@misc{BuesingD'AndreagiovanniRaymond, author = {B{\"u}sing, Christina and D'Andreagiovanni, Fabio and Raymond, Annie}, title = {0-1 Multiband Robust Optimization}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-44093}, abstract = {We provide an overview of new theoretical results that we obtained while further investigating multiband robust optimization, a new model for robust optimization that we recently proposed to tackle uncertainty in mixed-integer linear programming. This new model extends and refines the classical Gamma-robustness model of Bertsimas and Sim and is particularly useful in the common case of arbitrary asymmetric distributions of the uncertainty. Here, we focus on uncertain 0-1 programs and we analyze their robust counterparts when the uncertainty is represented through a multiband set. Our investigations were inspired by the needs of our industrial partners in the research project ROBUKOM.}, language = {en} } @misc{Shestakov, type = {Master Thesis}, author = {Shestakov, Alexey}, title = {A Deep Learning Method for Automated Detection of Meniscal Tears in Meniscal Sub-Regions in 3D MRI Data}, pages = {96}, abstract = {This work presents a fully automated pipeline, centered around a deep neural network, as well as a method to train that network in an efficient manner, that enables accurate detection of lesions in meniscal anatomical subregions. The network architecture is based on a transformer encoder/decoder. It is trained on DESS and tuned on IW TSE 3D MRI scans sourced from the Osteoarthritis Initiative. Furthermore, it is trained in a multilabel, and multitask fashion, using an auxiliary detection head. The former enables implicit localisation of meniscal defects, that to the best of my knowledge, has not yet been reported elsewhere. The latter enables efficient learning on the entire 3D MRI volume. Thus, the proposed method does not require any expert knowledge at inference. Aggregated inference results from two datasets resulted in an overall AUCROC result of 0.90, 0.91 and 0.93 for meniscal lesion detection anywhere in the knee, in medial and in lateral menisci respectively. These results compare very well to the related work, even though only a fraction of the data has been utilized. Clinical applicability and benefit is yet to be determined.}, language = {en} } @misc{D'AndreagiovanniKrolikowskiPulaj, author = {D'Andreagiovanni, Fabio and Krolikowski, Jonatan and Pulaj, Jonad}, title = {A hybrid primal heuristic for Robust Multiperiod Network Design}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-44081}, abstract = {We investigate the Robust Multiperiod Network Design Problem, a generalization of the classical Capacitated Network Design Problem that additionally considers multiple design periods and provides solutions protected against traffic uncertainty. Given the intrinsic difficulty of the problem, which proves challenging even for state-of-the art commercial solvers, we propose a hybrid primal heuristic based on the combination of ant colony optimization and an exact large neighborhood search. Computational experiments on a set of realistic instances from the SNDlib show that our heuristic can find solutions of extremely good quality with low optimality gap.}, language = {en} } @misc{PaskinBaumDeanetal., author = {Paskin, Martha and Baum, Daniel and Dean, Mason N. and von Tycowicz, Christoph}, title = {A Kendall Shape Space Approach to 3D Shape Estimation from 2D Landmarks -- Source Code and Data}, doi = {10.12752/8730}, abstract = {Source code and novel dataset of basking shark head skeletons facilitating the reproduction of the results presented in 'A Kendall Shape Space Approach to 3D Shape Estimation from 2D Landmarks' - ECCV 2022.}, language = {en} } @misc{BuesingD'Andreagiovanni, author = {B{\"u}sing, Christina and D'Andreagiovanni, Fabio}, title = {A new theoretical framework for Robust Optimization under multi-band uncertainty}, issn = {1438-0064}, doi = {10.1007/978-3-319-00795-3_17}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42644}, abstract = {We provide an overview of our main results about studying Linear Programming Problems whose coefficient matrix is subject to uncertainty and the uncertainty is modeled through a multi-band set. Such an uncertainty set generalizes the classical one proposed by Bertsimas and Sim and is particularly suitable in the common case of arbitrary non-symmetric distributions of the parameters. Our investigations were inspired by practical needs of our industrial partner in ongoing projects with focus on the design of robust telecommunications networks.