@misc{HaslerAmrheinKlindtetal.2017, author = {Hasler, Tim and Amrhein, Kilian and Klindt, Marco and Oltmanns, Elias and Peters-Kottig, Wolfgang}, title = {Backup ist KEINE Langzeitverf{\"u}gbarkeit}, doi = {10.12752/9954}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-99548}, year = {2017}, abstract = {Diese Handreichung im Flyerformat soll mit den verschiedenen Missverst{\"a}ndnissen aufr{\"a}umen, die einem im Alltag begegnen, wenn man es mit digitaler Langzeitverf{\"u}gbarkeit zu tun hat.}, language = {de} } @article{DonatiHartmannKeller2017, author = {Donati, Luca and Hartmann, Carsten and Keller, Bettina G.}, title = {Girsanov reweighting for path ensembles and Markov state models}, volume = {146}, journal = {The Journal of Chemical Physics}, number = {24}, doi = {10.1063/1.4989474}, pages = {244112}, year = {2017}, abstract = {The sensitivity of molecular dynamics on changes in the potential energy function plays an important role in understanding the dynamics and function of complex molecules. We present a method to obtain path ensemble averages of a perturbed dynamics from a set of paths generated by a reference dynamics. It is based on the concept of path probability measure and the Girsanov theorem, a result from stochastic analysis to estimate a change of measure of a path ensemble. Since Markov state models (MSMs) of the molecular dynamics can be formulated as a combined phase-space and path ensemble average, the method can be extended to reweight MSMs by combining it with a reweighting of the Boltzmann distribution. We demonstrate how to efficiently implement the Girsanov reweighting in a molecular dynamics simulation program by calculating parts of the reweighting factor "on the fly" during the simulation, and we benchmark the method on test systems ranging from a two-dimensional diffusion process and an artificial many-body system to alanine dipeptide and valine dipeptide in implicit and explicit water. The method can be used to study the sensitivity of molecular dynamics on external perturbations as well as to reweight trajectories generated by enhanced sampling schemes to the original dynamics.}, language = {en} } @masterthesis{Loebel2017, type = {Bachelor Thesis}, author = {L{\"o}bel, Fabian}, title = {Solving Integrated Timetabling and Passenger Routing Problems Using the Modulo Network Simplex Algorithm}, year = {2017}, abstract = {Common models and solving approaches for the problem of periodic timetabling, that is, determining periodic arrival and departure times of a given public transportation network's lines so that the total weighted travel time of all passengers is minimized, fail to take passenger behavior into account. Current research is attempting to resolve this issue and first results show a positive impact on solution quality. This thesis aims to give a brief overview of literature on the topic of timetabling and to then state a heuristic approach to Integrated Timetabling by blending passenger behavior into the Modulo Network Simplex algorithm, which is part of the research carried out by the author's study group at the Zuse Institut Berlin in the framework of MATHEON's research project MI-3 supported by the Einstein Foundation Berlin.}, language = {en} } @inproceedings{RoyXuPokutta2017, author = {Roy, Aurko and Xu, Huan and Pokutta, Sebastian}, title = {Reinforcement Learning under Model Mismatch}, booktitle = {Proceedings of NIPS}, arxiv = {http://arxiv.org/abs/1706.04711}, year = {2017}, language = {en} } @inproceedings{BaermannPokuttaSchneider2017, author = {B{\"a}rmann, Andreas and Pokutta, Sebastian and Schneider, Oskar}, title = {Emulating the Expert: Inverse Optimization through Online Learning}, booktitle = {Proceedings of the International Conference on Machine Learning (ICML)}, arxiv = {http://arxiv.org/abs/1810.12997}, year = {2017}, language = {en} } @inproceedings{BraunPokuttaZink2017, author = {Braun, G{\´a}bor and Pokutta, Sebastian and Zink, Daniel}, title = {Lazifying Conditional Gradient Algorithms}, booktitle = {Proceedings of the International Conference on Machine Learning (ICML)}, arxiv = {http://arxiv.org/abs/1610.05120}, year = {2017}, language = {en} } @inproceedings{ArumugamKadampotTahmasbietal.2017, author = {Arumugam, Keerthi Suria Kumar and Kadampot, Ishaque Ashar and Tahmasbi, Mehrdad and Shah, Shaswat and Bloch, Matthieu and Pokutta, Sebastian}, title = {Modulation Recognition Using Side Information and Hybrid Learning}, booktitle = {Proceedings of IEEE DySPAN}, year = {2017}, language = {en} } @inproceedings{LanPokuttaZhouetal.2017, author = {Lan, G. and Pokutta, Sebastian and Zhou, Y. and Zink, Daniel}, title = {Conditional Accelerated Lazy Stochastic Gradient Descent}, booktitle = {Proceedings of the International Conference on Machine Learning (ICML)}, arxiv = {http://arxiv.org/abs/1703.05840}, year = {2017}, language = {en} } @article{RoyPokutta2017, author = {Roy, Aurko and Pokutta, Sebastian}, title = {Hierarchical Clustering via Spreading Metrics}, volume = {18}, journal = {Journal of Machine Learning Research (JMLR)}, arxiv = {http://arxiv.org/abs/1610.09269}, pages = {1 -- 35}, year = {2017}, language = {en} } @article{BodurDel PiaDeyetal.2017, author = {Bodur, Merve and Del Pia, Alberto and Dey, Santanu Sabush and Molinaro, Marco and Pokutta, Sebastian}, title = {Aggregation-based cutting-planes for packing and covering Integer Programs}, journal = {to appear in Mathematical Programming A}, arxiv = {http://arxiv.org/abs/1606.08951}, year = {2017}, language = {en} } @article{BazziFioriniPokuttaetal.2017, author = {Bazzi, Abbas and Fiorini, Samuel and Pokutta, Sebastian and Svensson, Ola}, title = {Small linear programs cannot approximate Vertex Cover within a factor of 2 - epsilon}, journal = {to appear in Mathematics of Operations Research}, arxiv = {http://arxiv.org/abs/1503.00753}, year = {2017}, language = {en} } @article{BraunGuzmanPokutta2017, author = {Braun, G{\´a}bor and Guzm{\´a}n, C. and Pokutta, Sebastian}, title = {Unifying Lower Bounds on the Oracle Complexity of Nonsmooth Convex Optimization}, volume = {63}, journal = {IEEE Transactions of Information Theory}, number = {7}, arxiv = {http://arxiv.org/abs/1407.5144}, pages = {4709 -- 4724}, year = {2017}, language = {en} } @article{BraunJainLeeetal.2017, author = {Braun, G{\´a}bor and Jain, R. and Lee, T. and Pokutta, Sebastian}, title = {Information-theoretic approximations of the nonnegative rank}, volume = {26}, journal = {Computational Complexity}, number = {1}, pages = {147 -- 197}, year = {2017}, language = {en} } @article{ChristensenKhanPokuttaetal.2017, author = {Christensen, H. and Khan, A. and Pokutta, Sebastian and Tetali, P.