@misc{BorndoerferKarbstein2015, author = {Bornd{\"o}rfer, Ralf and Karbstein, Marika}, title = {Neue Planungsinstrumente nutzen: Das Verkehrsangebot verbessern und Kosten sparen}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-55439}, year = {2015}, abstract = {Wir illustrieren anhand des Liniennetzes der Stadt Potsdam das Potenzial mathematischer Methoden der Angebotsplanung. Wir zeigen, dass das "bestm{\"o}gliche" Verkehrsangebot stark von planerischen Vorgaben beeinflusst wird, mit denen man die Erreichung unterschiedlicher und teilweise gegenl{\"a}ufiger Ziele steuern kann. Die Komplexit{\"a}t des Systems f{\"u}hrt zum Auftreten von R{\"u}ckkoppelungseffekten, die man nicht mit Hilfe von Daumenregeln beherrschen kann. Vielmehr ist der Einsatz moderner Planungsverfahren in einer interdisziplin{\"a}ren Zusammenarbeit von politischen Entscheidungstr{\"a}gern, Verkehrsingenieuren und Mathematikern notwendig, um die aktuellen Herausforderungen in der Verkehrsplanung zu meistern. Der Artikel dokumentiert einen Beitrag zum 7. {\"O}PNV Innovationskongress des Ministeriums f{\"u}r Verkehr und Infrastruktur des Landes Baden-W{\"u}rttemberg, der vom 9.-11. M{\"a}rz 2015 in Freiburg stattfand.}, language = {de} } @misc{BorndoerferSagnolSchwartz2015, author = {Bornd{\"o}rfer, Ralf and Sagnol, Guillaume and Schwartz, Stephan}, title = {An Extended Network Interdiction Problem for Optimal Toll Control}, issn = {1438-0064}, doi = {10.1016/j.endm.2016.03.040}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-55405}, year = {2015}, abstract = {We study an extension of the shortest path network interdiction problem and present a novel real-world application in this area. We consider the problem of determining optimal locations for toll control stations on the arcs of a transportation network. We handle the fact that drivers can avoid control stations on parallel secondary roads. The problem is formulated as a mixed integer program and solved using Benders decomposition. We present experimental results for the application of our models to German motorways.}, language = {en} } @misc{BorndoerferHoppmannKarbstein2015, author = {Bornd{\"o}rfer, Ralf and Hoppmann, Heide and Karbstein, Marika}, title = {Timetabling and Passenger Routing in Public Transport}, journal = {Appeard in: Proceedings of Conference on Advanced Systems in Public Transport 2015 (CASPT2015)}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-55305}, year = {2015}, abstract = {The task of timetabling is to schedule the trips in a public transport system by determining periodic arrival and departure times at every station. The goal is to provide a service that is both attractive for passengers and can be operated economically. To date, timetable optimization is generally done with respect to fixed passenger routes, i.e., it is assumed that passengers do not respond to changes in the timetable. This is unrealistic and ignores potentially valuable degrees of freedom. We investigate in this paper periodic timetabling models with integrated passenger routing. We propose several models that differ in the allowed passenger paths and the objectives. We compare these models theoretically and report on computations on real-world instances for the city of Wuppertal.}, language = {en} } @misc{GleixnerSteffyWolter2015, author = {Gleixner, Ambros and Steffy, Daniel and Wolter, Kati}, title = {Iterative Refinement for Linear Programming}, issn = {1438-0064}, doi = {10.1287/ijoc.2016.0692}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-55118}, year = {2015}, abstract = {We describe an iterative refinement procedure for computing extended precision or exact solutions to linear programming problems (LPs). Arbitrarily precise solutions can be computed by solving a sequence of closely related LPs with limited precision arithmetic. The LPs solved share the same constraint matrix as the original problem instance and are transformed only by modification of the objective function, right-hand side, and variable bounds. Exact computation is used to compute and store the exact representation of the transformed problems, while numeric computation is used for solving LPs. At all steps of the algorithm the LP bases encountered in the transformed problems correspond directly to LP bases in the original problem description. We show that this algorithm is effective in practice for computing extended precision solutions and that it leads to a direct improvement of the best known methods for solving LPs exactly over the rational numbers. Our implementation is publically available as an extension of the academic LP solver SoPlex.}, language = {en} } @misc{Schaefer2015, author = {Sch{\"a}fer, Patrick}, title = {Bag-Of-SFA-Symbols in Vector Space (BOSS VS)}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54984}, year = {2015}, abstract = {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.}, language = {en} } @misc{TaentzerGolas2015, author = {Taentzer, Gabriele and Golas, Ulrike}, title = {Local Confluence Analysis for Amalgamated Graph Transformation: Long Version}, issn = {1438-0064}, doi = {10.1007/978-3-319-21145-9_5}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54943}, year = {2015}, abstract = {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.}, language = {en} } @misc{GamrathKochMaheretal.2015, author = {Gamrath, Gerald and Koch, Thorsten and Maher, Stephen J. and Rehfeldt, Daniel and Shinano, Yuji}, title = {SCIP-Jack - A solver for STP and variants with parallelization extensions}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54648}, year = {2015}, abstract = {The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. While often a strong relationship between different Steiner tree problem variants can be observed, solution approaches employed so far have been prevalently problem specific. In contrast, this paper introduces a general purpose solver that can be used to solve both the classical Steiner tree problem and many of its variants without modification. This is achieved by transforming various problem variants into a general form and solving them using a state-of-the-art MIP-framework. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances.}, language = {en} } @misc{Hendel2015, author = {Hendel, Gregor}, title = {Enhancing MIP branching decisions by using the sample variance of pseudo-costs}, issn = {1438-0064}, doi = {10.1007/978-3-319-18008-3_14}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54591}, year = {2015}, abstract = {The selection of a good branching variable is crucial for small search trees in Mixed Integer Programming. Most modern solvers employ a strategy guided by history information, mainly the variable pseudo-costs, which are used to estimate the objective gain. At the beginning of the search, such information is usually collected via an expensive look-ahead strategy called strong-branching until variables are considered reliable. The reliability notion is thereby mostly based on fixed-number thresholds, which may lead to ineffective branching decisions on problems with highly varying objective gains. We suggest two new notions of reliability motivated by mathematical statistics that take into account the sample variance of the past observations on each variable individually. The first method prioritizes additional strong-branching look-aheads on variables whose pseudo-costs show a large variance by measuring the relative error of a pseudo-cost confidence interval. The second method performs a two-sample Student-t test for filtering branching candidates with a high probability to be better than the best history candidate. Both methods were implemented in the MIP-solver SCIP and computational results on standard MIP test sets are presented.