}, language = {en} } @misc{Wolf, author = {Wolf, Thomas}, title = {A Study of Genetic Algorithms solving a combinatorial Puzzle}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-3445}, number = {SC-98-01}, abstract = {The suitability of Genetic Algorithms (GAs) to solve a combinatorial problem with only one solution is investigated. The dependence of the performance is studied for GA-hard and GA-soft fitness functions, both with a range of different parameter values and different encodings.}, language = {en} } @misc{PfeufferWerner, author = {Pfeuffer, Frank and Werner, Axel}, title = {Adaptive telecommunication network operation with a limited number of reconfigurations}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-55547}, abstract = {Rising traffic in telecommunication networks lead to rising energy costs for the network operators. Meanwhile, increased flexibility of the networking hardware may help to realize load-adaptive operation of the networks to cut operation costs. To meet network operators' concerns over stability, we propose to switch network configurations only a limited number of times per day. We present a method for the integrated computation of optimal switching times and network configurations that alternatingly solves mixed-integer programs and constrained shortest cycle problems in a certain graph. Similarly to the Branch \& Bound Algorithm, it uses lower and upper bounds on the optimum value and allows for pivoting strategies to guide the computation and avoid the solution of irrelevant subproblems. The algorithm can act as a framework to be adapted and applied to suitable problems of different origin.}, language = {en} } @misc{QuerDonatiKelleretal., author = {Quer, Jannes and Donati, Luca and Keller, Bettina and Weber, Marcus}, title = {An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-62075}, abstract = {In this article we propose an adaptive importance sampling scheme for dynamical quantities of high dimensional complex systems which are metastable. The main idea of this article is to combine a method coming from Molecular Dynamics Simulation, Metadynamics, with a theorem from stochastic analysis, Girsanov's theorem. The proposed algorithm has two advantages compared to a standard estimator of dynamic quantities: firstly, it is possible to produce estimators with a lower variance and, secondly, we can speed up the sampling. One of the main problems for building importance sampling schemes for metastable systems is to find the metastable region in order to manipulate the potential accordingly. Our method circumvents this problem by using an assimilated version of the Metadynamics algorithm and thus creates a non-equilibrium dynamics which is used to sample the equilibrium quantities.}, language = {en} } @misc{Hoffmann, type = {Master Thesis}, author = {Hoffmann, Marie}, title = {Approximate Algorithms for Distributed Systems}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42370}, school = {Zuse Institute Berlin (ZIB)}, pages = {75}, abstract = {Peer-to-peer (P2P) systems form a special class of distributed systems. Typically, nodes in a P2P system are flat and share the same responsabilities. In this thesis we focus on three problems that occur in P2P systems: the storage of data replicates, quantile computation on distributed data streams, and churn rate estimation. Data replication is one of the oldest techniques to maintain stored data in a P2P system and to reply to read requests. Applications, which use data replication are distributed databases. They are part of an abstract overlay network and do not see the underlying network topology. The question is how to place a set of data replicates in a distributed system such that response