}, title = {Multidimensional Bin Packing and Other Related Problems: A survey}, journal = {to appear in Computer Science Review}, year = {2017}, language = {en} } @article{MartinMuellerPapeetal.2017, author = {Martin, Alex and M{\"u}ller, J. and Pape, S. and Peter, A. and Pokutta, Sebastian and Winter, T.}, title = {Pricing and clearing combinatorial markets with singleton and swap orders}, volume = {85}, journal = {Mathematical Methods of Operations Research}, number = {2}, arxiv = {http://arxiv.org/abs/1404.6546}, pages = {155 -- 177}, year = {2017}, language = {en} } @article{KnuevenOstrowskiPokutta2017, author = {Knueven, B. and Ostrowski, J. and Pokutta, Sebastian}, title = {Detecting Almost Symmetries in Graphs}, journal = {to appear in Mathematical Programming C}, year = {2017}, language = {en} } @article{BraunBrownCohenHuqetal.2017, author = {Braun, G{\´a}bor and Brown-Cohen, Jonah and Huq, Arefin and Pokutta, Sebastian and Raghavendra, Prasad and Weitz, Benjamin and Zink, Daniel}, title = {The matching problem has no small symmetric SDP}, volume = {165}, journal = {Mathematical Programming A}, number = {2}, arxiv = {http://arxiv.org/abs/1504.00703}, pages = {643 -- 662}, year = {2017}, language = {en} } @misc{ChristofConradRempelDegkwitzetal.2017, author = {Christof, J{\"u}rgen and Conrad-Rempel, Steffi and Degkwitz, Andreas and Goltz-Fellgiebel, Julia Alexandra and Happel, Hans-Gerd and Hasler, Tim and Heiss, Alexandra and Kaminsky, Uta and Kant, Oliver and Kende, Jiř{\´i} and Koch, Thorsten and Kuberek, Monika and Lohrum, Stefan and M{\"u}ller, Anja and Mutter, Moritz and Peters-Kottig, Wolfgang and Quitzsch, Nicole and Rusch, Beate and Schwidder, Jens and Stanek, Ursula and Weihe, Signe and Zeyns, Andrea}, title = {KOBV Jahresbericht 2015-2016}, volume = {2015-2016}, number = {2015-2016}, organization = {Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV)}, issn = {0934-5892}, pages = {1 -- 64}, year = {2017}, abstract = {Der KOBV-Jahresbericht informiert r{\"u}ckblickend im 2-Jahres-Rhythmus {\"u}ber die bibliothekarisch-fachlichen Entwicklungen im Verbund und die Projekte des Kooperativen Bibliotheksverbunds Berlin-Brandenburg (KOBV).}, language = {de} } @article{BernalVigerskeTrespalaciosetal.2017, author = {Bernal, David E. and Vigerske, Stefan and Trespalacios, Francisco and Grossmann, Ignacio E.}, title = {Improving the performance of DICOPT in convex MINLP problems using a feasibility pump}, journal = {Optimization Methods and Software}, year = {2017}, abstract = {The solver DICOPT is based on an outer-approximation algorithm used for solving mixed- integer nonlinear programming (MINLP) problems. This algorithm is very effective for solving some types of convex MINLPs. However, there are certain problems that are diffcult to solve with this algorithm. One of these problems is when the nonlinear constraints are so restrictive that the nonlinear subproblems produced by the algorithm are infeasible. This problem is addressed in this paper with a feasibility pump algorithm, which modifies the objective function in order to efficiently find feasible solutions. It has been implemented as a preprocessing algorithm for DICOPT. Computational comparisons with previous versions of DICOPT and other MINLP solvers on a set of convex MINLPs demonstrate the effectiveness of the proposed algorithm in terms of solution quality and solving time.}, language = {en} } @misc{SakuraiHegeKuhnetal.2017, author = {Sakurai, Daisuke and Hege, Hans-Christian and Kuhn, Alexander and Rust, Henning and Kern, Bastian and Breitkopf, Tom-Lukas}, title = {An Application-Oriented Framework for Feature Tracking in Atmospheric Sciences}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-72617}, year = {2017}, abstract = {In atmospheric sciences, sizes of data sets grow continuously due to increasing resolutions. A central task is the comparison of spatiotemporal fields, to assess different simulations and to compare simulations with observations. A significant information reduction is possible by focusing on geometric-topological features of the fields or on derived meteorological objects. Due to the huge size of the data sets, spatial features have to be extracted in time slices and traced over time. Fields with chaotic component, i.e. without 1:1 spatiotemporal correspondences, can be compared by looking upon statistics of feature properties. Feature extraction, however, requires a clear mathematical definition of the features - which many meteorological objects still lack. Traditionally, object extractions are often heuristic, defined only by implemented algorithms, and thus are not comparable. This work surveys our framework designed for efficient development of feature tracking methods and for testing new feature definitions. The framework supports well-established visualization practices and is being used by atmospheric researchers to diagnose and compare data.