TY - GEN A1 - Özel, M. Neset A1 - Kulkarni, Abhishek A1 - Hasan, Amr A1 - Brummer, Josephine A1 - Moldenhauer, Marian A1 - Daumann, Ilsa-Maria A1 - Wolfenberg, Heike A1 - Dercksen, Vincent J. A1 - Kiral, F. Ridvan A1 - Weiser, Martin A1 - Prohaska, Steffen A1 - von Kleist, Max A1 - Hiesinger, Peter Robin T1 - Serial synapse formation through filopodial competition for synaptic seeding factors N2 - Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses. T3 - ZIB-Report - 19-45 KW - filopodia KW - growth cone dynamics KW - brain wiring KW - 2-photon microscopy KW - model Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74397 SN - 1438-0064 ER - TY - GEN A1 - Zakrzewska, Anna A1 - D'Andreagiovanni, Fabio A1 - Ruepp, Sarah A1 - Berger, Michael S. T1 - Biobjective Optimization of Radio Access Technology Selection and Resource Allocation in Heterogeneous Wireless Networks N2 - 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. T3 - ZIB-Report - 13-63 KW - Heterogeneous Wireless Networks, Biobjective Optimization, Mixed Integer Linear Programming, Simulation Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42675 UR - http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6576416&isnumber=6576384 SN - 1438-0064 ER - TY - GEN A1 - Wolf, Thomas T1 - A Study of Genetic Algorithms solving a combinatorial Puzzle N2 - 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. T3 - ZIB-Report - SC-98-01 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3445 ER - TY - THES A1 - Witzig, Jakob T1 - Reoptimization Techniques in MIP Solvers N2 - Many optimization problems can be modeled as Mixed Integer Programs (MIPs). In general, MIPs cannot be solved efficiently, since solving MIPs is NP-hard, see, e.g., Schrijver, 2003. Common methods for solving NP-hard problems are branch-and-bound and column generation. In the case of column generation, the original problem becomes decomposed or re-formulated into one ore more smaller subproblems, which are easier to solve. Each of these subproblems is solved separately and recurrently, which can be interpreted as solving a sequence of optimization problems. In this thesis, we consider a sequence of MIPs which only differ in the respective objective functions. Furthermore, we assume each of these MIPs get solved with a branch-and-bound algorithm. This thesis aims to figure out whether the solving process of a given sequence of MIPs can be accelerated by reoptimization. As reoptimization we understand starting the solving process of a MIP of this sequence at a given frontier of a search tree corresponding to another MIP of this sequence. At the beginning we introduce an LP-based branch-and-bound algorithm. This algorithm is inspired by the reoptimizing algorithm of Hiller, Klug, and the author of this thesis, 2013. Since most of the state-of-the-art MIP solvers come to decisions based on dual information, which leads to the loss of feasible solutions after changing the objective function, we present a technique to guarantee optimality despite using these information. A decision is based on a dual information if this decision is valid for at least one feasible solution, whereas a decision is based on a primal information if this decision is valid for all feasible solutions. Afterwards, we consider representing the search frontier of the tree by a set of nodes of a given size. We call this the Tree Compression Problem. Moreover, we present a criterion characterizing the similarity of two objective functions. To evaluate our approach of reoptimization we extend the well-known and well-maintained MIP solver SCIP to an LP-based branch-and-bound framework, introduce two heuristics for solving the Tree Compression Problem, and a primal heuristic which is especially fitted to column generation. Finally, we present computational experiments on several problem classes, e.g., the Vertex Coloring and k-Constrained Shortest Path. Our experiments show, that a straightforward reoptimization, i.e., without additional heuristics, provides no benefit in general. However, in combination with the techniques and methods presented in this thesis, we can accelerate the solving of a given sequence up to the factor 14. For this purpose it is essential to take the differences of the objective functions into account and to restart the reoptimization, i.e., solve the subproblem from scratch, if the objective functions are not similar enough. Finally, we discuss the possibility to parallelize the solving process of the search frontier at the beginning of each solving process. