of Computational Physics N2 - A classic Discontinuous Galerkin Method with low-order polynomials and explicit as well as semi-implicit time-stepping is applied to an atmospheric model employing the Euler equations on the β plane. The method, which was initially proposed without regard for the source terms and their balance with the pressure gradient that dominates atmospheric dynamics, needs to be adapted to be able to keep the combined geostrophic and hydrostatic balance in three spatial dimensions. This is achieved inside the discretisation through a polynomial mapping of both source and flux terms without imposing filters between time steps. After introduction and verification of this balancing, the realistic development of barotropic and baroclinic waves in the model is demonstrated, including the formation of a retrograde Rossby wave pattern. A prerequesite is the numerical solution of the thermal wind equation to construct geostrophically balanced initial states in z coordinates with arbitrary prescribed zonal wind profile, offering a new set of test cases for atmospheric models employing z coordinates. The resulting simulations demonstrate that the balanced low-order Discontinous Galerkin discretisation with polynomial degrees down to k=1 can be a viable option for atmospheric modelling. Y1 - 2017 U6 - https://doi.org/10.1016/j.jcp.2017.03.029 VL - 339 SP - 461 EP - 481 ER - TY - GEN T1 - Annual Report 2016 T3 - Jahresbericht - 2016 KW - Jahresbericht Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64339 SN - 0934-5892 VL - 2016 ER - TY - GEN A1 - Rohr, Ulrich-Peter A1 - Herrmann, Pia A1 - Ilm, Katharina A1 - Zhang, Hai A1 - Lohmann, Sabine A1 - Reiser, Astrid A1 - Muranyi, Andrea A1 - Smith, Janice A1 - Burock, Susen A1 - Osterland, Marc A1 - Leith, Katherine A1 - Singh, Shalini A1 - Brunhoeber, Patrick A1 - Bowermaster, Rebecca A1 - Tie, Jeanne A1 - Christie, Michael A1 - Wong, Hui-Li A1 - Waring, Paul A1 - Shanmugam, Kandavel A1 - Gibbs, Peter A1 - Stein, Ulrike T1 - Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies N2 - Background We assessed the novel MACC1 gene to further stratify stage II colon cancer patients with proficient mismatch repair (pMMR). Patients and methods Four cohorts with 596 patients were analyzed: Charité 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charité 2 comparison cohort was used to translate MACC1 qRT- PCR analyses to FFPE samples. In the BIOGRID 1 training cohort MACC1 mRNA levels were related to MACC1 protein levels from immunohistochemistry in FFPE sections; also analyzed for MMR. Chemotherapy-naïve pMMR patients were stratified by MACC1 mRNA and protein expression to establish risk groups based on recurrence-free survival (RFS). Risk stratification from BIOGRID 1 was confirmed in the BIOGRID 2 validation cohort. Pooled BIOGRID datasets produced a best effect-size estimate. Results In BIOGRID 1, using qRT-PCR and immunohistochemistry for MACC1 detection, pMMR/MACC1-low patients had a lower recurrence probability versus pMMR/MACC1-high patients (5-year RFS of 92% and 67% versus 100% and 68%, respectively). In BIOGRID 2, longer RFS was confirmed for pMMR/MACC1-low versus pMMR/MACC1-high patients (5-year RFS of 100% versus 90%, respectively). In the pooled dataset, 6.5% of patients were pMMR/MACC1-low with no disease recurrence, resulting in a 17% higher 5-year RFS (95% CI (12.6-21.3%)) versus pMMR/MACC1-high patients (P=0.037). Outcomes were similar for pMMR/MACC1-low and deficient MMR (dMMR) patients (5-year RFS of 100% and 96%, respectively). Conclusions MACC1 expression stratifies colon cancer patients with unfavorable pMMR status. Stage II colon cancer patients with pMMR/MACC1-low tumors have a similar favorable prognosis to those with dMMR with potential implications for the role of adjuvant therapy. T3 - ZIB-Report - 17-28 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64184 SN - 1438-0064 ER - TY - JOUR A1 - Rohr, Ulrich-Peter A1 - Herrmann, Pia A1 - Ilm, Katharina A1 - Zhang, Hai A1 - Lohmann, Sabine A1 - Reiser, Astrid A1 - Muranyi, Andrea A1 - Smith, Janice A1 - Burock, Susen A1 - Osterland, Marc A1 - Leith, Katherine A1 - Singh, Shalini A1 - Brunhoeber, Patrick A1 - Bowermaster, Rebecca A1 - Tie, Jeanne A1 - Christie, Michael A1 - Wong, Hui-Li A1 - Waring, Paul A1 - Shanmugam, Kandavel A1 - Gibbs, Peter A1 - Stein, Ulrike T1 - Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies JF - Annals of Oncology N2 - Background We assessed the novel MACC1 gene to further stratify stage II colon cancer patients with proficient mismatch repair (pMMR). Patients and methods Four cohorts with 596 patients were analyzed: Charité 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charité 2 comparison cohort was used to translate MACC1 qRT-PCR analyses to FFPE samples. In the BIOGRID 1 training cohort MACC1 mRNA levels were related to MACC1 protein levels from immunohistochemistry in FFPE sections; also analyzed for MMR. Chemotherapy-naïve pMMR patients were stratified by MACC1 mRNA and protein expression to establish risk groups based on recurrence-free survival (RFS). Risk stratification from BIOGRID 1 was confirmed in the BIOGRID 2 validation cohort. Pooled BIOGRID datasets produced a best effect-size estimate. Results In BIOGRID 1, using qRT-PCR and immunohistochemistry for MACC1 detection, pMMR/MACC1-low patients had a lower recurrence probability versus pMMR/MACC1-high patients (5-year RFS of 92% and 67% versus 100% and 68%, respectively). In BIOGRID 2, longer RFS was confirmed for pMMR/MACC1-low versus pMMR/MACC1-high patients (5-year RFS of 100% versus 