}, language = {en} } @article{ChraparyDalitzNeunetal.2017, author = {Chrapary, Hagen and Dalitz, Wolfgang and Neun, Winfried and Sperber, Wolfram}, title = {Design, Concepts, and State of the Art of the swMATH Service}, volume = {11}, journal = {Mathematics in Computer Science}, number = {3-4}, doi = {10.1007/s11786-017-0305-5}, pages = {469 -- 481}, year = {2017}, abstract = {In this paper, the concepts and design for an efficient information service for mathematical software and further mathematical research data are presented. The publication-based approach and the web-based approach are the main building blocks of the service and will be discussed. Heuristic methods are used for identification, extraction, and ranking of information about software and other mathematical research data. The methods provide not only information about the research data but also link software and mathematical research data to the scientific context.}, language = {en} } @article{SeeberConradHoppeetal.2017, author = {Seeber, L. and Conrad, Tim and Hoppe, Christian and Obermeier, Patrick and Chen, X. and Karsch, K. and Muehlhans, S. and Tief, Franziska and Boettcher, Sindy and Diedrich, S. and Schweiger, Brunhilde and Rath, Barbara}, title = {Educating parents about the vaccination status of their children: A user-centered mobile application}, volume = {5}, journal = {Preventive Medicine Reports}, doi = {10.1016/j.pmedr.2017.01.002}, pages = {241 -- 250}, year = {2017}, abstract = {Parents are often uncertain about the vaccination status of their children. In times of vaccine hesitancy, vaccination programs could benefit from active patient participation. The Vaccination App (VAccApp) was developed by the Vienna Vaccine Safety Initiative, enabling parents to learn about the vaccination status of their children, including 25 different routine, special indication and travel vaccines listed in the WHO Immunization Certificate of Vaccination (WHO-ICV). Between 2012 and 2014, the VAccApp was validated in a hospital-based quality management program in Berlin, Germany, in collaboration with the Robert Koch Institute. Parents of 178 children were asked to transfer the immunization data of their children from the WHO-ICV into the VAccApp. The respective WHO-ICV was photocopied for independent, professional data entry (gold standard). Demonstrating the status quo in vaccine information reporting, a Recall Group of 278 parents underwent structured interviews for verbal immunization histories, without the respective WHO-ICV. Only 9\% of the Recall Group were able to provide a complete vaccination status; on average 39\% of the questions were answered correctly. Using the WHO-ICV with the help of the VAccApp resulted in 62\% of parents providing a complete vaccination status; on average 95\% of the questions were answered correctly. After using the VAccApp, parents were more likely to remember key aspects of the vaccination history. User-friendly mobile applications empower parents to take a closer look at the vaccination record, thereby taking an active role in providing accurate vaccination histories. Parents may become motivated to ask informed questions and to keep vaccinations up-to-date.}, language = {en} } @article{ConradGenzelCvetkovicetal.2017, author = {Conrad, Tim and Genzel, Martin and Cvetkovic, Nada and Wulkow, Niklas and Vybiral, Jan and Kutyniok, Gitta and Sch{\"u}tte, Christof}, title = {Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data}, volume = {18}, journal = {BMC Bioinformatics}, number = {160}, doi = {10.1186/s12859-017-1565-4}, pages = {1 -- 20}, year = {2017}, abstract = {Motivation: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested how MS spectra dier between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust to noise and outliers, and the identied feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA), based on the theory of Compressed Sensing that allows to identify a minimal discriminating set of features from mass spectrometry data-sets. We show how our method performs on artificial and real-world data-sets.}, language = {en} } @article{BorongCannistraciConrad2017, author = {Borong, Shao and Cannistraci, Carlo and Conrad, Tim}, title = {Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data}, volume = {3}, journal = {Genomics and Computational Biology}, number = {3}, doi = {http://dx.doi.org/10.18547/gcb.2017.vol3.iss3.e57}, pages = {1 -- 13}, year = {2017}, abstract = {Epithelial mesenchymal transition (EMT) process has been shown as highly relevant to cancer prognosis. However, although different biological network-based biomarker identification methods have been proposed to predict cancer prognosis, EMT network has not been directly used for this purpose. In this study, we constructed an EMT regulatory network consisting of 87 molecules and tried to select features that are useful for prognosis prediction in Lung Adenocarcinoma (LUAD). To incorporate multiple molecular profiles, we obtained four types of molecular data including mRNA-Seq, copy number alteration (CNA), DNA methylation, and miRNA-Seq data from The Cancer Genome Atlas. The data were mapped to the EMT network in three alternative ways: mRNA-Seq and miRNA-Seq, DNA methylation, and CNA and miRNA-Seq. Each mapping was employed to extract five different sets of features using discretization and network-based biomarker identification methods. Each feature set was then used to predict prognosis with SVM and logistic regression classifiers. We measured the prediction accuracy with AUC and AUPR values using 10 times 10-fold cross validation. For a more comprehensive evaluation, we also measured the prediction accuracies of clinical features, EMT plus clinical features, randomly picked 87 molecules from each data mapping, and using all molecules from each data type. Counter-intuitively, EMT features do not always outperform randomly selected features and the prediction accuracies of the five feature sets are mostly not significantly different. Clinical features are shown to give the highest prediction accuracies. In addition, the prediction accuracies of both EMT features and random features are comparable as using all features (more than 17,000) from each data type.