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  <doc>
    <id>1554</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2012-07-02</completedDate>
    <publishedDate>2012-07-02</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A General Attribution Concept for Models in M- adhesive Transformation Systems: Long Version</title>
    <abstract language="eng">Attributes are an important concept for modeling data in practical applications. Up to now there is no adequate way to define attributes for different kinds of models used in M-adhesive transformation systems, which are a special kind of graph transformation systems based on M-adhesive categories. Especially a proper representation and definition of attributes and their values as well as a suitable handling of the data does not fit well with other graph transformation formalisms.&#13;
In this paper, we propose a new method to define attributes in a natural, but still formally precise and widely applicable way. We define a new kind of adhesive category, called W-adhesive, that can be used for transformations of attributes, while the underlying models are still M-adhesive ones. As a result, attributed models can be used as they are intended to be, but with a formal background and proven well-behavior.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-15547</identifier>
    <identifier type="doi">10.1007/978-3-642-33654-6_13</identifier>
    <enrichment key="SourceTitle">A short version appeared in:  Graph Transformation,  6th International Conference, ICGT 2012, Bremen, Germany, September 24-29, 2012, Proceedings. Lecture Notes in Computer Science, Vol. 7562 . 2012. Pp.187-202</enrichment>
    <author>Ulrike Golas</author>
    <submitter>Ulrike Golas</submitter>
    <series>
      <title>ZIB-Report</title>
      <number>12-22</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>graph transformation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>attribution</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>adhesive categories</value>
    </subject>
    <collection role="ccs" number="F.">Theory of Computation</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/1554/ZR-12-22.pdf</file>
  </doc>
  <doc>
    <id>4218</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2013-08-26</completedDate>
    <publishedDate>2013-08-26</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU</title>
    <abstract language="eng">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&#13;
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&#13;
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&#13;
describe an MPI version of the algorithm on Xeon Phi and CPU, respectively. Significant performance improvements over known im&#13;
plementations of the Swendsen-Wang algorithm are demonstrated.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-42187</identifier>
    <identifier type="doi">10.1145/2503210.2503254</identifier>
    <enrichment key="SourceTitle">Appeared in: Proceeding SC '13 Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis Article No. 83 ACM New York, NY, USA, 2013</enrichment>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Florian Wende</author>
    <submitter>Florian Wende</submitter>
    <author>Thomas Steinke</author>
    <series>
      <title>ZIB-Report</title>
      <number>13-44</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Swendsen-Wang Multi-Cluster Algorithm</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Ising Model</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Xeon Phi</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>GPGPU</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Connected Component Labeling</value>
    </subject>
    <collection role="ccs" number="B.">Hardware</collection>
    <collection role="ccs" number="J.">Computer Applications</collection>
    <collection role="pacs" number="80.00.00">INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="msc" number="82-XX">STATISTICAL MECHANICS, STRUCTURE OF MATTER</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="steinke">Steinke, Thomas</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/4218/wende_steinke.pdf</file>
  </doc>
  <doc>
    <id>4206</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2013-08-21</completedDate>
    <publishedDate>2013-08-21</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Übersicht über die Datenhaltung im ZIB und die Möglichkeiten einer Nutzung durch Projekte</title>
    <abstract language="deu">Dieser Bericht beschreibt in allgemein&#13;
verständlicher Form die Struktur der&#13;
Datenhaltung im Zuse‐Institut Berlin (ZIB) und&#13;
die aktuell verwendeten Strategien im Umgang&#13;
mit immer stärker wachsenden Datenmengen,&#13;
sowie der Herausforderung der Speicherung&#13;
unwiederbringlicher Daten über im Grunde&#13;
unbegrenzte Zeit.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-42060</identifier>
    <author>Wolfgang Pyszkalski</author>
    <submitter>Wolfgang Pyszkalski</submitter>
    <series>
      <title>ZIB-Report</title>
      <number>13-16</number>