}, language = {en} } @misc{DuarteSagnolOliveira2015, author = {Duarte, Belmiro P.M. and Sagnol, Guillaume and Oliveira, Nuno M.C.}, title = {A robust minimax Semidefinite Programming formulation for optimal design of experiments for model parametrization}, issn = {1438-0064}, doi = {10.1016/B978-0-444-63578-5.50146-8}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54626}, year = {2015}, abstract = {Model-based optimal design of experiments (M-bODE) is a crucial step in model parametrization since it encloses a framework that maximizes the amount of information extracted from a battery of lab experiments. We address the design of M-bODE for dynamic models considering a continuous representation of the design. We use Semidefinite Programming (SDP) to derive robust minmax formulations for nonlinear models, and extend the formulations to other criteria. The approaches are demonstrated for a CSTR where a two-step reaction occurs.}, language = {en} } @misc{WillenbockelSchuette2015, author = {Willenbockel, Christian Tobias and Sch{\"u}tte, Christof}, title = {A Variational Bayesian Algorithm for Clustering of Large and Complex Networks}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54588}, year = {2015}, abstract = {We propose the Blockloading algorithm for the clustering of large and complex graphs with tens of thousands of vertices according to a Stochastic Block Model (SBM). Blockloading is based on generalized Variational Bayesian EM (VBEM) schemes and works for weighted and unweighted graphs. Existing Variational (Bayesian) EM methods have to consider each possible number of clusters sepa- rately to determine the optimal number of clusters and are prone to converge to local optima making multiple restarts necessary. These factors impose a severe restriction on the size and complexity of graphs these methods can handle. In con- trast, the Blockloading algorithm restricts restarts to subnetworks in a way that provides error correction of an existing cluster assignment. The number of clusters need not be specified in advance because Blockloading will return it as a result. We show that Blockloading outperforms all other variational methods regarding reliability of the results and computational efficiency.}, language = {en} } @misc{MuellerBartholmeiFischeretal.2014, author = {M{\"u}ller, Anja and Bartholmei, Stephan and Fischer, Barbara and Hahn, Helene}, title = {Der GLAM-Hackathon "Coding da Vinci"}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54566}, year = {2014}, abstract = {Coding da Vinci, der erste deutsche Kultur-Hackathon, wurde gemeinsam von der Open Knowledge Foundation Deutschland, der Servicestelle Digitalisierung Berlin, Wikimedia Deutschland und der Deutschen Digitalen Bibliothek veranstaltet. Zwischen Ende April und Anfang Juli haben 150 Teilnehmer (Coder, Webdesigner, Kulturinteressierte u.a.) an Webseiten, mobilen Apps,Spielen, Hardwareprojekten und anderen Anwendungen offener Daten gearbeitet. Die Daten wurden von 16 Kultur-Einrichtungen bereitgestellt. Im Verlauf des Hackathons wurden daraus 17 funktionsf{\"a}hige Prototypen entwickelt, {\"o}ffentlich pr{\"a}sentiert und f{\"u}nf davon auch pr{\"a}miert.Doch was genau ist ein Hackathon? Wie kommen Kulturinstitutionen und Hacker zusammen? Wie gelangt eine Kulturinstitution zu offenen Daten? Welche Herausforderungen und Chancen bietet ein Hackathon f{\"u}r den Kulturbereich? Welche neue Qualit{\"a}t erw{\"a}chst aus einem partizipativen Zugang zum digitalen Kulturerbe und der M{\"o}glichkeit mit Daten zu arbeiten? Was bleibt zu tun,um die Ergebnisse nachhaltig zu sichern? Diese Fragen sollen anhand der Ergebnisse von CdV diskutiert werden. Unter dem Motto „lessons learned" wagen wir den Ausblick auf Coding da Vinci 2015.}, language = {de} } @misc{WitzigGamrathHiller2015, author = {Witzig, Jakob and Gamrath, Gerald and Hiller, Benjamin}, title = {Reoptimization Techniques in MIP Solvers}, issn = {1438-0064}, doi = {10.1007/978-3-319-20086-6_14}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54375}, year = {2015}, abstract = {Recently, there have been many successful applications of optimization algorithms that solve a sequence of quite similar mixed-integer programs (MIPs) as subproblems. Traditionally, each problem in the sequence is solved from scratch. In this paper we consider reoptimization techniques that try to benefit from information obtained by solving previous problems of the sequence. We focus on the case that subsequent MIPs differ only in the objective function or that the feasible region is reduced. We propose extensions of the very complex branch-and-bound algorithms employed by general MIP solvers based on the idea to ``warmstart'' using the final search frontier of the preceding solver run. We extend the academic MIP solver SCIP by these techniques to obtain a reoptimizing branch-and-bound solver and report computational results which show the effectiveness of the approach.}, language = {en} } @misc{AboulhassanBaumWodoetal.2015, author = {Aboulhassan, Amal and Baum, Daniel and Wodo, Olga and Ganapathysubramanian, Baskar and Amassian, Aram and Hadwiger, Markus}, title = {A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54353}, year = {2015}, abstract = {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.}, language = {en} } @misc{GulSchuetteBernhard2015, author = {Gul, Raheem and Sch{\"u}tte, Christof and Bernhard, Stefan}, title = {Mathematical modeling and sensitivity analysis of arterial anastomosis in arm arteries}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54339}, year = {2015}, abstract = {Cardiovascular diseases are one of the major problems in medicine today and the number of patients increases worldwide. To find the most efficient treatment, prior knowledge about function and dysfunction of the cardiovas- cular system is required and methods need to be developed that identify the disease in an early stage. Mathematical modeling is a powerful tool for prediction and investigation of cardiovascular diseases. It has been shown that the Windkessel model, being based on an analogy between electrical circuits and fluid flow, is a simple but effective method to model the human cardiovascular system. In this paper, we have applied parametric local sensitivity analysis (LSA) to a linear elastic model of the arm arteries, to find and rank sensitive param- eters that may be helpful in clinical diagnosis. A computational model for end-to-side anastomosis (superior ulnar collateral anastomosis with posterior ulnar recurrent, SUC-PUR) is carried out to study the effects of some clinically relevant haemodynamic parameters like blood flow resistance and terminal re- sistance on pressure and flow at different locations of the arm artery. In this context, we also discuss the spatio-temporal dependency of local sensitivities. The sensitivities with respect to cardiovascular parameters reveal the flow resistance and diameter of the vessels as most sensitive parameters. These parameters play a key role in diagnosis of severe stenosis and aneurysms. In contrast, wall thickness and elastic modulus are found to be less sensitive.