times and failure probabilities become minimal without a priori knowledge of the topology of the underlying hardware nodes? We show how to utilize an agglomerative clustering procedure to reach this goal. State-of-the-art algorithms for aggregation of distributed data or data streams require at some point synchronization, or merge data aggregates hierarchically, which does not accompany the basic principle of P2P systems. We test whether randomized communication and merging of data aggregates are able to produce the same results. These data aggregates serve for quantile queries. Constituting and maintaining a P2P overlay network requires frequent message passing. It is a goal to minimize the number of maintenance messages since they consume bandwidth which might be missing for other applications. The lower bound of the frequency for mainte- nance messages is highly dependent on the churn rate of peers. We show how to estimate the mean lifetime of peers and to reduce the frequency for maintenance messages without destabilizing the infrastructure of the constituting overlay.}, language = {en} } @misc{WeberTranfieldHoeoegetal., 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}, 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{Schaefer, 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}, 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{ZakrzewskaD'AndreagiovanniRueppetal., author = {Zakrzewska, Anna and D'Andreagiovanni, Fabio and Ruepp, Sarah and Berger, Michael S.}, title = {Biobjective Optimization of Radio Access Technology Selection and Resource Allocation in Heterogeneous Wireless Networks}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42675}, abstract = {We propose a novel optimization model for resource assignment in heterogeneous wireless network. The model adopts two objective functions maximizing the number of served users and the minimum granted utility at once. A distinctive feature of our new model is to consider two consecutive time slots, in order to include handover as an additional decision dimension. Furthermore, the solution algorithm that we propose refines a heuristic solution approach recently proposed in literature, by considering a real joint optimization of the considered resources. The simulation study shows that the new model leads to a significant reduction in handover frequency, when compared to a traditional scheme based on maximum SNR.}, language = {en} } @misc{ShinanoRehfeldtKoch, author = {Shinano, Yuji and Rehfeldt, Daniel and Koch, Thorsten}, title = {Building Optimal Steiner Trees on Supercomputers by using up to 43,000 Cores}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-71118}, abstract = {SCIP-JACK is a customized, branch-and-cut based solver for Steiner tree and related problems. ug [SCIP-JACK, MPI] extends SCIP-JACK to a massively par- allel solver by using the Ubiquity Generator (UG) framework. ug [SCIP-JACK, MPI] was the only solver that could run on a distributed environment at the (latest) 11th DIMACS Challenge in 2014. Furthermore, it could solve three well-known open instances and updated 14 best known solutions to instances from the bench- mark libary STEINLIB. After the DIMACS Challenge, SCIP-JACK has been con- siderably improved. However, the improvements were not reflected on ug [SCIP- JACK, MPI]. This paper describes an updated version of ug [SCIP-JACK, MPI], especially branching on constrains and a customized racing ramp-up. Furthermore, the different stages of the solution process on a supercomputer are described in detail. We also show the latest results on open instances from the STEINLIB.