    </series>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Langfristige Datenhaltung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Speichersysteme</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Magnetband</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Vertrauenswürdigkeit des Langzeitspeichers</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Sicherstellung der Lesbarkeit des Bandmaterials</value>
    </subject>
    <collection role="ccs" number="H.3">INFORMATION STORAGE AND RETRIEVAL</collection>
    <collection role="msc" number="68P20">Information storage and retrieval</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="institutes" number="ITS">IT-Service</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/4206/LFDimZIB-TR13-16.pdf</file>
  </doc>
  <doc>
    <id>7089</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2018-11-15</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Efficient Stiff Integration of Density Driven Flow Problems</title>
    <abstract language="eng">The paper investigates the efficient use of a linearly implicit stiff integrator for the numerical solution of density driven flow problems. Upon choosing a one-step method of extrapolation type (code LIMEX), the use of full Jacobians and reduced approximations are discussed. Numerical experiments include nonlinear density flow problems such as diffusion from a salt dome (2D), a (modified) Elder problem (3D), the saltpool benchmark (3D) and a real life salt dome problem (2D). The arising linear equations are solved using either a multigrid preconditioner from the software package UG4 or the sparse matrix solver SuperLU.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-70891</identifier>
    <author>Arne Nägel</author>
    <submitter>Erlinda Körnig</submitter>
    <author>Peter Deuflhard</author>
    <author>Gabriel Wittum</author>
    <series>
      <title>ZIB-Report</title>
      <number>18-54</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>stiff integration for PDEs</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>linearly implicit Euler discretization</value>
    </subject>
    <collection role="msc" number="65L80">Methods for differential-algebraic equations</collection>
    <collection role="msc" number="65M20">Method of lines</collection>
    <collection role="msc" number="65M55">Multigrid methods; domain decomposition</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="deuflhard">Deuflhard, Peter</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/7089/ZIB-Report_1854.pdf</file>
  </doc>
  <doc>
    <id>6182</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-01-25</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Revealing hidden text in rolled and folded papyri</title>
    <abstract language="eng">Ancient Egyptian papyri are often folded, rolled up or kept as small packages, sometimes even sealed. Physically unrolling or unfolding these packages might severely damage them. We demonstrate a way to get access to the hidden script without physical unfolding by employing computed tomography and mathematical algorithms for virtual unrolling and unfolding. Our algorithmic approaches are combined with manual interaction. This provides the necessary flexibility to enable the unfolding of even complicated and partly damaged papyrus packages. In addition, it allows us to cope with challenges posed by the structure of ancient papyrus, which is rather irregular, compared to other writing substrates like metallic foils or parchment. Unfolding of packages is done in two stages. In the first stage, we virtually invert the physical folding process step by step until the partially unfolded package is topologically equivalent to a scroll or a papyrus sheet folded only along one fold line. To minimize distortions at this stage, we apply the method of moving least squares. In the second stage, the papyrus is simply flattened, which requires the definition of a medial surface. We have applied our software framework to several papyri. In this work, we present the results of applying our approaches to mockup papyri that were either rolled or folded along perpendicular fold lines. In the case of the folded papyrus, our approach represents the first attempt to address the unfolding of such complicated folds.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-61826</identifier>
    <identifier type="doi">10.1007/s00339-017-0808-6</identifier>
    <enrichment key="SourceTitle">Appeared in: Applied Physics A 123 (2017) pp. 171</enrichment>
    <author>Daniel Baum</author>
    <submitter>Daniel Baum</submitter>
    <author>Norbert Lindow</author>
    <author>Hans-Christian Hege</author>
    <author>Verena Lepper</author>
    <author>Tzulia Siopi</author>
    <author>Frank Kutz</author>
    <author>Kristin Mahlow</author>
    <author>Heinz-Eberhard Mahnke</author>
    <series>
      <title>ZIB-Report</title>
      <number>17-02</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>unfolding, papyri, computed tomography</value>
    </subject>
    <collection role="ccs" number="J.">Computer Applications</collection>
    <collection role="pacs" number="80.00.00">INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="persons" number="norbert.lindow">Lindow, Norbert</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6182/ZR-17-02.pdf</file>
  </doc>
  <doc>