}, language = {en} } @misc{SchuetteSarich2015, author = {Sch{\"u}tte, Christof and Sarich, Marco}, title = {A Critical Appraisal of Markov State Models}, issn = {1438-0064}, doi = {10.1140/epjst/e2015-02421-0}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54218}, year = {2015}, abstract = {Markov State Modelling as a concept for a coarse grained description of the essential kinetics of a molecular system in equilibrium has gained a lot of atten- tion recently. The last 10 years have seen an ever increasing publication activity on how to construct Markov State Models (MSMs) for very different molecular systems ranging from peptides to proteins, from RNA to DNA, and via molecu- lar sensors to molecular aggregation. Simultaneously the accompanying theory behind MSM building and approximation quality has been developed well be- yond the concepts and ideas used in practical applications. This article reviews the main theoretical results, provides links to crucial new developments, outlines the full power of MSM building today, and discusses the essential limitations still to overcome.}, language = {en} } @misc{BanischDjurdjevacConradSchuette2015, author = {Banisch, Ralf and Djurdjevac Conrad, Natasa and Sch{\"u}tte, Christof}, title = {Reactive flows and unproductive cycles for random walks on complex networks}, issn = {1438-0064}, doi = {10.1140/epjst/e2015-02417-8}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54239}, year = {2015}, abstract = {We present a comprehensive theory for analysis and understanding of transition events between an initial set A and a target set B for general ergodic finite-state space Markov chains or jump processes, including random walks on networks as they occur, e.g., in Markov State Modelling in molecular dynamics. The theory allows us to decompose the probability flow generated by transition events between the sets A and B into the productive part that directly flows from A to B through reaction pathways and the unproductive part that runs in loops and is supported on cycles of the underlying network. It applies to random walks on directed networks and nonreversible Markov processes and can be seen as an extension of Transition Path Theory. Information on reaction pathways and unproductive cycles results from the stochastic cycle decomposition of the underlying network which also allows to compute their corresponding weight, thus characterizing completely which structure is used how often in transition events. The new theory is illustrated by an application to a Markov State Model resulting from weakly damped Langevin dynamics where the unproductive cycles are associated with periodic orbits of the underlying Hamiltonian dynamics.}, language = {en} } @misc{EhlkeHeylandMaerdianetal.2015, author = {Ehlke, Moritz and Heyland, Mark and M{\"a}rdian, Sven and Duda, Georg and Zachow, Stefan}, title = {Assessing the Relative Positioning of an Osteosynthesis Plate to the Patient-Specific Femoral Shape from Plain 2D Radiographs}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54268}, year = {2015}, abstract = {We present a novel method to derive the surface distance of an osteosynthesis plate w.r.t. the patient­specific surface of the distal femur based on 2D X­ray images. Our goal is to study from clinical data, how the plate­to­bone distance affects bone healing. The patient­specific 3D shape of the femur is, however, seldom recorded for cases of femoral osteosynthesis since this typically requires Computed Tomography (CT), which comes at high cost and radiation dose. Our method instead utilizes two postoperative X­ray images to derive the femoral shape and thus can be applied on radiographs that are taken in clinical routine for follow­up. First, the implant geometry is used as a calibration object to relate the implant and the individual X­ray images spatially in a virtual X­ray setup. In a second step, the patient­specific femoral shape and pose are reconstructed in the virtual setup by fitting a deformable statistical shape and intensity model (SSIM) to the images. The relative positioning between femur and implant is then assessed in terms of displacement between the reconstructed 3D shape of the femur and the plate. A preliminary evaluation based on 4 cadaver datasets shows that the method derives the plate­to­bone distance with a mean absolute error of less than 1mm and a maximum error of 4.7 mm compared to ground truth from CT. We believe that the approach presented in this paper constitutes a meaningful tool to elucidate the effect of implant positioning on fracture healing.}, language = {en} } @misc{Wende2015, author = {Wende, Florian}, title = {SIMD Enabled Functions on Intel Xeon CPU and Intel Xeon Phi Coprocessor}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54163}, year = {2015}, abstract = {To achieve high floating point compute performance, modern processors draw on short vector SIMD units, as found e.g. in Intel CPUs (SSE, AVX1, AVX2 as well as AVX-512 on the roadmap) and the Intel Xeon Phi coprocessor, to operate an increasingly larger number of operands simultaneously. Making use of SIMD vector operations therefore is essential to get close to the processor's floating point peak performance. Two approaches are typically used by programmers to utilize the vector units: compiler driven vectorization via directives and code annotations, and manual vectorization by means of SIMD intrinsic operations or assembly. In this paper, we investigate the capabilities of the current Intel compiler (version 15 and later) to generate vector code for non-trivial coding patterns within loops. Beside the more or less uniform data-parallel standard loops or loop nests, which are typical candidates for SIMDfication, the occurrence of e.g. (conditional) function calls including branching, and early returns from functions may pose difficulties regarding the effective use of vector operations. Recent improvements of the compiler's capabilities involve the generation of SIMD-enabled functions. We will study the effectiveness of the vector code generated by the compiler by comparing it against hand-coded intrinsics versions of different kinds of functions that are invoked within innermost loops.}, language = {en} } @misc{LubkollSchielaWeiser2015, author = {Lubkoll, Lars and Schiela, Anton and Weiser, Martin}, title = {An affine covariant composite step method for optimization with PDEs as equality constraints}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53954}, year = {2015}, abstract = {We propose a composite step method, designed for equality constrained optimization with partial differential equations. Focus is laid on the construction of a globalization scheme, which is based on cubic regularization of the objective and an affine covariant damped Newton method for feasibility. We show finite termination of the inner loop and fast local convergence of the algorithm. We discuss preconditioning strategies for the iterative solution of the arising linear systems with projected conjugate gradient. Numerical results are shown for optimal control problems subject to a nonlinear heat equation and subject to nonlinear elastic equations arising from an implant design problem in craniofacial surgery.