@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{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{AmbellanHanikvonTycowicz, author = {Ambellan, Felix and Hanik, Martin and von Tycowicz, Christoph}, title = {Morphomatics: Geometric morphometrics in non-Euclidean shape spaces}, doi = {10.12752/8544}, abstract = {Morphomatics is an open-source Python library for (statistical) shape analysis developed within the geometric data analysis and processing research group at Zuse Institute Berlin. It contains prototype implementations of intrinsic manifold-based methods that are highly consistent and avoid the influence of unwanted effects such as bias due to arbitrary choices of coordinates.}, language = {en} } @misc{Shinano, author = {Shinano, Yuji}, title = {UG - Ubiquity Generator Framework v0.9.1}, doi = {10.12752/8508}, 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. For MIP solving, ParaSCIP and FiberSCIP are well debugged and should be stable. For MINLP solving, they are relatively stable, but not as thoroughly debugged. This release version should handle branch-and-cut approaches where subproblems are defined by variable bounds and also by constrains for ug[SCIP,*] ParaSCIP and FiberSCIP). Therefore, problem classes other than MIP or MINLP can be handled, but they have not been tested yet. v0.9.1: Update orbitope cip files.}, 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} } @misc{EhlkeRammLameckeretal., author = {Ehlke, Moritz and Ramm, Heiko and Lamecker, Hans and Hege, Hans-Christian and Zachow, Stefan}, title = {Fast Generation of Virtual X-ray Images from Deformable Tetrahedral Meshes}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41896}, abstract = {We propose a novel GPU-based approach to render virtual X-ray projections of deformable tetrahedral meshes. These meshes represent the shape and the internal density distribution of a particular anatomical structure and are derived from statistical shape and intensity models (SSIMs). We apply our method to improve the geometric reconstruction of 3D anatomy (e.g.\ pelvic bone) from 2D X-ray images. For that purpose, shape and density of a tetrahedral mesh are varied and virtual X-ray projections are generated within an optimization process until the similarity between the computed virtual X-ray and the respective anatomy depicted in a given clinical X-ray is maximized. The OpenGL implementation presented in this work deforms and projects tetrahedral meshes of high resolution (200.000+ tetrahedra) at interactive rates. It generates virtual X-rays that accurately depict the density distribution of an anatomy of interest. Compared to existing methods that accumulate X-ray attenuation in deformable meshes, our novel approach significantly boosts the deformation/projection performance. The proposed projection algorithm scales better with respect to mesh resolution and complexity of the density distribution, and the combined deformation and projection on the GPU scales better with respect to the number of deformation parameters. The gain in performance allows for a larger number of cycles in the optimization process. Consequently, it reduces the risk of being stuck in a local optimum. We believe that our approach contributes in orthopedic surgery, where 3D anatomy information needs to be extracted from 2D X-rays to support surgeons in better planning joint replacements.}, 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{Keidel, type = {Master Thesis}, author = {Keidel, Stefan}, title = {Snapshots in Scalaris}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42282}, school = {Zuse Institute Berlin (ZIB)}, pages = {87}, abstract = {Eines der gr{\"o}ßten Hindernisse beim praktischen Einsatz von Scalaris, einer skalierbaren Implementierung einer verteilten Hashtabelle mit Unterst{\"u}tzung f{\"u}r Transaktionen, ist das Fehlen eines Verfahrens zur Aufnahme eines konsistenten Zustandes des gesamten Systems. Wir stellen in dieser Arbeit ein einfaches Protokoll vor, dass diese Aufgabe erf{\"u}llt und sich, auf Grund der von uns gew{\"a}hlten Herangehensweise, leicht implementieren l{\"a}sst. Als Ausgangspunkt daf{\"u}r w{\"a}hlen wir aus einer Reihe von „klassischen" Snapshot-Algorithmen ein 1993 von Mattern entworfenes Verfahren, welches auf dem Algorithmus von Lai und Yang basiert, aus. Diese Entscheidung basiert auf einer gr{\"u}ndlichen Analyse der Protokolle unter Ber{\"u}cksichtigung der Architektur der existierenden Software. Im n{\"a}chsten Arbeitsschritt benutzen wir unser vollst{\"a}ndiges Wissen {\"u}ber die Interna des Transaktionssystems von Scalaris und vereinfachen damit das Verfahren hinsichtlich Benutzbarkeit und Implementierungskomplexit{\"a}t, ohne die Anforderungen an den aufgenommenen Zustand aufzuweichen. Statt einer losen Anh{\"a}ufung lokaler Zust{\"a}nde der einzelnen Teilnehmerknoten k{\"o}nnen wir am Ende eine große Schl{\"u}ssel-Wert-Tabelle als Ergebnis erzeugen, die konsistent ist, sich leicht weiterverarbeiten l{\"a}sst und die einem Zustand entspricht, in dem sich das System einmal befunden haben k{\"o}nnte. Nachdem wir das Verfahren dann in Software umgesetzt haben, werten wir die Ergebnisse hinsichtlich des Einflusses auf die Performanz des Gesamtsystems aus und diskutieren m{\"o}gliche Weiterentwicklungen.}, language = {de} } @misc{ItoShinano, author = {Ito, Satoshi and Shinano, Yuji}, title = {Calculation of clinch and elimination numbers for sports leagues with multiple tiebreaking criteria}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-70591}, abstract = {The clinch (elimination) number is a minimal number of future wins (losses) needed to clinch (to be eliminated from) a specified place in a sports league. Several optimization models and computational results are shown in this paper for calculating clinch and elimination numbers in the presence of predefined multiple tiebreaking criteria. The main subject of this paper is to provide a general algorithmic framework based on integer programming with utilizing possibly multilayered upper and lower bounds.}, language = {en} } @misc{CostaMantonOstrovskyetal., author = {Costa, Marta and Manton, James D. and Ostrovsky, Aaron D. and Prohaska, Steffen and Jefferis, Gregory S.X.E.}, title = {NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases}, issn = {1438-0064}, doi = {10.1016/j.neuron.2016.06.012}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59672}, abstract = {Neural circuit mapping is generating datasets of 10,000s of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types including searching neurons against transgene expression patterns. Finally we show that NBLAST is effective with data from other invertebrates and zebrafish.}, language = {en} }