    <id>1497</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2012-04-03</completedDate>
    <publishedDate>2012-04-03</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A cubic regularization algorithm for nonconvex optimization in function space (in preparation)</title>
    <abstract language="eng">We propose a cubic regularization algorithm that is constructed to deal with nonconvex minimization&#13;
problems in function space. It allows for a flexible choice of the regularization term and thus accounts for the fact &#13;
that in such problems one often has to deal with more than one norm. Global and local convergence results are established&#13;
in a general framework. Moreover, several variants of step computations are compared. In the context of nonlinear &#13;
elasticity it turns out the a cg method applied to an augmented Hessian is more robust than truncated cg.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <author>Anton Schiela</author>
    <submitter>Anton Schiela</submitter>
    <series>
      <title>ZIB-Report</title>
      <number>12-16</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>nonconvex optimization</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>optimization in function space</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>nonlinear elasticity</value>
    </subject>
    <collection role="msc" number="49M37">Methods of nonlinear programming type [See also 90C30, 65Kxx]</collection>
    <collection role="msc" number="74B20">Nonlinear elasticity</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="projects" number="no-project">no-project</collection>
  </doc>
  <doc>
    <id>6023</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-08-23</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Cameron--Martin theorems for sequences of Cauchy-distributed random variables</title>
    <abstract language="eng">Given a sequence of Cauchy-distributed random variables defined by a sequence of location parameters and a sequence of scale parameters, we consider another sequence of random variables that is obtained by perturbing the location or scale parameter sequences. Using a result of Kakutani on equivalence of infinite product measures, we provide sufficient conditions for the equivalence of laws of the two sequences.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-60230</identifier>
    <author>Han Cheng Lie</author>
    <submitter>Han Cheng Lie</submitter>
    <author>T. J. Sullivan</author>
    <series>
      <title>ZIB-Report</title>
      <number>16-40</number>
    </series>
    <collection role="msc" number="60-XX">PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="persons" number="lie">Lie, Han</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6023/ZIB_report.pdf</file>
  </doc>
  <doc>
    <id>5942</id>
    <completedYear>2016</completedYear>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Well-posed Bayesian inverse problems and heavy-tailed stable Banach space priors</title>
    <abstract language="eng">This article extends the framework of Bayesian inverse problems in infinite-dimensional parameter spaces, as advocated by Stuart (Acta Numer. 19:451–559, 2010) and others, to the case of a heavy-tailed prior measure in the family of stable distributions, such as an infinite-dimensional Cauchy distribution, for which polynomial moments are infinite or undefined.  It is shown that analogues of the Karhunen–Loève expansion for square-integrable random variables can be used to sample such measures.  Furthermore, under weaker regularity assumptions than those used to date, the Bayesian posterior measure is shown to depend Lipschitz continuously in the Hellinger metric upon perturbations of the misfit function and observed data.</abstract>
    <identifier type="urn">urn:nbn:de:0297-zib-59422</identifier>
    <identifier type="doi">10.3934/ipi.2017040</identifier>
    <identifier type="issn">1438-0064</identifier>
    <enrichment key="SourceTitle">Appeared in: Inverse Problems and Imaging</enrichment>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>T. J. Sullivan</author>
    <submitter>T. J. Sullivan</submitter>
    <series>
      <title>ZIB-Report</title>
      <number>16-30</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Bayesian inverse problems</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>heavy-tailed distribution</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Karhunen–Loève expansion</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>stable distribution</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>uncertainty quantification</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>well-posedness</value>
    </subject>
    <collection role="msc" number="28-XX">MEASURE AND INTEGRATION (For analysis on manifolds, see 58-XX)</collection>
    <collection role="msc" number="35-XX">PARTIAL DIFFERENTIAL EQUATIONS</collection>
    <collection role="msc" number="60-XX">PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)</collection>
    <collection role="msc" number="62-XX">STATISTICS</collection>
    <collection role="msc" number="65-XX">NUMERICAL ANALYSIS</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="uq">Uncertainty Quantification</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5942/stable_bip.pdf</file>