}, language = {en} } @misc{NielsenWeber, 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}, 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} } @article{NielsenWeber, author = {Nielsen, Adam and Weber, Marcus}, title = {Computing the nearest reversible Markov chain}, series = {Numerical Linear Algebra with Applications}, volume = {22}, journal = {Numerical Linear Algebra with Applications}, number = {3}, doi = {10.1002/nla.1967}, pages = {483 -- 499}, 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{ChraparyDalitzNeunetal., author = {Chrapary, Hagen and Dalitz, Wolfgang and Neun, Winfried and Sperber, Wolfram}, title = {Design, concepts, and state of the art of the swMATH service}, issn = {1438-0064}, doi = {10.1007/s11786-017-0305-5}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-62263}, 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} } @misc{BeckerHiller, author = {Becker, Kai-Helge and Hiller, Benjamin}, title = {Efficient Enumeration of Acyclic Graph Orientations with Sources or Sinks Revisited}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-77684}, abstract = {In a recent paper, Conte et al. [CGMR2017] presented an algorithm for enumerating all acyclic orientations of a graph G=(V,E) with a single source (and related orientations) with delay O(|V||E|). In this paper we revisit the problem by going back to an early paper by de Fraysseix et al. [FMR1995], who proposed an algorithm for enumerating all bipolar orientations of a graph based on a recursion formula. We first formalize de Fraysseix et al.'s algorithm for bipolar orientations and determine that its delay is also O(|V||E|). We then apply their recursion formula to the case of Conte et al.'s enumeration problem and show that this yields a more efficient enumeration algorithm with delay O(\sqrt(|V|)|E|). Finally, a way to further streamline the algorithm that leads to a particularly simple implementation is suggested.}, language = {en} } @masterthesis{Witzig, type = {Bachelor Thesis}, author = {Witzig, Jakob}, title = {Effiziente Reoptimierung in Branch\&Bound-Verfahren f{\"u}r die Steuerung von Aufz{\"u}gen}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42210}, school = {Zuse Institute Berlin (ZIB)}, pages = {111}, abstract = {Heutzutage ist eine Vielzahl der mehrst{\"o}ckigen Geb{\"a}ude mit Personenaufzugsgruppen ausgestattet. Uns wohl bekannt sind die sogenannten konventionellen Systeme. Bei diesen Systemen bet{\"a}tigt jeder ankommende Passagier eine der beiden Richtungstasten und teilt dem dahinterstehenden Steuerungsalgorithmus seine gew{\"u}nschte Startetage und Fahrtrichtung mit. Betreten wird der zuerst auf der Startetage ankommende Aufzug mit gleicher Fahrtrichtung und ausreichend Kapazit{\"a}t. Die entsprechende Zieletage wird dem System erst nach dem Betreten der Fahrgastkabine mitgeteilt. Neben diesen konventionellen Systemen gibt es Aufzugsgruppen mit Zielrufsteuerung. Die Besonderheit eines zielrufgesteuerten Systems ist, dass ein ankommender Passagier bereits auf der Startetage seine gew{\"u}nschte Zieletage angibt und eine R{\"u}ckmeldung vom System erh{\"a}lt, welchen Aufzug er nutzen soll. Diese Zuweisung durch das System hat das Ziel, die Warte- und Reisezeiten der Passagiere zu minimieren. Ein wesentlicher Faktor bei der Berechnung warte- und reisezeitminimaler Fahrpl{\"a}ne ist das momentane Verkehrsmuster. Eine Einteilung der Verkehrsszenarien l{\"a}sst sich am besten bei B{\"u}rogeb{\"a}uden vornehmen. So ist es typisch f{\"u}r die Morgenstunden, dass jeder Passagier auf einer Zugangsebene seine Fahrt beginnt und alle Passagiere die gleiche Fahrtrichtung haben. Unter einer Zugangsebene ist z. B. der Haupteingang oder ein Parkdeck zu verstehen. Ein weiterer wesentlicher Punkt bei Zielrufsystemen ist die Art der Zuweisung der Passagiere durch das System. Zum einen gibt es unmittelbar zuweisende (UZ-) Systeme. In einem UZ-System wird nach jeder Ankunft eines Passagiers eine Momentaufnahme des momentanen Verkehrs erstellt und es findet eine Neuplanung und Zuweisung statt. Eine solche Momentaufnahme werden wir im sp{\"a}teren Verkauf als Schnappschussproblem bezeichnen. Jeder Passagier bekommt im Anschluss an die L{\"o}sung des Schnappschussproblems eine Mitteilung vom System, z. B. {\"u}ber ein Display, welchen Aufzug er benutzen soll. Zum anderen gibt es verz{\"o}gert zuweisende (VZ-) Systeme. In diesen Systemen wird die Erstellung und L{\"o}sung eines Schnappschussproblems bis kurz vor Ankunft eines Aufzuges auf einer Etage verz{\"o}gert. In einem VZ-System teilt das System allen wartenden Passagieren die geplanten Zieletagen des ankommenden Aufzugs mit. Jeder Passagier, der einen Ruf get{\"a}tigt hat und zu einer dieser Zieletagen