}, language = {en} } @misc{GamrathMelchioriBertholdetal.2015, author = {Gamrath, Gerald and Melchiori, Anna and Berthold, Timo and Gleixner, Ambros and Salvagnin, Domenico}, title = {Branching on multi-aggregated variables}, issn = {1438-0064}, doi = {10.1007/978-3-319-18008-3_10}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53829}, year = {2015}, abstract = {In mixed-integer programming, the branching rule is a key component to a fast convergence of the branch-and-bound algorithm. The most common strategy is to branch on simple disjunctions that split the domain of a single integer variable into two disjoint intervals. Multi-aggregation is a presolving step that replaces variables by an affine linear sum of other variables, thereby reducing the problem size. While this simplification typically improves the performance of MIP solvers, it also restricts the degree of freedom in variable-based branching rules. We present a novel branching scheme that tries to overcome the above drawback by considering general disjunctions defined by multi-aggregated variables in addition to the standard disjunctions based on single variables. This natural idea results in a hybrid between variable- and constraint-based branching rules. Our implementation within the constraint integer programming framework SCIP incorporates this into a full strong branching rule and reduces the number of branch-and-bound nodes on a general test set of publicly available benchmark instances. For a specific class of problems, we show that the solving time decreases significantly.}, language = {en} } @misc{BeckenbachBorndoerferKnobenetal.2015, author = {Beckenbach, Isabel and Bornd{\"o}rfer, Ralf and Knoben, Loes and Kretz, David and Uetz, Marc}, title = {The S-Bahn Challenge in Berlin}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53792}, year = {2015}, abstract = {The S-Bahn Challenge in Berlin is a challenge in which one has to travel the entire S-Bahn network of Berlin in the shortest possible time. We explain how the problem can be modeled and solved mathematically. Furthermore, we report on our record attempt on January 10, 2015.}, language = {en} } @misc{UsluWerner2015, author = {Uslu, Svenja and Werner, Axel}, title = {A Two-Phase Method for the Biobjective k-Architecture Connected Facility Location Problem and Hypervolume Computation}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53753}, year = {2015}, abstract = {We apply customized versions of the ε-constraint Method and the Two-Phase Method to a problem originating in access network planning. We introduce various notions of quality measures for approximated/partial sets of nondominated points, utilizing the concept of hypervolume for biobjective problems. We report on computations to assess the performance of the two methods in terms of these measures.}, language = {en} } @misc{BorndoerferKlugLamorgeseetal.2015, author = {Bornd{\"o}rfer, Ralf and Klug, Torsten and Lamorgese, Leonardo and Mannino, Carlo and Reuther, Markus and Schlechte, Thomas}, title = {Recent Success Stories on Optimization of Railway Systems}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53726}, year = {2015}, abstract = {Planning and operating railway transportation systems is an extremely hard task due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense size of the problem instances. Because of that, however, mathematical models and optimization techniques can result in large gains for both railway cus- tomers and operators, e.g., in terms of cost reductions or service quality improvements. In the last years a large and growing group of researchers in the OR community have devoted their attention to this domain devel- oping mathematical models and optimization approaches to tackle many of the relevant problems in the railway planning process. However, there is still a gap to bridge between theory and practice, with a few notable exceptions. In this paper we address three success stories, namely, long-term freight train routing (part I), mid-term rolling stock rotation planning (part II), and real-time train dispatching (part III). In each case, we describe real-life, successful implementations. We will dis- cuss the individual problem setting, survey the optimization literature, and focus on particular aspects addressed by the mathematical models. We demonstrate on concrete applications how mathematical optimization can support railway planning and operations. This gives proof that math- ematical optimization can support the planning of rolling stock resources. Thus, mathematical models and optimization can lead to a greater effi- ciency of railway operations and will serve as a powerful and innovative tool to meet recent challenges of the railway industry.}, language = {en} } @misc{EhlkeFrenzelRammetal.2015, author = {Ehlke, Moritz and Frenzel, Thomas and Ramm, Heiko and Shandiz, Mohsen Akbari and Anglin, Carolyn and Zachow, Stefan}, title = {Towards Robust Measurement of Pelvic Parameters from AP Radiographs using Articulated 3D Models}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53707}, year = {2015}, abstract = {Patient-specific parameters such as the orientation of the acetabulum or pelvic tilt are useful for custom planning for total hip arthroplasty (THA) and for evaluating the outcome of surgical interventions. The gold standard in obtaining pelvic parameters is from three-dimensional (3D) computed tomography (CT) imaging. However, this adds time and cost, exposes the patient to a substantial radiation dose, and does not allow for imaging under load (e.g. while the patient is standing). If pelvic parameters could be reliably derived from the standard anteroposterior (AP) radiograph, preoperative planning would be more widespread, and research analyses could be applied to retrospective data, after a postoperative issue is discovered. The goal of this work is to enable robust measurement of two surgical parameters of interest: the tilt of the anterior pelvic plane (APP) and the orientation of the natural acetabulum. We present a computer-aided reconstruction method to determine the APP and natural acetabular orientation from a single, preoperative X-ray. It can easily be extended to obtain other important preoperative and postoperative parameters solely based on a single AP radiograph.}, language = {en} } @misc{HarmanSagnol2015, author = {Harman, Radoslav and Sagnol, Guillaume}, title = {Computing D-optimal experimental designs for estimating treatment contrasts under the presence of a nuisance time trend}, issn = {1438-0064}, doi = {10.1007/978-3-319-13881-7_10}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53640}, year = {2015}, abstract = {We prove a mathematical programming characterisation of approximate partial D-optimality under general linear constraints. We use this characterisation with a branch-and-bound method to compute a list of all exact D-optimal designs for estimating a pair of treatment contrasts in the presence of a nuisance time trend up to the size of 24 consecutive trials.