  </doc>
  <doc>
    <id>5967</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-06-15</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases</title>
    <abstract language="eng">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.&#13;
&#13;
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.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-59672</identifier>
    <identifier type="doi">10.1016/j.neuron.2016.06.012</identifier>
    <enrichment key="SourceTitle">appeared also as bioRxiv preprint http://dx.doi.org/10.1101/006346 and in revised form in Neuron</enrichment>
    <author>Marta Costa</author>
    <submitter>Steffen Prohaska</submitter>
    <author>James D. Manton</author>
    <author>Aaron D. Ostrovsky</author>
    <author>Steffen Prohaska</author>
    <author>Gregory S.X.E. Jefferis</author>
    <series>
      <title>ZIB-Report</title>
      <number>16-34</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>neuroinformatics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>NBLAST</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>neuron similarity</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>cell type</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>clustering</value>
    </subject>
    <collection role="ccs" number="J.">Computer Applications</collection>
    <collection role="pacs" number="80.00.00">INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="msc" number="92-XX">BIOLOGY AND OTHER NATURAL SCIENCES</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5967/zibreport-16-34_v1.pdf</file>
  </doc>
  <doc>
    <id>5970</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-06-22</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Effective Dynamics Along Given Reaction Coordinates, and Reaction Rate Theory</title>
    <abstract language="eng">In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature. In this article, we contribute to this discussion: We first show that if we start with an ergodic diffusion processes whose invariant measure is unique then these properties are inherited by the effective dynamics. Then, we give equations for the effective dynamics, discuss whether the dominant timescales and reaction rates inferred from the effective dynamics are accurate approximations of such quantities for the full dynamics, and compare our findings to results from approaches like Zwanzig-Mori, averaging, or homogenization. Finally, by discussing the algorithmic realization of the effective dynamics, we demonstrate that recent algorithmic techniques like the ”equation-free” approach and the ”heterogeneous multiscale method” can be seen as special cases of our approach.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-59706</identifier>
    <identifier type="doi">10.1039/C6FD00147E</identifier>
    <author>Wei Zhang</author>
    <submitter>Paulina Bressel</submitter>
    <author>Carsten Hartmann</author>
    <author>Christof Schütte</author>
    <series>
      <title>ZIB-Report</title>
      <number>16-35</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Ergodic diffusion</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>reaction coordinate</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>effective dynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>model reduction</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>equation-free</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>heterogeneous multiscale method</value>
    </subject>
    <collection role="msc" number="58J65">Diffusion processes and stochastic analysis on manifolds [See also 35R60, 60H10, 60J60]</collection>
    <collection role="msc" number="62P35">Applications to physics</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5970/ZIB_16-35.pdf</file>
  </doc>
  <doc>
    <id>5951</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-05-25</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Probabilistic Meshless Methods for Partial Differential Equations and Bayesian Inverse Problems</title>
    <abstract language="eng">This paper develops a class of meshless methods that are well-suited to statistical inverse problems involving partial differential equations (PDEs).  The methods discussed in this paper view the forcing term in the PDE as a random field that induces a probability distribution over the residual error of a symmetric collocation method.  This construction enables the solution of challenging inverse problems while accounting, in a rigorous way, for the impact of the discretisation of the forward problem.  In particular, this confers robustness to failure of meshless methods, with statistical inferences driven to be more conservative in the presence of significant solver error.  In addition, (i) a principled learning-theoretic approach to minimise the impact of solver error is developed, and (ii) the challenging setting of inverse problems with a non-linear forward model is considered.  The method is applied to parameter inference problems in which non-negligible solver error must be accounted for in order to draw valid statistical conclusions.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-59513</identifier>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-59513</enrichment>