}, language = {en} } @inproceedings{JayrannejadConrad2017, author = {Jayrannejad, Fahrnaz and Conrad, Tim}, title = {Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining}, booktitle = {Springer Lecture Notes in Artificial Intelligence}, pages = {studi}, year = {2017}, abstract = {Recent advances in -omics technology has yielded in large data-sets in many areas of biology, such as mass spectrometry based proteomics. However, analyzing this data is still a challenging task mainly due to the very high dimensionality and high noise content of the data. One of the main objectives of the analysis is the identification of relevant patterns (or features) which can be used for classification of new samples to healthy or diseased. So, a method is required to find easily interpretable models from this data. To gain the above mentioned goal, we have adapted the disjunctive association rule mining algorithm, TitanicOR, to identify emerging patterns from our mass spectrometry proteomics data-sets. Comparison to five state-of-the-art methods shows that our method is advantageous them in terms of identifying the inter-dependency between the features and the TP-rate and precision of the features selected. We further demonstrate the applicability of our algorithm to one previously published clinical data-set.}, language = {en} } @misc{Jeschke2017, type = {Master Thesis}, author = {Jeschke, Bj{\"o}rn-Marcel}, title = {Alternativen zum Dijkstra Algorithmus in der (Nah-) Verkehrsoptimierung}, pages = {74}, year = {2017}, abstract = {In dieser Arbeit betrachten wir das Problem, f{\"u}r den Fahrplan eines (Nah-) Verkehrsnetzes schnellste Wege zu berechnen. Da die Verkehrsmittel zu unterschiedlichen Zeiten von den einzelnen Haltestellen/Bahnh{\"o}fen abfahren, kann das Problem nicht ohne Weiteres mit einem „statischen" Graphen modelliert werden. Es gibt zwei unterschiedliche Ans{\"a}tze f{\"u}r dieses zeitabh{\"a}ngige Problem: Erstens k{\"o}nnen die verschiedenen An-/Abfahrtereignisse an einem Halt durch „Kopien" dargestellt werden, das ist das zeit-expandierte Modell. Zweitens k{\"o}nnen die Gewichte der Kanten zeitabh{\"a}ngig sein, das ist das zeitabh{\"a}ngige Modell. Wir untersuchen in dieser Arbeit, wie der „klassische" Dijkstra-Algorithmus und der A* Algorithmus mit einer geeigneten Heuristik im Vergleich abschneiden. Die gew{\"a}hlte Heuristik ist der Abstand zum Zielknoten, wenn die Abfahrtszeiten ignoriert werden. Nach unseren Untersuchungen zeigt sich, dass der A* Algorithmus dem Dijkstra-Algorithmus weit {\"u}berlegen ist f{\"u}r gen{\"u}gend große Nahverkehrsnetze. Wir testen anhand der echten Verkehrsnetze von Berlin und Aachen. Unsere Berechnungen zeigen, dass die gew{\"a}hlte Heuristik besonders gut ist f{\"u}r Start- und Zielknoten, welche unabh{\"a}ngig von ihrer Distanz nur 1-2 verschiedene m{\"o}gliche k{\"u}rzeste Pfade f{\"u}r alle Zeitschritte haben. Dort ist der A* Algorithmus bis zu 20-mal schneller. Dies kommt aber nicht h{\"a}ufig in unseren Testinstanzen vor. Die einzelnen Laufzeitvergleich zeigen, dass der A* Algorithmus durchschnittlich 7-mal so schnell ist wie der Dikstra-Algorithmus.}, language = {de} } @article{ApprichDieterichHoelligetal.2017, author = {Apprich, Christian and Dieterich, Annegret and H{\"o}llig, Klaus and Nava-Yazdani, Esfandiar}, title = {Cubic spline approximation of a circle with maximal smoothness and accuracy}, volume = {56}, journal = {Computer Aided Geometric Design}, publisher = {Elsevier B.V.}, doi = {10.1016/j.cagd.2017.05.001}, pages = {1 -- 3}, year = {2017}, abstract = {We construct cubic spline approximations of a circle which are four times continuously differentiable and converge with order six.}, language = {en} } @misc{SahuDillMukhopadyayetal.2017, author = {Sahu, Manish and Dill, Sabrina and Mukhopadyay, Anirban and Zachow, Stefan}, title = {Surgical Tool Presence Detection for Cataract Procedures}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-69110}, year = {2017}, abstract = {This article outlines the submission to the CATARACTS challenge for automatic tool presence detection [1]. Our approach for this multi-label classification problem comprises labelset-based sampling, a CNN architecture and temporal smothing as described in [3], which we call ZIB-Res-TS.}, language = {en} } @article{D'AndreagiovanniMettNardinetal.2017, author = {D'Andreagiovanni, Fabio and Mett, Fabian and Nardin, Antonella and Pulaj, Jonad}, title = {Integrating LP-guided variable fixing with MIP heuristics in the robust design of hybrid wired-wireless FTTx access networks}, volume = {61}, journal = {Applied Soft Computing}, doi = {10.1016/j.asoc.2017.07.018}, pages = {1074 -- 1087}, year = {2017}, abstract = {This study investigates how to model and solve the problem of optimally designing FTTx telecommunications access networks integrating wired and wireless technologies, while taking into account the uncertainty of wireless signal propagation. We propose an original robust optimization model for the related robust 3-architecture Connected Facility Location problem, which includes additional variables and constraints to model wireless signal coverage represented through signal-to-interference ratios. Since the resulting robust problem can prove very challenging even for a modern state-of-the art optimization solver, we propose to solve it by an original primal heuristic that combines a probabilistic variable fixing procedure, guided by peculiar Linear Programming relaxations, with a Mixed Integer Programming heuristic, based on an exact very large neighborhood search. A numerical study carried out on a set of realistic instances show that our heuristic can find solutions of much higher quality than a state-of-the-art solver.