90%, respectively). In the pooled dataset, 6.5% of patients were pMMR/MACC1-low with no disease recurrence, resulting in a 17% higher 5-year RFS (95% CI (12.6-21.3%)) versus pMMR/MACC1-high patients (P=0.037). Outcomes were similar for pMMR/MACC1-low and deficient MMR (dMMR) patients (5-year RFS of 100% and 96%, respectively). Conclusions MACC1 expression stratifies colon cancer patients with unfavorable pMMR status. Stage II colon cancer patients with pMMR/MACC1-low tumors have a similar favorable prognosis to those with dMMR with potential implications for the role of adjuvant therapy. Y1 - 2017 U6 - https://doi.org/10.1093/annonc/mdx207 VL - 28 IS - 8 SP - 1869 EP - 1875 ER - TY - THES A1 - Agarwal, Animesh T1 - Path Integral Techniques in Molecular Dynamics Simulations of Open Boundary Systems Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000103020-4 ER - TY - THES A1 - Badowski, Tomasz T1 - Adaptive importance sampling via minimization of estimators of cross-entropy, mean square and inefficiency constants Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000102823-3 ER - TY - THES A1 - Daragmeh, Adman T1 - Model Order Reduction of Linear Control Systems: Comparison of Balance Truncation and Singular Perturbation Approximation with Application to Optimal Control Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000102586-2 ER - TY - THES A1 - Gul, Raheem T1 - Mathematical Modeling and Sensitivity Analysis of Lumped­ Parameter Model of the Human Cardiovascular System Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000101271-2 ER - TY - THES A1 - Lie, Han Cheng T1 - On a strongly convex approximation of a stochastic optimal control problem for importance sampling of metastable diffusions Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000101680-4 ER - TY - THES A1 - Sriwattanaworachai, Nisara T1 - Spectral approach to metastability of non-reversible complex processes Y1 - 2016 ER - TY - THES A1 - Vega, Iliusi T1 - Reconstruction and analysis of the state space for the identification of dynamical states in real-world time-series Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000104520-1 ER - TY - GEN A1 - Koltai, Péter A1 - Schütte, Christof T1 - A multi scale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics N2 - We investigate metastable dynamical systems subject to non-stationary forcing as they appear in molecular dynamics for systems driven by external fields. We show, that if the strength of the forcing is inversely proportional to the length of the slow metastable time scales of the unforced system, then the effective behavior of the forced system on slow time scales can be described by a low-dimensional reduced master equation. Our construction is explicit and uses the multiscale perturbation expansion method called two-timing, or method of multiple scales. The reduced master equation—a Markov state model—can be assembled by constructing two equilibrium Markov state models; one for the unforced system, and one for a slightly perturbed one. T3 - ZIB-Report - 17-49 KW - Markov state model KW - non-equilibrium molecular dynamics KW - two timescale master equation KW - non-stationary forcing KW - metastability Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64868 SN - 1438-0064 ER - TY - GEN A1 - Wolf, Thomas A1 - Amadi, Chimaobi T1 - Rational Solutions of Underdetermined Polynomial Equations N2 - In this paper we report on an application of computer algebra in which mathematical puzzles are generated of a type that had been widely used in mathematics contests by a large number of participants worldwide. The algorithmic aspect of our work provides a method to compute rational solutions of single polynomial equations that are typically large with 10^2 ... 10^5 terms and that are heavily underdetermined. It was possible to obtain this functionality by adding a number of new modules for a new type of splitting of equations to the existing package CRACK that is normally used to solve polynomial algebraic and differential systems of equations. T3 - ZIB-Report - 17-33 KW - underdetermined polynomial systems, rational solutions, computer algebra, recreational mathematics Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64488 SN - 1438-0064 ER - TY - JOUR A1 - Leeners, Brigitte A1 - Krüger, Tillmann H. C. A1 - Geraedts, Kirsten A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Ille, Fabian A1 - Egli, Marcel A1 - Röblitz, Susanna A1 - Saleh, Lanja A1 - Spanhaus, K. A1 - Schippert, Cordula A1 - Zhang, Y. A1 - Hengartner, M. P. T1 - Lack of association between female hormone levels and visuospatial working memory, divided attention and cognitive bias across two consecutive menstrual cycles JF - Front. Behav. Neurosci. Y1 - 2017 U6 - https://doi.org/10.3389/fnbeh.2017.00120 ER - TY - JOUR A1 - Hermann, Frank A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Orejas, Fernando T1 - Formal Analysis of Model Transformations Based on Triple Graph Grammars JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000370 VL - 24 IS - 4 SP - 1 EP - 57 ER - TY - JOUR A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Habel, A. A1 - Lambers, L. A1 - Orejas, Fernando T1 - M-Adhesive Transformation Systems with Nested Application Conditions. Part 1: Parallelism, Concurreny and Amalgamation JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000357 VL - 24 IS - 4 SP - 1 EP - 48 ER - TY - JOUR A1 - Gabriel, Karsten A1 - Braatz, Benjamin A1 - Ehrig, Hartmut A1 - Golas, Ulrike T1 - Finitary M-Adhesive Categories JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000321 VL - 24 IS - 4 SP - 1 EP - 40 ER -