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54067 ER - TY - THES A1 - Witzig, Jakob T1 - Effiziente Reoptimierung in Branch&Bound-Verfahren für die Steuerung von Aufzügen N2 - Heutzutage ist eine Vielzahl der mehrstöckigen Gebäude mit Personenaufzugsgruppen ausgestattet. Uns wohl bekannt sind die sogenannten konventionellen Systeme. Bei diesen Systemen betätigt jeder ankommende Passagier eine der beiden Richtungstasten und teilt dem dahinterstehenden Steuerungsalgorithmus seine gewünschte Startetage und Fahrtrichtung mit. Betreten wird der zuerst auf der Startetage ankommende Aufzug mit gleicher Fahrtrichtung und ausreichend Kapazität. 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 gewünschte Zieletage angibt und eine Rückmeldung vom System erhält, 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 Fahrpläne ist das momentane Verkehrsmuster. Eine Einteilung der Verkehrsszenarien lässt sich am besten bei Bürogebäuden vornehmen. So ist es typisch für 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 späteren Verkauf als Schnappschussproblem bezeichnen. Jeder Passagier bekommt im Anschluss an die Lösung des Schnappschussproblems eine Mitteilung vom System, z. B. über ein Display, welchen Aufzug er benutzen soll. Zum anderen gibt es verzögert zuweisende (VZ-) Systeme. In diesen Systemen wird die Erstellung und Lösung eines Schnappschussproblems bis kurz vor Ankunft eines Aufzuges auf einer Etage verzögert. In einem VZ-System teilt das System allen wartenden Passagieren die geplanten Zieletagen des ankommenden Aufzugs mit. Jeder Passagier, der einen Ruf getätigt hat und zu einer dieser Zieletagen fahren will, kann jetzt diesen Aufzug betreten. Durch die Verzögerung muss im Vergleich zu einem UZ-System eine weitaus größere Menge von Passagieren zugewiesen werden. Dadurch kann der Lösungsprozess bedeutend aufwändiger werden. Vorteil eines VZ-Systems ist hingegen der größere Freiheitsgrad bei der Optimierung, da aufgrund der späten Zuweisung die weitere Verkehrsentwicklung mit einbezogen werden kann. VZ-Systeme sind aufgrund des größeren Freiheitsgrades interessant für die Praxis ist, wir uns demzufolge in dieser Arbeit mit einer effizienteren Lösung dieser Art von Schnappschussproblemen befassen. Es genügt dabei den Lösungsprozess eines Schnappschussproblems zu betrachten. Das Ziel ist eine Reduzierung der benötigten Rechenzeit. Unter Reoptimierung verstehen wir die Konstruktion zulässiger Spalten in den jeweiligen Iterationsrunden der Spaltengenerierung innerhalb eines Schnappschussproblems. Als eine Iterationsrunde bezeichnet wir einer Menge zulässiger 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 gehört der konstruierte Suchbaum der vorherigen Iterationsrunde mit seinen ausgeloteten (abgeschnittenen) Blättern sowie konstruierten Touren bzw. Spalten, welche in der Iterationsrunde ihrer Konstruktion nicht zur Lösung des Teilproblems der Spaltengenerierung beitrugen. Eine solche Wiederverwendung und Aufbereitung von Informationen nennen wir Warmstart. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42210 ER - TY - GEN A1 - Wiebel, Alexander A1 - Vos, Frans M. A1 - Hege, Hans-Christian T1 - Perception-Oriented Picking of Structures in Direct Volumetric Renderings N2 - Radiologists from all application areas are trained to read slice-based visualizations of 3D medical image data. Despite the numerous examples of sophisticated three-dimensional renderings, especially all variants of direct volume rendering, such methods are often considered not very useful by radiologists who prefer slice-based visualization. Just recently there have been attempts to bridge this gap between 2D and 3D renderings. These attempts include specialized techniques for volume picking that result in repositioning slices. In this paper, we present a new volume picking technique that, in contrast to previous work, does not require pre-segmented data or metadata. The positions picked by our method are solely based on the data itself, the transfer function and, most importantly, on the way the volumetric rendering is perceived by viewers. To demonstrate the usefulness of the proposed method we apply it for automatically repositioning slices in an abdominal MRI scan, a data set from a flow simulation and a number of other volumetric scalar fields. Furthermore we discuss how the method can be implemented in combination with various different volumetric rendering techniques. T3 - ZIB-Report - 11-45 KW - DVR KW - picking KW - pointing KW - direct volume rendering Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14343 SN - 1438-0064 ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas T1 - Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU N2 - Simulations of the critical Ising model by means of local update algorithms suffer from critical slowing down. One way to partially compensate for the influence of this phenomenon on the runtime of simulations is using increasingly faster and parallel computer hardware. Another approach is using algorithms