}, language = {en} } @phdthesis{Reuther2017, author = {Reuther, Markus}, title = {Mathematical Optimization of Rolling Stock Rotations}, year = {2017}, abstract = {We show how to optimize rolling stock rotations that are required for the operation of a passenger timetable. The underlying mathematical ptimization problem is called rolling stock rotation problem (RSRP) and the leitmotiv of the thesis is RotOR, i.e., a highly integrated optimization algorithm for the RSRP. RotOR is used by DB Fernverkehr AG (DBF) in order to optimize intercity express (ICE) rotations for the European high-speed network. In this application, RSRPs have to be solved which (A) require many different aspects to be simultaneously considered, (B) are typically of large scale, and (C) include constraints that have a difficult combinatorial structure. This thesis suggests answers to these issues via the following concepts. (A) The main model, which RotOR uses, relies on a hypergraph. The hypergraph provides an easy way to model manifold industrial railway requirements in great detail. This includes well known vehicle composition requirements as well as relatively unexplored regularity stipulations. At the same time, the hypergraph directly leads to a mixed-integer programming (MIP) model for the RSRP. (B) The main algorithmic ingredient to solve industrial instances of the RSRP is a coarse-to-fine (C2F) column generation procedure. In this approach, the hypergraph is layered into coarse and fine layers that distinguish different levels of detail of the RSRP. The coarse layers are algorithmically utilized while pricing fine columns until proven optimality. Initially, the C2F approach is presented in terms of pure linear programming in order to provide an interface for other applications. (C) Rolling stock rotations have to comply to resource constraints in order to ensure, e.g., enough maintenance inspections along the rotations. These constraints are computationally hard, but are well known in the literature on the vehicle routing problem (VRP). We define an interface problem in order to bridge between the RSRP and the VRP and derive a straightforward algorithmic concept, namely regional search (RS), from their common features and, moreover, differences. Our RS algorithms show promising results for classical VRPs and RSRPs. In the first part of the thesis we present these concepts, which encompass its main mathematical contribution. The second part explains all modeling and solving components of RotOR that turn out to be essential in its industrial application. The thesis concludes with a solution to a complex re-optimization RSRP that RotOR has computed successfully for DBF. In this application all ICE vehicles of the ICE-W fleets of DBF had to be redirected past a construction site on a high-speed line in the heart of Germany.}, language = {en} } @article{Sullivan2017, author = {Sullivan, T. J.}, title = {Well-posed Bayesian inverse problems and heavy-tailed stable quasi-Banach space priors}, volume = {11}, journal = {Inverse Problems and Imaging}, number = {5}, arxiv = {http://arxiv.org/abs/1605.05898}, doi = {10.3934/ipi.2017040}, pages = {857 -- 874}, year = {2017}, language = {en} } @inproceedings{Sullivan2017, author = {Sullivan, T. J.}, title = {Well-posedness of Bayesian inverse problems in quasi-Banach spaces with stable priors}, volume = {17}, booktitle = {88th Annual Meeting of the International Association of Applied Mathematics and Mechanics (GAMM), Weimar 2017}, number = {1}, arxiv = {http://arxiv.org/abs/1710.05610}, doi = {10.1002/pamm.201710402}, pages = {871 -- 874}, year = {2017}, language = {en} } @article{JayrannejadConrad2017, author = {Jayrannejad, Fahrnaz and Conrad, Tim}, title = {Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining}, journal = {Springer Lecture Notes in Artificial Intelligence}, year = {2017}, abstract = {Recent advances in -omics technology has yielded in large data-sets in many areas of biology, such as mass spectrometry based proteomics. However, analyzing this data is still a challenging task mainly due to the very high dimensionality and high noise content of the data. One of the main objectives of the analysis is the identification of relevant patterns (or features) which can be used for classification of new samples to healthy or diseased. So, a method is required to find easily interpretable models from this data. To gain the above mentioned goal, we have adapted the disjunctive association rule mining algorithm, TitanicOR, to identify emerging patterns from our mass spectrometry proteomics data-sets. Comparison to five state-of-the-art methods shows that our method is advantageous them in terms of identifying the inter-dependency between the features and the TP-rate and precision of the features selected. We further demonstrate the applicability of our algorithm to one previously published clinical data-set.}, language = {en} } @article{ShaoCannistraciConrad2017, author = {Shao, Borong and Cannistraci, Carlo Vittorio and Conrad, Tim}, title = {Epithelial Mesenchymal Transition Network-Based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data}, volume = {3}, journal = {Genomics and Computational Biology}, number = {3}, doi = {10.18547/gcb.2017.vol3.iss3.e57}, pages = {e57}, year = {2017}, abstract = {Epithelial mesenchymal transition (EMT) process has been shown as highly relevant to cancer prognosis. However, although different biological network-based biomarker identification methods have been proposed to predict cancer prognosis, EMT network has not been directly used for this purpose. In this study, we constructed an EMT regulatory network consisting of 87 molecules and tried to select features that are useful for prognosis prediction in Lung Adenocarcinoma (LUAD). To incorporate multiple molecular profiles, we obtained four types of molecular data including mRNA-Seq, copy number alteration (CNA), DNA methylation, and miRNA-Seq data from The Cancer Genome Atlas. The data were mapped to the EMT network in three alternative ways: mRNA-Seq and miRNA-Seq, DNA methylation, and CNA and miRNA-Seq. Each mapping was employed to extract five different sets of features using discretization and network-based biomarker identification methods. Each feature set was then used to predict prognosis with SVM and logistic regression classifiers. We measured the prediction accuracy with AUC and AUPR values using 10 times 10-fold cross validation. For a more comprehensive evaluation, we also measured the prediction accuracies of clinical features, EMT plus clinical features, randomly picked 87 molecules from each data mapping, and using all molecules from each data type. Counter-intuitively, EMT features do not always outperform randomly selected features and the prediction accuracies of the five feature sets are mostly not significantly different. Clinical features are shown to give the highest prediction accuracies. In addition, the prediction accuracies of both EMT features and random features are comparable as using all features (more than 17,000) from each data type.