}, language = {en} } @misc{FuegenschuhJunoszaSzaniawskiKlugetal.2015, author = {F{\"u}genschuh, Armin and Junosza-Szaniawski, Konstanty and Klug, Torsten and Kwasiborski, Slawomir and Schlechte, Thomas}, title = {Fastest, average and quantile schedule}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53592}, year = {2015}, abstract = {We consider problems concerning the scheduling of a set of trains on a single track. For every pair of trains there is a minimum headway, which every train must wait before it enters the track after another train. The speed of each train is also given. Hence for every schedule - a sequence of trains - we may compute the time that is at least needed for all trains to travel along the track in the given order. We give the solution to three problems: the fastest schedule, the average schedule, and the problem of quantile schedules. The last problem is a question about the smallest upper bound on the time of a given fraction of all possible schedules. We show how these problems are related to the travelling salesman problem. We prove NP-completeness of the fastest schedule problem, NP-hardness of quantile of schedules problem, and polynomiality of the average schedule problem. We also describe some algorithms for all three problems. In the solution of the quantile problem we give an algorithm, based on a reverse search method, generating with polynomial delay all Eulerian multigraphs with the given degree sequence and a bound on the number of such multigraphs. A better bound is left as an open question.}, language = {en} } @misc{WendeSteinkeReinefeld2015, author = {Wende, Florian and Steinke, Thomas and Reinefeld, Alexander}, title = {The Impact of Process Placement and Oversubscription on Application Performance: A Case Study for Exascale Computing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53560}, year = {2015}, abstract = {With the growing number of hardware components and the increasing software complexity in the upcoming exascale computers, system failures will become the norm rather than an exception for long-running applications. Fault-tolerance can be achieved by the creation of checkpoints during the execution of a parallel program. Checkpoint/Restart (C/R) mechanisms allow for both task migration (even if there were no hardware faults) and restarting of tasks after the occurrence of hardware faults. Affected tasks are then migrated to other nodes which may result in unfortunate process placement and/or oversubscription of compute resources. In this paper we analyze the impact of unfortunate process placement and oversubscription of compute resources on the performance and scalability of two typical HPC application workloads, CP2K and MOM5. Results are given for a Cray XC30/40 with Aries dragonfly topology. Our results indicate that unfortunate process placement has only little negative impact while oversubscription substantially degrades the performance. The latter might be only (partially) beneficial when placing multiple applications with different computational characteristics on the same node.}, language = {en} } @misc{DraegertEisenblaetterGamrathetal.2015, author = {Draegert, Andreas and Eisenbl{\"a}tter, Andreas and Gamrath, Inken and Werner, Axel}, title = {Optimal Battery Controlling for Smart Grid Nodes}, issn = {1438-0064}, doi = {10.1007/978-4-431-55420-2_6}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53550}, year = {2015}, abstract = {Energy storages can be of great value when added to power grids. They introduce the possibility to store and release energy whenever this is favorable. This is particularly relevant, for example, if power supply is volatile (as is the case with renewable energy) and the network is small (so that there are few other nodes that might balance fluctuations in consumption or production). We present models and methods from mathematical optimization for computing an optimized storage schedule for this purpose. We look at alternative optimization objectives, such as smallest possible peak load, low energy costs, or the close approximation of a prescribed load curve. The optimization needs to respect general operational and economic constraints as well as limitations in the use of storage, which are imposed by the chosen storage technology. We therefore introduce alternative approaches for modeling the non-linear properties of energy storages and study their impact on the efficiency of the optimization process. Finally, we present a computational study with batteries as storage devices. We use this to highlight the trade-off between solution quality and computational tractability. A version of the model for the purpose of leveling peaks and instabilities has been implemented into a control system for an office-building smart grid scenario.}, language = {en} } @misc{BorndoerferKarbstein2015, author = {Bornd{\"o}rfer, Ralf and Karbstein, Marika}, title = {Metric Inequalities for Routings on Direct Connections with Application in Line Planning}, issn = {1438-0064}, doi = {10.1016/j.disopt.2015.07.004}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53507}, year = {2015}, abstract = {We consider multi-commodity flow problems in which capacities are installed on paths. In this setting, it is often important to distinguish between flows on direct connection routes, using single paths, and flows that include path switching. We derive a feasibility condition for path capacities supporting such direct connection flows similar to the feasibility condition for arc capacities in ordinary multi-commodity flows. The concept allows to solve large-scale real-world line planning problems in public transport including a novel passenger routing model that favors direct connections over connections with transfers.}, language = {en} } @misc{Humpola2015, author = {Humpola, Jesco}, title = {Sufficient Pruning Conditions for MINLP in Gas Network Design}, doi = {10.1007/s13675-016-0077-8}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53489}, year = {2015}, abstract = {One quarter of Europe's energy demand is provided by natural gas distributed through a vast pipeline network covering the whole of Europe. At a cost of 1 million Euros per kilometer the extension of the European pipeline network is already a multi billion Euro business. Therefore, automatic planning tools that support the decision process are desired. We model the topology extension problem in gas networks by a mixed-integer nonlinear program (MINLP). This gives rise to a so-called active transmission problem, a continuous nonlinear non-convex feasibility problem which emerges from the MINLP model by fixing all integral variables. In this article we offer novel sufficient conditions for proving the infeasibility of this active transmission problem. These conditions can be expressed in the form of a mixed-integer program (MILP), i.e., the infeasibility of a non-convex NLP can be certified by solving an MILP. These results provide an efficient bounding procedure in a branch-and-bound algorithm. Our computational results demonstrate a substantial speed-up for the necessary computations.