fahren will, kann jetzt diesen Aufzug betreten. Durch die Verz{\"o}gerung muss im Vergleich zu einem UZ-System eine weitaus gr{\"o}ßere Menge von Passagieren zugewiesen werden. Dadurch kann der L{\"o}sungsprozess bedeutend aufw{\"a}ndiger werden. Vorteil eines VZ-Systems ist hingegen der gr{\"o}ßere Freiheitsgrad bei der Optimierung, da aufgrund der sp{\"a}ten Zuweisung die weitere Verkehrsentwicklung mit einbezogen werden kann. VZ-Systeme sind aufgrund des gr{\"o}ßeren Freiheitsgrades interessant f{\"u}r die Praxis ist, wir uns demzufolge in dieser Arbeit mit einer effizienteren L{\"o}sung dieser Art von Schnappschussproblemen befassen. Es gen{\"u}gt dabei den L{\"o}sungsprozess eines Schnappschussproblems zu betrachten. Das Ziel ist eine Reduzierung der ben{\"o}tigten Rechenzeit. Unter Reoptimierung verstehen wir die Konstruktion zul{\"a}ssiger Spalten in den jeweiligen Iterationsrunden der Spaltengenerierung innerhalb eines Schnappschussproblems. Als eine Iterationsrunde bezeichnet wir einer Menge zul{\"a}ssiger Touren mit negativen reduzierten Kosten. Eine effiziente Reoptimierung zeichnet sich durch die Wiederverwendung und Aufbereitung von Informationen aus vorangegangenen Iterationsrunden desselben Schnappschussproblems aus. Zu den wichtigen Informationen geh{\"o}rt der konstruierte Suchbaum der vorherigen Iterationsrunde mit seinen ausgeloteten (abgeschnittenen) Bl{\"a}ttern sowie konstruierten Touren bzw. Spalten, welche in der Iterationsrunde ihrer Konstruktion nicht zur L{\"o}sung des Teilproblems der Spaltengenerierung beitrugen. Eine solche Wiederverwendung und Aufbereitung von Informationen nennen wir Warmstart.}, language = {de} } @misc{Paskin, type = {Master Thesis}, author = {Paskin, Martha}, title = {Estimating 3D Shape of the Head Skeleton of Basking Sharks Using Annotated Landmarks on a 2D Image}, abstract = {Basking sharks are thought to be one of the most efficient filter-feeding fish in terms of the throughput of water filtered through their gills. Details about the underlying morphology of their branchial region have not been studied due to various challenges in acquiring real-world data. The present thesis aims to facilitate this, by developing a mathematical shape model which constructs the 3D structure of the head skeleton of a basking shark using annotated landmarks on a single 2D image. This is an ill-posed problem as estimating the depth of a 3D object from a single 2D view is, in general, not possible. To reduce this ambiguity, we create a set of pre-defined training shapes in 3D from CT scans of basking sharks. First, the damaged structures of the sharks in the scans are corrected via solving a set of optimization problems, before using them as accurate 3D representations of the object. Then, two approaches are employed for the 2D-to-3D shape fitting problem-an Active Shape Model approach and a Kendall's Shape Space approach. The former represents a shape as a point on a high-dimensional Euclidean space, whereas the latter represents a shape as an equivalence class of points in this Euclidean space. Kendall's shape space approach is a novel technique that has not yet been applied in this context, and a comprehensive comparison of the two approaches suggests this approach to be superior for the problem at hand. This can be credited to an improved interpolation of the training shapes.}, language = {en} } @misc{OrlowskiWernerWessaely, author = {Orlowski, Sebastian and Werner, Axel and Wess{\"a}ly, Roland}, title = {Estimating trenching costs in FTTx network planning}, issn = {1438-0064}, doi = {10.1007/978-3-642-29210-1_15}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-14884}, abstract = {In this paper we assess to which extent trenching costs of an FTTx network are unavoidable, even if technical side constraints are neglected. For that purpose we present an extended Steiner tree model. Using a variety of realistic problem instances we demonstrate that the total trenching cost can only be reduced by about 5 percent in realistic scenarios. This work has been funded by BMBF (German Federal Ministry of Education and Research) within the program "KMU-innovativ".}, language = {en} }