}, language = {en} } @article{RathConradMylesetal.2017, author = {Rath, Barbara and Conrad, Tim and Myles, Puja and Alchikh, Maren and Ma, Xiaolin and Hoppe, Christian and Tief, Franziska and Chen, Xi and Obermeier, Patrick and Kisler, Bron and Schweiger, Brunhilde}, title = {Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials}, volume = {15}, journal = {Expert Review of Anti-infective Therapy}, number = {6}, doi = {10.1080/14787210.2017.1295847}, pages = {545 -- 568}, year = {2017}, abstract = {Introduction: Influenza-Like Illness is a leading cause of hospitalization in children. Disease burden due to influenza and other respiratory viral infections is reported on a population level, but clinical scores measuring individual changes in disease severity are urgently needed. Areas covered: We present a composite clinical score allowing individual patient data analyses of disease severity based on systematic literature review and WHO-criteria for uncomplicated and complicated disease. The 22-item ViVI Disease Severity Score showed a normal distribution in a pediatric cohort of 6073 children aged 0-18 years (mean age 3.13; S.D. 3.89; range: 0 to 18.79). Expert commentary: The ViVI Score was correlated with risk of antibiotic use as well as need for hospitalization and intensive care. The ViVI Score was used to track children with influenza, respiratory syncytial virus, human metapneumovirus, human rhinovirus, and adenovirus infections and is fully compliant with regulatory data standards. The ViVI Disease Severity Score mobile application allows physicians to measure disease severity at the point-of care thereby taking clinical trials to the next level.}, language = {en} } @inproceedings{PapazovHege2017, author = {Papazov, Chavdar and Hege, Hans-Christian}, title = {Blue-noise Optimized Point Sets Based on Procrustes Analysis}, booktitle = {SIGGRAPH Asia 2017 Technical Briefs}, doi = {10.1145/3145749.3149442}, pages = {20:1 -- 20:4}, year = {2017}, language = {en} } @misc{WeberDurmazSabrietal.2017, author = {Weber, Marcus and Durmaz, Vedat and Sabri, Peggy and Reidelbach, Marco}, title = {Supplementary simulation data for Science Manuscript ai8636}, doi = {10.12752/5.MWB.1.0}, year = {2017}, abstract = {The simulation data has been produced by Vedat Durmaz, Peggy Sabri and Marco Reidelbach inside the "Computational Molecular Design" Group headed by Marcus Weber at Zuse-Institut Berlin, Takustr. 7, D-14195 Berlin, Germany. The file contains classical simulation data for different fentanyl derivates in the MOR binding pocket at different pHs. It also includes instruction files for quantum-chemical pKa-value estimations and a description of how we derived the pKa-values from the Gaussian09 log-files.}, language = {en} } @phdthesis{Pulaj2017, author = {Pulaj, Jonad}, title = {Cutting Planes for Union-Closed Families}, year = {2017}, abstract = {Frankl's (union-closed sets) conjecture states that for any nonempty finite union-closed (UC) family of distinct sets there exists an element in at least half of the sets. Poonen's Theorem characterizes the existence of weights which determine whether a given UC family ensures Frankl's conjecture holds for all UC families which contain it. The weight systems are nontrivial to identify for a given UC family, and methods to determine such weight systems have led to several other open questions and conjectures regarding structures in UC families. We design a cutting-plane method that computes the explicit weights which imply the existence conditions of Poonen's Theorem using computational integer programming coupled with redundant verification routines that ensure correctness. We find over one hundred previously unknown families of sets which ensure Frankl's conjecture holds for all families that contain any of them. This improves significantly on all previous results of the kind. Our framework allows us to answer several open questions and conjectures regarding structural properties of UC families, including proving the 3-sets conjecture of Morris from 2006 which characterizes the minimum number of 3-sets that ensure Frankl's conjecture holds for all families that contain them. Furthermore, our method provides a general algorithmic road-map for improving other known results and uncovering structures in UC families.}, language = {en} } @misc{Schubert2017, type = {Master Thesis}, author = {Schubert, Christoph}, title = {Multi-Level Lookahead Branching}, year = {2017}, language = {en} } @masterthesis{Wischlinsky2017, type = {Bachelor Thesis}, author = {Wischlinsky, William}, title = {Feasibility-based bound tightening via linear programming}, year = {2017}, language = {en} } @inproceedings{CheungGleixnerSteffy2017, author = {Cheung, Kevin K. H. and Gleixner, Ambros and Steffy, Daniel}, title = {Verifying Integer Programming Results}, volume = {10328}, booktitle = {F. Eisenbrand and J. Koenemann, eds., Integer Programming and Combinatorial Optimization: 19th International Conference, IPCO 2017}, doi = {10.1007/978-3-319-59250-3_13}, pages = {148 -- 160}, year = {2017}, abstract = {Software for mixed-integer linear programming can return incorrect results for a number of reasons, one being the use of inexact floating-point arithmetic. Even solvers that employ exact arithmetic may suffer from programming or algorithmic errors, motivating the desire for a way to produce independently verifiable certificates of claimed results. Due to the complex nature of state-of-the-art MIP solution algorithms, the ideal form of such a certificate is not entirely clear. This paper proposes such a certificate format designed with simplicity in mind, which is composed of a list of statements that can be sequentially verified using a limited number of inference rules. We present a supplementary verification tool for compressing and checking these certificates independently of how they were created. We report computational results on a selection of MIP instances from the literature. To this end, we have extended the exact rational version of the MIP solver SCIP to produce such certificates.