}, language = {en} } @misc{BrettHobergPachecoetal.2015, author = {Brett, Charles and Hoberg, Rebecca and Pacheco, Meritxell and Smith, Kyle and Bornd{\"o}rfer, Ralf and Euler, Ricardo and Gamrath, Gerwin and Grimm, Boris and Heismann, Olga and Reuther, Markus and Schlechte, Thomas and Tesch, Alexander}, title = {G-RIPS 2014 RailLab - Towards robust rolling stock rotations}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53475}, year = {2015}, abstract = {The Graduate-Level Research in Industrial Projects (G-RIPS) Program provides an opportunity for high-achieving graduate-level students to work in teams on a real-world research project proposed by a sponsor from industry or the public sector. Each G-RIPS team consists of four international students (two from the US and two from European universities), an academic mentor, and an industrial sponsor. This is the report of the Rail-Lab project on the definition and integration of robustness aspects into optimizing rolling stock schedules. In general, there is a trade-off for complex systems between robustness and efficiency. The ambitious goal was to explore this trade-off by implementing numerical simulations and developing analytic models. In rolling stock planning a very large set of industrial railway requirements, such as vehicle composition, maintenance constraints, infrastructure capacity, and regularity aspects, have to be considered in an integrated model. General hypergraphs provide the modeling power to tackle those requirements. Furthermore, integer programming approaches are able to produce high quality solutions for the deterministic problem. When stochastic time delays are considered, the mathematical programming problem is much more complex and presents additional challenges. Thus, we started with a basic variant of the deterministic case, i.e., we are only considering hypergraphs representing vehicle composition and regularity. We transfered solution approaches for robust optimization from the airline industry to the setting of railways and attained a reasonable measure of robustness. Finally, we present and discuss different methods to optimize this robustness measure.}, language = {en} } @misc{HoerthBaumKnoeteletal.2015, author = {Hoerth, Rebecca M. and Baum, Daniel and Kn{\"o}tel, David and Prohaska, Steffen and Willie, Bettina M. and Duda, Georg and Hege, Hans-Christian and Fratzl, Peter and Wagermaier, Wolfgang}, title = {Registering 2D and 3D Imaging Data of Bone during Healing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53426}, year = {2015}, abstract = {Purpose/Aims of the Study: Bone's hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro computed tomography (μCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. Materials and Methods: We investigated bone during healing by means of μCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue's calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. Results: We present an approach for the registration of 2D data in a 3D μCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into μCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. Conclusions: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.}, language = {en} } @misc{NielsenWeber2014, author = {Nielsen, Adam and Weber, Marcus}, title = {Computing the nearest reversible Markov chain}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53292}, year = {2014}, abstract = {Reversible Markov chains are the basis of many applications. However, computing transition probabilities by a finite sampling of a Markov chain can lead to truncation errors. Even if the original Markov chain is reversible, the approximated Markov chain might be non-reversible and will lose important properties, like the real valued spectrum. In this paper, we show how to find the closest reversible Markov chain to a given transition matrix. It turns out that this matrix can be computed by solving a convex minimization problem.}, language = {en} } @misc{WangSchuette2014, author = {Wang, Han and Sch{\"u}tte, Christof}, title = {Building Markov State Models for Periodically Driven Non-Equilibrium Systems}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53167}, year = {2014}, abstract = {Recent years have seen an increased interest in non-equilibrium molecular dynamics (NEMD) simulations, especially for molecular systems with periodic forcing by external fields, e.g., in the context of studying effects of electromagnetic radiation on the human body tissue. Lately, an NEMD methods with local thermostating has been proposed that allows for studying non-equilibrium processes in a statistically reliable and thermodynamically consistent way. In this article, we demonstrate how to construct Markov State Models (MSMs) for such NEMD simulations. MSM building has been well-established for systems in equilibrium where MSMs with just a few (macro-)states allow for accurate reproduction of the essential kinetics of the molecular system under consideration. Non-equilibrium MSMs have been lacking so far. The article presents how to construct such MSMs and illustrates their validity and usefulness for the case of conformation dynamics of alanine dipeptide in an external electric field.}, language = {en} } @misc{EggerDercksenUdvaryetal.2014, author = {Egger, Robert and Dercksen, Vincent J. and Udvary, Daniel and Hege, Hans-Christian and Oberlaender, Marcel}, title = {Generation of dense statistical connectomes from sparse morphological data}, issn = {1438-0064}, doi = {10.3389/fnana.2014.00129}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53075}, year = {2014}, abstract = {Sensory-evoked signal flow, at cellular and network levels, is primarily determined by the synaptic wiring of the underlying neuronal circuitry. Measurements of synaptic innervation, connection probabilities and sub-cellular organization of synaptic inputs are thus among the most active fields of research in contemporary neuroscience. Methods to measure these quantities range from electrophysiological recordings over reconstructions of dendrite-axon overlap at light-microscopic levels to dense circuit reconstructions of small volumes at electron-microscopic resolution. However, quantitative and complete measurements at subcellular resolution and mesoscopic scales to obtain all local and long-range synaptic in/outputs for any neuron within an entire brain region are beyond present methodological limits. Here, we present a novel concept, implemented within an interactive software environment called NeuroNet, which allows (i) integration of sparsely sampled (sub)cellular morphological data into an accurate anatomical reference frame of the brain region(s) of interest, (ii) up-scaling to generate an average dense model of the neuronal circuitry within the respective brain region(s) and (iii) statistical measurements of synaptic innervation between all neurons within the model. We illustrate our approach by generating a dense average model of the entire rat vibrissal cortex, providing the required anatomical data, and illustrate how to measure synaptic innervation statistically. Comparing our results with data from paired recordings in vitro and in vivo, as well as with reconstructions of synaptic contact sites at light- and electron-microscopic levels, we find that our in silico measurements are in line with previous results.