@misc{DercksenHegeOberlaender2013, author = {Dercksen, Vincent J. and Hege, Hans-Christian and Oberlaender, Marcel}, title = {The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology}, issn = {1438-0064}, doi = {10.1007/s12021-013-9213-2}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-43157}, year = {2013}, abstract = {Neuroanatomical analysis, such as classification of cell types, depends on reliable reconstruction of large numbers of complete 3D dendrite and axon morphologies. At present, the majority of neuron reconstructions are obtained from preparations in a single tissue slice in vitro, thus suffering from cut off dendrites and, more dramatically, cut off axons. In general, axons can innervate volumes of several cubic millimeters and may reach path lengths of tens of centimeters. Thus, their complete reconstruction requires in vivo labeling, histological sectioning and imaging of large fields of view. Unfortunately, anisotropic background conditions across such large tissue volumes, as well as faintly labeled thin neurites, result in incomplete or erroneous automated tracings and even lead experts to make annotation errors during manual reconstructions. Consequently, tracing reliability renders the major bottleneck for reconstructing complete 3D neuron morphologies. Here, we present a novel set of tools, integrated into a software environment named 'Filament Editor', for creating reliable neuron tracings from sparsely labeled in vivo datasets. The Filament Editor allows for simultaneous visualization of complex neuronal tracings and image data in a 3D viewer, proof-editing of neuronal tracings, alignment and interconnection across sections, and morphometric analysis in relation to 3D anatomical reference structures. We illustrate the functionality of the Filament Editor on the example of in vivo labeled axons and demonstrate that for the exemplary dataset the final tracing results after proof-editing are independent of the expertise of the human operator.}, language = {en} } @misc{Shinano, author = {Shinano, Yuji}, title = {The Ubiquity Generator Framework: 7 Years of Progress in Parallelizing Branch-and-Bound}, issn = {1438-0064}, doi = {10.1007/978-3-319-89920-6_20}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65545}, abstract = {Mixed integer linear programming (MIP) is a general form to model combinatorial optimization problems and has many industrial applications. The performance of MIP solvers has improved tremendously in the last two decades and these solvers have been used to solve many real-word problems. However, against the backdrop of modern computer technology, parallelization is of pivotal importance. In this way, ParaSCIP is the most successful parallel MIP solver in terms of solving previously unsolvable instances from the well-known benchmark instance set MIPLIB by using supercomputers. It solved two instances from MIPLIB2003 and 12 from MIPLIB2010 for the first time to optimality by using up to 80,000 cores on supercomputers. ParaSCIP has been developed by using the Ubiquity Generator (UG) framework, which is a general software package to parallelize any state-of-the-art branch-and-bound based solver. This paper discusses 7 years of progress in parallelizing branch-and-bound solvers with UG.}, 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{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{WendeSteinke, author = {Wende, Florian and Steinke, Thomas}, title = {Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU}, issn = {1438-0064}, doi = {10.1145/2503210.2503254}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42187}, abstract = {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.}, language = {en} } @misc{Shinano, author = {Shinano, Yuji}, title = {UG - Ubiquity Generator Framework v1.0.0beta}, doi = {10.12752/8521}, abstract = {UG is a generic framework to parallelize branch-and-bound based solvers (e.g., MIP, MINLP, ExactIP) in a distributed or shared memory computing environment. It exploits the powerful performance of state-of-the-art "base solvers", such as SCIP, CPLEX, etc. without the need for base solver parallelization. UG framework, ParaSCIP(ug[SCIP,MPI]) and FiberSCIP (ug[SCIP,Pthreads]) are available as a beta version. v1.0.0: new documentation and cmake, generalization of ug framework, implementation of selfsplitrampup for fiber- and parascip, better memory and time limit handling.}, language = {en} } @misc{MunguiaOxberryRajanetal., author = {Munguia, Lluis-Miquel and Oxberry, Geoffrey and Rajan, Deepak and Shinano, Yuji}, title = {Parallel PIPS-SBB: Multi-Level Parallelism For Stochastic Mixed-Integer Programs}, number = {ZIB-Report 17-58}, issn = {1438-0064}, doi = {10.1007/s10589-019-00074-0}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65517}, abstract = {PIPS-SBB is a distributed-memory parallel solver with a scalable data distribution paradigm. It is designed to solve MIPs with a dual-block angular structure, which is characteristic of deterministic-equivalent Stochastic Mixed-Integer Programs (SMIPs). In this paper, we present two different parallelizations of Branch \& Bound (B\&B), implementing both as extensions of PIPS-SBB, thus adding an additional layer of parallelism. In the first of the proposed frameworks, PIPS-PSBB, the coordination and load-balancing of the different optimization workers is done in a decentralized fashion. This new framework is designed to ensure all available cores are processing the most promising parts of the B\&B tree. The second, ug[PIPS-SBB,MPI], is a parallel implementation using the Ubiquity Generator (UG), a universal framework for parallelizing B\&B tree search that has been successfully applied to other MIP solvers. We show the effects of leveraging multiple levels of parallelism in potentially improving scaling performance beyond thousands of cores.}, language = {en} } @misc{GriewankStreubelLehmannetal., author = {Griewank, Andreas and Streubel, Tom and Lehmann, Lutz and Hasenfelder, Richard and Radons, Manuel}, title = {Piecewise linear secant approximation via Algorithmic Piecewise Differentiation}, issn = {1438-0064}, doi = {10.1080/10556788.2017.1387256}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-61642}, abstract = {It is shown how piecewise differentiable functions \(F: R^n → R^m\) that are defined by evaluation programs can be approximated locally by a piecewise linear model based on a pair of sample points x̌ and x̂. We show that the discrepancy between function and model at any point x is of the bilinear order O(||x - x̌|| ||x - x̂||). This is a little surprising since x ∈ R^n may vary over the whole Euclidean space, and we utilize only two function samples F̌ = F(x̌) and F̂ = F(x̂), as well as the intermediates computed during their evaluation. As an application of the piecewise linearization procedure we devise a generalized Newton's method based on successive piecewise linearization and prove for it sufficient conditions for convergence and convergence rates equaling those of semismooth Newton. We conclude with the derivation of formulas for the numerically stable implementation of the aforedeveloped piecewise linearization methods.}, language = {en} } @misc{LindnerReisch, author = {Lindner, Niels and Reisch, Julian}, title = {Parameterized Complexity of Periodic Timetabling}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-78314}, abstract = {Public transportation networks are typically operated with a periodic timetable. The Periodic Event Scheduling Problem (PESP) is the standard mathematical modelling tool for periodic timetabling. Since PESP can be solved in linear time on trees, it is a natural question to ask whether there are polynomial-time algorithms for input networks of bounded treewidth. We show that deciding the feasibility of a PESP instance is NP-hard even when the treewidth is 2, the branchwidth is 2, or the carvingwidth is 3. Analogous results hold for the optimization of reduced PESP instances, where the feasibility problem is trivial. To complete the picture, we present two pseudo-polynomial-time dynamic programming algorithms solving PESP on input networks with bounded tree- or branchwidth. We further analyze the parameterized complexity of PESP with bounded cyclomatic number, diameter, or vertex cover number. For event-activity networks with a special -- but standard -- structure, we give explicit and sharp bounds on the branchwidth in terms of the maximum degree and the carvingwidth of an underlying line network. Finally, we investigate several parameters on the smallest instance of the benchmarking library PESPlib.}, language = {en} } @misc{Witzig, type = {Master Thesis}, author = {Witzig, Jakob}, title = {Reoptimization Techniques in MIP Solvers}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54067}, pages = {176}, abstract = {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.}, language = {en} }