}, language = {en} } @article{VierhausFuegenschuhGottwaldetal.2017, author = {Vierhaus, Ingmar and F{\"u}genschuh, Armin and Gottwald, Robert Lion and Gr{\"o}sser, Stefan}, title = {Using white-box nonlinear optimization methods in system dynamics policy improvement}, volume = {33}, journal = {System Dynamics Review}, number = {2}, doi = {10.1002/sdr.1583}, pages = {138 -- 168}, year = {2017}, abstract = {We present a new strategy for the direct optimization of the values of policy functions. This approach is particularly well suited to model actors with a global perspective on the system and relies heavily on modern mathematical white-box optimization methods. We demonstrate our strategy on two classical models: market growth and World2. Each model is first transformed into an optimization problem by defining how the actor can influence the models' dynamics and by choosing objective functions to measure improvements. To improve comparability between different runs, we also introduce a comparison measure for possible interventions. We solve the optimization problems, discuss the resulting policies and compare them to the existing results from the literature. In particular, we present a run of the World2 model which significantly improves the published "towards a global equilibrium" run with equal cost of intervention.}, language = {en} } @inproceedings{YokoyamaShinanoWakayamaetal.2017, author = {Yokoyama, Ryohei and Shinano, Yuji and Wakayama, Yuki and Wakui, Tetsuya}, title = {Multiobjective Optimal Design of a Gas Turbine Cogeneration Plant by a Revised Hierarchical Optimization Method}, volume = {3}, booktitle = {ASME Turbo Expo 2017: Turbomachinery Technical Conference and Exposition}, doi = {doi:10.1115/GT2017-64296}, pages = {1 -- 14}, year = {2017}, abstract = {To attain the highest performance of energy supply systems, it is necessary to rationally determine design specifications in consideration of operational strategies corresponding to energy demands. Mixed-integer linear programming (MILP) approaches have been applied widely to such optimal design problems. A MILP method utilizing the hierarchical relationship between design and operation variables have been proposed to solve them efficiently. However, it cannot necessarily be effective to multi-objective optimal design problems because of the existence of a large number of competing design candidates. In this paper, the hierarchical MILP method is revised from the viewpoint of computation efficiency so that it can be applied practically to multi-objective optimal design problems. At the lower level, the order of the optimal operation problems to be solved is changed based on incumbents obtained previously to increase a lower bound for the optimal value of the combined objective function and reduce the number of the optimal operation problems to be solved. At the upper level, a lower bound for the optimal value of the combined objective function is incorporated into the solution method to reduce the number of the design candidates to be generated. This revised hierarchical MILP method is applied to a multiobjective optimal design of a gas turbine cogeneration plant, and its validity and effectiveness are clarified.}, language = {en} } @article{Dierkes2017, author = {Dierkes, Thomas}, title = {Ist die Umsetzung der Open-Access-Komponente in Allianz-Lizenzvertr{\"a}gen wirklich so kompliziert?}, volume = {37}, journal = {ABI Technik}, number = {3}, doi = {10.1515/abitech-2017-0051}, pages = {237}, year = {2017}, abstract = {Thomas Dierkes ist promovierter Mathematiker und als Entwickler beim Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) am Zuse-Institut Berlin (ZIB) t{\"a}tig. Er arbeitet dort an der Entwicklung einer „Datendrehscheibe" f{\"u}r die Umsetzung der Open-Access-Komponente in Allianz-Lizenzen. Er beantwortet die aktuelle Abi Technikfrage: „Ist die Umsetzung der Open-Access-Komponente in Allianz-Lizenzvertr{\"a}gen wirklich so kompliziert?"}, language = {de} } @inproceedings{GottwaldMaherShinano2017, author = {Gottwald, Robert Lion and Maher, Stephen J. and Shinano, Yuji}, title = {Distributed Domain Propagation}, volume = {75}, booktitle = {16th International Symposium on Experimental Algorithms (SEA 2017)}, doi = {10.4230/LIPIcs.SEA.2017.6}, pages = {6:1 -- 6:11}, year = {2017}, abstract = {Portfolio parallelization is an approach that runs several solver instances in parallel and terminates when one of them succeeds in solving the problem. Despite its simplicity, portfolio parallelization has been shown to perform well for modern mixed-integer programming (MIP) and boolean satisfiability problem (SAT) solvers. Domain propagation has also been shown to be a simple technique in modern MIP and SAT solvers that effectively finds additional domain reductions after the domain of a variable has been reduced. In this paper we introduce distributed domain propagation, a technique that shares bound tightenings across solvers to trigger further domain propagations. We investigate its impact in modern MIP solvers that employ portfolio parallelization. Computational experiments were conducted for two implementations of this parallelization approach. While both share global variable bounds and solutions, they communicate differently. In one implementation the communication is performed only at designated points in the solving process and in the other it is performed completely asynchronously. Computational experiments show a positive performance impact of communicating global variable bounds and provide valuable insights in communication strategies for parallel solvers.