}, language = {en} } @misc{Karbstein2014, author = {Karbstein, Marika}, title = {Integrated Line Planning and Passenger Routing: Connectivity and Transfers}, issn = {1438-0064}, doi = {10.1007/978-3-319-28697-6_37}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52986}, year = {2014}, abstract = {The integrated line planning and passenger routing problem is an important planning problem in service design of public transport. A major challenge is the treatment of transfers. A main property of a line system is its connectivity. In this paper we show that analysing the connecvitiy aspect of a line plan gives a new idea to handle the transfer aspect of the line planning problem.}, language = {en} } @misc{WeberTranfieldHoeoegetal.2014, author = {Weber, Britta and Tranfield, Erin M. and H{\"o}{\"o}g, Johanna L. and Baum, Daniel and Antony, Claude and Hyman, Tony and Verbavatz, Jean-Marc and Prohaska, Steffen}, title = {Automated stitching of microtubule centerlines across serial electron tomograms}, issn = {1438-0064}, doi = {10.1371/journal.pone.0113222}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52958}, year = {2014}, abstract = {Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts' opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort.}, language = {en} } @misc{D'AndreagiovanniKrolikowskiPulaj2014, author = {D'Andreagiovanni, Fabio and Krolikowski, Jonatan and Pulaj, Jonad}, title = {A Fast Hybrid Primal Heuristic for Multiband Robust Capacitated Network Design with Multiple Time Periods}, issn = {1438-0064}, doi = {10.1016/j.asoc.2014.10.016}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52862}, year = {2014}, abstract = {We investigate the Robust Multiperiod Network Design Problem, a generalization of the Capacitated Network Design Problem (CNDP) that, besides establishing flow routing and network capacity installation as in a canonical CNDP, also considers a planning horizon made up of multiple time periods and protection against fluctuations in traffic volumes. As a remedy against traffic volume uncertainty, we propose a Robust Optimization model based on Multiband Robustness (B{\"u}sing and D'Andreagiovanni, 2012), a refinement of classical Gamma-Robustness by Bertsimas and Sim (2004) that uses a system of multiple deviation bands. Since the resulting optimization problem may prove very challenging even for instances of moderate size solved by a state-of-the-art optimization solver, we propose a hybrid primal heuristic that combines a randomized fixing strategy inspired by ant colony optimization and an exact large neighbourhood search. Computational experiments on a set of realistic instances from the SNDlib (2010) show that our original heuristic can run fast and produce solutions of extremely high quality associated with low optimality gaps.}, language = {en} } @misc{SagnolHarman2014, author = {Sagnol, Guillaume and Harman, Radoslav}, title = {Optimal Designs for Steady-state Kalman filters}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52808}, year = {2014}, abstract = {We consider a stationary discrete-time linear process that can be observed by a finite number of sensors. The experimental design for the observations consists of an allocation of available resources to these sensors. We formalize the problem of selecting a design that maximizes the information matrix of the steady-state of the Kalman filter, with respect to a standard optimality criterion, such as \$D-\$ or \$A-\$optimality. This problem generalizes the optimal experimental design problem for a linear regression model with a finite design space and uncorrelated errors. Finally, we show that under natural assumptions, a steady-state optimal design can be computed by semidefinite programming.}, language = {en} } @misc{SagnolBorndoerferSchlechteetal.2014, author = {Sagnol, Guillaume and Bornd{\"o}rfer, Ralf and Schlechte, Thomas and Swarat, Elmar}, title = {The Price of Spite in Spot-checking games}, issn = {1438-0064}, doi = {10.1007/978-3-662-44803-8}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52775}, year = {2014}, abstract = {We introduce the class of spot-checking games (SC games). These games model problems where the goal is to distribute fare inspectors over a toll network. Although SC games are not zero-sum, we show that a Nash equilibrium can be computed by linear programming. The computation of a strong Stackelberg equilibrium is more relevant for this problem, but we show that this is NP-hard. However, we give some bounds on the \emph{price of spite}, which measures how the payoff of the inspector degrades when committing to a Nash equilibrium. Finally, we demonstrate the quality of these bounds for a real-world application, namely the enforcement of a truck toll on German motorways.}, language = {en} } @misc{BorndoerferKarbsteinMehrgardtetal.2014, author = {Bornd{\"o}rfer, Ralf and Karbstein, Marika and Mehrgardt, Julika and Reuther, Markus and Schlechte, Thomas}, title = {The Cycle Embedding Problem}, issn = {1438-0064}, doi = {10.1007/978-3-319-28697-6_65}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52788}, year = {2014}, abstract = {Given two hypergraphs, representing a fine and a coarse "layer", and a cycle cover of the nodes of the coarse layer, the cycle embedding problem (CEP) asks for an embedding of the coarse cycles into the fine layer. The CEP is NP-hard for general hypergraphs, but it can be solved in polynomial time for graphs. We propose an integer rogramming formulation for the CEP that provides a complete escription of the CEP polytope for the graphical case. The CEP comes up in railway vehicle rotation scheduling. We present computational results for problem instances of DB Fernverkehr AG that justify a sequential coarse-first-fine-second planning approach.}, language = {en} } @misc{BetkerGamrathKosiankowskietal.2014, author = {Betker, Andreas and Gamrath, Inken and Kosiankowski, Dirk and Lange, Christoph and Lehmann, Heiko and Pfeuffer, Frank and Simon, Felix and Werner, Axel}, title = {Comprehensive Topology and Traffic Model of a Nation-wide Telecommunication Network}, issn = {1438-0064}, doi = {10.1364/JOCN.6.001038}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52670}, year = {2014}, abstract = {As a basis for meaningful simulation and optimization efforts with regard to traffic engineering or energy consumption in telecommunication networks, suitable models are indispensable. This concerns not only realistic network topologies, but also models for the geographical distribution and the temporal dynamics of traffic, as well as the assumptions on network components and technology. This paper derives such a model from the practice of a large national carrier. Applying the network and traffic model, we demonstrate its use by presenting various optimization cases related to energy-efficient telecommunication. Here, we focus on load-adaptivity by employing sleep modes to the network hardware, where several constraints on the reconfigurability of the network over time are considered.