that do not suffer from critical slowing down, such as cluster algorithms. This paper reports on the Swendsen-Wang multi-cluster algorithm on Intel Xeon Phi coprocessor 5110P, Nvidia Tesla M2090 GPU, and x86 multi-core CPU. We present shared memory versions of the said algorithm for the simulation of the two- and three-dimensional Ising model. We use a combination of local cluster search and global label reduction by means of atomic hardware primitives. Further, we describe an MPI version of the algorithm on Xeon Phi and CPU, respectively. Significant performance improvements over known im plementations of the Swendsen-Wang algorithm are demonstrated. T3 - ZIB-Report - 13-44 KW - Swendsen-Wang Multi-Cluster Algorithm KW - Ising Model KW - Xeon Phi KW - GPGPU KW - Connected Component Labeling Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42187 SN - 1438-0064 ER - TY - GEN A1 - Weber, Britta A1 - Tranfield, Erin M. A1 - Höög, Johanna L. A1 - Baum, Daniel A1 - Antony, Claude A1 - Hyman, Tony A1 - Verbavatz, Jean-Marc A1 - Prohaska, Steffen T1 - Automated stitching of microtubule centerlines across serial electron tomograms N2 - 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. T3 - ZIB-Report - 14-41 KW - electron tomography KW - microtubules KW - serial sectioning KW - image analysis KW - geometry reconstruction KW - image and geometry alignment KW - point correspondence Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52958 SN - 1438-0064 ER - TY - GEN A1 - Tateiwa, Nariaki A1 - Shinano, Yuji A1 - Yasuda, Masaya A1 - Kaji, Shizuo A1 - Yamamura, Keiichiro A1 - Fujisawa, Katsuki T1 - Massively parallel sharing lattice basis reduction N2 - For cryptanalysis in lattice-based schemes, the performance evaluation of lattice basis reduction using high-performance computers is becoming increasingly important for the determination of the security level. We propose a distributed and asynchronous parallel reduction algorithm based on randomization and DeepBKZ, which is an improved variant of the block Korkine-Zolotarev (BKZ) reduction algorithm. Randomized copies of a lattice basis are distributed to up to 103,680 cores and independently reduced in parallel, while some basis vectors are shared asynchronously among all processes via MPI. There is a trade-off between randomization and information sharing; if a substantial amount of information is shared, all processes will work on the same problem, thereby diminishing the benefit of parallelization. To monitor this balance between randomness and sharing, we propose a metric to quantify the variety of lattice bases. We empirically find an optimal parameter of sharing for high-dimensional lattices. We demonstrate the efficacy of our proposed parallel algorithm and implementation with respect to both performance and scalability through our experiments. T3 - ZIB-Report - 21-38 KW - Discrete optimization KW - Lattice problem KW - Lattice-based cryptography KW - Shortest vector problem KW - Parallel algorithms KW - Ubiquity Generator Framework Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85209 SN - 1438-0064 N1 - under review ER - TY - GEN A1 - Tateiwa, Nariaki A1 - Shinano, Yuji A1 - Yamamura, Keiichiro A1 - Yoshida, Akihiro A1 - Kaji, Shizuo A1 - Yasuda, Masaya A1 - Fujisawa, Katsuki T1 - CMAP-LAP: Configurable Massively Parallel Solver for Lattice Problems N2 - Lattice problems are a class of optimization problems that are notably hard. There are no classical or quantum algorithms known to solve these problems efficiently. Their hardness has made lattices a major cryptographic primitive for post-quantum cryptography. Several different approaches have been used for lattice problems with different computational profiles; some suffer from super-exponential time, and others require exponential space. This motivated us to develop a novel lattice problem solver, CMAP-LAP, based on the clever coordination of different algorithms that run massively in parallel. With our flexible framework, heterogeneous modules run asynchronously in parallel on a large-scale distributed system while exchanging information, which drastically boosts the overall performance. We also implement full checkpoint-and-restart functionality, which is vital to high-dimensional lattice problems. Through numerical experiments with up to 103,680 cores, we evaluated the performance and stability of our system and demonstrated its high capability for future massive-scale experiments. T3 - ZIB-Report - 21-16 KW - Discrete optimization KW - Lattice problem KW - Lattice-based cryptography KW - Shortest vector problem KW - Parallel algorithms KW - Ubiquity Generator Framework Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-82802 SN - 1438-0064 N1 - Revised version is accepted to HiPC 2021 ER -