}, language = {en} } @masterthesis{Clausecker2017, type = {Bachelor Thesis}, author = {Clausecker, Robert}, title = {Notes on the Construction of Tablebases}, year = {2017}, language = {en} } @inproceedings{SeblanyHombergVincensetal.2017, author = {Seblany, Feda and Homberg, Ulrike and Vincens, Eric and Winkler, Paul and Witt, Karl Josef}, title = {Merging criteria for the definition of a local pore and the CSD computation of granular materials}, booktitle = {Proceedings of the 25th meeting of the Working Group on Internal Erosion in embankment dams and their foundations}, publisher = {Deltares}, address = {Delft, Netherlands}, isbn = {978-90-827468-1-5 | 978-90-827468-0-8}, pages = {150 -- 159}, year = {2017}, language = {en} } @phdthesis{Schweiger2017, author = {Schweiger, Jonas}, title = {Exploiting structure in non-convex quadratic optimization and gas network planning under uncertainty}, pages = {411}, year = {2017}, abstract = {The amazing success of computational mathematical optimization over the last decades has been driven more by insights into mathematical structures than by the advance of computing technology. In this vein, we address applications, where nonconvexity in the model and uncertainty in the data pose principal difficulties. The first part of the thesis deals with non-convex quadratic programs. Branch\&Bound methods for this problem class depend on tight relaxations. We contribute in several ways: First, we establish a new way to handle missing linearization variables in the well-known Reformulation-Linearization-Technique (RLT). This is implemented into the commercial software CPLEX. Second, we study the optimization of a quadratic objective over the standard simplex or a knapsack constraint. These basic structures appear as part of many complex models. Exploiting connections to the maximum clique problem and RLT, we derive new valid inequalities. Using exact and heuristic separation methods, we demonstrate the impact of the new inequalities on the relaxation and the global optimization of these problems. Third, we strengthen the state-of-the-art relaxation for the pooling problem, a well-known non-convex quadratic problem, which is, for example, relevant in the petrochemical industry. We propose a novel relaxation that captures the essential non-convex structure of the problem but is small enough for an in-depth study. We provide a complete inner description in terms of the extreme points as well as an outer description in terms of inequalities defining its convex hull (which is not a polyhedron). We show that the resulting valid convex inequalities significantly strengthen the standard relaxation of the pooling problem. The second part of this thesis focuses on a common challenge in real world applications, namely, the uncertainty entailed in the input data. We study the extension of a gas transport network, e.g., from our project partner Open Grid Europe GmbH. For a single scenario this maps to a challenging non-convex MINLP. As the future transport patterns are highly uncertain, we propose a robust model to best prepare the network operator for an array of scenarios. We develop a custom decomposition approach that makes use of the hierarchical structure of network extensions and the loose coupling between the scenarios. The algorithm used the single-scenario problem as black-box subproblem allowing the generalization of our approach to problems with the same structure. The scenario-expanded version of this problem is out of reach for today's general-purpose MINLP solvers. Yet our approach provides primal and dual bounds for instances with up to 256 scenarios and solves many of them to optimality. Extensive computational studies show the impact of our work.}, language = {en} } @inproceedings{MuellerGoetschelWeiseretal.2017, author = {M{\"u}ller, Jan and G{\"o}tschel, Sebastian and Weiser, Martin and Maierhofer, Christiane}, title = {Thermografie mit optimierter Anregung f{\"u}r die quantitative Untersuchung von Delaminationen in kohlenstofffaserverst{\"a}rkten Kunststoffen}, booktitle = {NDT.net Proc. DGZfP 2017}, year = {2017}, abstract = {Da kohlenstofffaserverst{\"a}rkte Kunststoffe (CFK) in anspruchsvollen sicherheitsrelevanten Einsatzgebieten wie im Automobilbau und in der Luftfahrt eingesetzt werden, besteht ein zunehmender Bedarf an zerst{\"o}rungsfreien Pr{\"u}fmethoden. Ziel ist die Gew{\"a}hrleistung der Sicherheit und Zuverl{\"a}ssigkeit der eingesetzten Bauteile. Aktive Thermografieverfahren erm{\"o}glichen die effiziente Pr{\"u}fung großer Fl{\"a}chen mit hoher Aufl{\"o}sung in wenigen Arbeitsschritten. Ein wichtiges Teilgebiet der Pr{\"u}fungen ist die Ortung und Charakterisierung von Delaminationen, die sowohl bereits in der Fertigung als auch w{\"a}hrend der Nutzung eines Bauteils auftreten k{\"o}nnen, und dessen strukturelle Integrit{\"a}t schw{\"a}chen. ;In diesem Beitrag werden CFK-Strukturen mit k{\"u}nstlichen und nat{\"u}rlichen Delaminationen mit Hilfe unterschiedlich zeitlich modulierter Strahlungsquellen experimentell untersucht. Verwendet werden dabei Anregungen mit Blitzlampen und mit frequenzmodulierten Halogenlampen. Mittels Filterfunktionen im Zeit- und Frequenzbereich wird das Kontrast-zu-Rausch-Verh{\"a}ltnis (CNR) der detektierten Fehlstellen optimiert. Verglichen werden anschließend die Nachweisempfindlichkeit, das CNR und die Ortsaufl{\"o}sung der zu charakterisierenden Delaminationen f{\"u}r die unterschiedlichen Anregungs- und Auswertungstechniken. Erg{\"a}nzt werden die Experimente durch numerische Simulationen des dreidimensionalen W{\"a}rmetransportes.}, language = {de} } @misc{Wulkow2017, type = {Master Thesis}, author = {Wulkow, Niklas}, title = {Modelling the Spread of Innovations by a Markov Process in a Bayesian Framework}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66869}, year = {2017}, language = {en} }