}, language = {en} } @misc{GamrathKochRehfeldtetal.2014, author = {Gamrath, Gerald and Koch, Thorsten and Rehfeldt, Daniel and Shinano, Yuji}, title = {SCIP-Jack - A massively parallel STP solver}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52293}, year = {2014}, abstract = {In this article we describe the impact from embedding a 15 year old model for solving the Steiner tree problem in graphs in a state-of-the-art MIP-Framework, making the result run in a massively parallel environment and extending the model to solve as many variants as possible. We end up with a high-perfomance solver that is capable of solving previously unsolved instances and, in contrast to its predecessor, is freely available for academic research.}, language = {en} } @misc{StoetzelApriRoeblitz2014, author = {St{\"o}tzel, Claudia and Apri, Mochamad and R{\"o}blitz, Susanna}, title = {A reduced ODE model of the bovine estrous cycle}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51594}, year = {2014}, abstract = {This work deals with the reduction of a previously developed ODE model for the bovine estrous cycle. After applying a method for exploring the parameter space by Apri et al. (2012), we perform structure-based reduction steps and several system specific adaptations. Overall, the original model consisting of 15 ODEs and 60 parameters is reduced to a model of 10 odes and 38 parameters. The reduced model qualitatively reproduces the state trajectories of the original model.}, language = {en} } @misc{SarichSchuette2014, author = {Sarich, Marco and Sch{\"u}tte, Christof}, title = {Utilizing hitting times for finding metastable sets in non-reversible Markov chains}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51209}, year = {2014}, abstract = {Techniques for finding metastable or almost invariant sets have been investigated, e.g., for deterministic dynamical systems in set-oriented numerics, for stochastic processes in molecular dynamics, and for random walks on complex networks. Most prominent algorithms are based on spectral apporaches and identify metastable sets via the doimant eigenvalues of the transfer operator associated with the dynamical system under consideration. These algorithms require the dominant eigenvalues to be real-valued. However, for many types of dynamics, e.g. for non-reversible Markov chains, this condition is not met. In this paper we utilize the hitting time apporach to metastable sets and demonstrate how the wellknown statements about optimal metastable decompositions of reversible chains can be reformulated for non-reversible chains if one switches from a spectral approach to an exit time approach. The performance of the resulting algorithm is illustrated by numerical experiments on random walks on complex networks.}, language = {en} } @misc{LindowBaumHege2014, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Ligand Excluded Surface: A New Type of Molecular Surface}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51194}, year = {2014}, abstract = {The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes - including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules.}, language = {en} } @misc{DjurdjevacConradBanischSchuette2014, author = {Djurdjevac Conrad, Natasa and Banisch, Ralf and Sch{\"u}tte, Christof}, title = {Modularity of Directed Networks: Cycle Decomposition Approach}, issn = {1438-0064}, doi = {10.3934/jcd.2015.2.1}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51166}, year = {2014}, abstract = {The problem of decomposing networks into modules (or clusters) has gained much attention in recent years, as it can account for a coarsegrained description of complex systems, often revealing functional subunits of these systems. A variety of module detection algorithms have been proposed, mostly oriented towards finding hard partitionings of undirected networks. Despite the increasing number of fuzzy clustering methods for directed networks, many of these approaches tend to neglect important directional information. In this paper, we present a novel random walk based approach for finding fuzzy partitions of directed, weighted networks, where edge directions play a crucial role in defining how well nodes in a module are interconnected. We will show that cycle decomposition of a random walk process connects the notion of network modules and information transport in a network, leading to a new, symmetric measure of node communication. Finally, we will use this measure to introduce a communication graph, for which we will show that although being undirected it inherits all necessary information about modular structures from the original network.}, language = {en} } @misc{BeckenbachBorndoerfer2014, author = {Beckenbach, Isabel and Bornd{\"o}rfer, Ralf}, title = {An Approximation Result for Matchings in Partitioned Hypergraphs}, doi = {10.1007/978-3-319-28697-6_5}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51083}, year = {2014}, abstract = {We investigate the matching and perfect matching polytopes of hypergraphs having a special structure, which we call partitioned hypergraphs. We show that the integrality gap of the standard LP-relaxation is at most \$2\sqrt{d}\$ for partitioned hypergraphs with parts of size \$\leq d\$. Furthermore, we show that this bound cannot be improved to \$\mathcal{O}(d^{0.5-\epsilon})\$.}, language = {en} } @misc{Schweiger2014, author = {Schweiger, Jonas}, title = {Gas network extension planning for multiple demand scenarios}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51030}, year = {2014}, abstract = {Today's gas markets demand more flexibility from the network operators which in turn have to invest into their network infrastructure. As these investments are very cost-intensive and long-living, network extensions should not only focus on one bottleneck scenario, but should increase the flexibility to fulfill different demand scenarios. We formulate a model for the network extension problem for multiple demand scenarios and propose a scenario decomposition. We solve MINLP single-scenario sub-problems and obtain valid bounds even without solving them to optimality. Heuristics prove capable of improving the initial solutions substantially. Results of computational experiments are presented.}, language = {en} } @misc{HeismannBorndoerfer2014, author = {Heismann, Olga and Bornd{\"o}rfer, Ralf}, title = {A Generalization of Odd Set Inequalities for the Set Packing Problem}, issn = {1438-0064}, doi = {10.1007/978-3-319-07001-8_26}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51010}, year = {2014}, abstract = {The set packing problem, sometimes also called the stable set problem, is a well-known NP-hard problem in combinatorial optimization with a wide range of applications and an interesting polyhedral structure, that has been the subject of intensive study. We contribute to this field by showing how, employing cliques, odd set inequalities for the matching problem can be generalized to valid inequalities for the set packing polytope with a clear combinatorial meaning.}, language = {en} }