    <submitter>T. J. Sullivan</submitter>
    <author>Jon Cockayne</author>
    <author>Chris Oates</author>
    <author>T. J. Sullivan</author>
    <author>Mark Girolami</author>
    <series>
      <title>ZIB-Report</title>
      <number>16-31</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Probabilistic Numerics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Partial Differential Equations</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Inverse Problems</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Meshless Methods</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Gaussian Processes</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Pseudo-Marginal MCMC</value>
    </subject>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="uq">Uncertainty Quantification</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5951/pmm_pde_bip.pdf</file>
  </doc>
  <doc>
    <id>6603</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-12-01</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">The Grand Four</title>
    <abstract language="eng">This paper gives a concise synopsis and some new insights concerning four&#13;
affine invariant globalizations of the local Newton method. The&#13;
invariance classes include: affine covariance, affine contravariance, affine&#13;
conjugacy, and affine similarity. In view of algorithmic robustness, each of these classes of algorithms is particularly suitable for some corresponding&#13;
problem class.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-66038</identifier>
    <author>Peter Deuflhard</author>
    <submitter>Julia Boltze</submitter>
    <series>
      <title>ZIB-Report</title>
      <number>17-70</number>
    </series>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="deuflhard">Deuflhard, Peter</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6603/ZR 17-70.pdf</file>
  </doc>
  <doc>
    <id>7477</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2019-10-21</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">MPI Passive Target Synchronization on a Non-Cache-Coherent Shared-Memory Processor</title>
    <abstract language="eng">MPI passive target synchronization offers exclusive and shared locks. These are the building blocks for the implementation of applications with Readers &amp; Writers semantic, like for example distributed hash tables. This paper discusses the implementation of MPI passive target synchronization on a non-cache-coherent multicore, the Intel Single-Chip Cloud Computer. The considered algorithms differ in their communication style (message based versus shared memory), their data structures (centralized versus distributed) and their semantics (with/without Writer preference). It is shown that shared memory approaches scale very well and deliver good performance, even in absence of cache coherence.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-74774</identifier>
    <identifier type="doi">10.12752/7477</identifier>
    <author>Steffen Christgau</author>
    <submitter>Steffen Christgau</submitter>
    <author>Bettina Schnor</author>
    <series>
      <title>ZIB-Report</title>
      <number>19-52</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>process synchronization</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>programming models and systems for manycores</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>MPI</value>
    </subject>
    <collection role="ccs" number="">Multiple-instruction-stream, multiple-data-stream processors (MIMD)</collection>
    <collection role="ccs" number="">Parallel programming</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="persons" number="christgau">Christgau, Steffen</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/7477/ZIB_TR_19-52.pdf</file>
  </doc>
  <doc>
    <id>7774</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2020-03-04</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Making spherical-harmonics-based Geometric Morphometrics (SPHARM) approachable for 3D images containing large cavity openings using Ambient Occlusion - a study using hermit crab claw shape variability</title>
    <abstract language="eng">An advantageous property of mesh-based geometric morphometrics (GM) towards landmark-based approaches, is the possibility of precisely examining highly irregular shapes and highly topographic surfaces. In case of spherical-harmonics-based GM the main requirement is a completely closed mesh surface, which often is not given, especially when dealing with natural objects. Here we present a methodological workflow to prepare 3D segmentations containing large cavity openings for the conduction of spherical-harmonics-based GM. This will be exemplified with a case study on claws of hermit crabs (Paguroidea, Decapoda, Crustacea), whereby joint openings – between manus and “movable finger” – typify the large-cavity-opening problem. We found a methodology including an ambient-occlusion-based segmentation algorithm leading to results precise and suitable to study the inter- and intraspecific differences in shape of hermit crab claws. Statistical analyses showed a significant separation between all examined diogenid and pagurid claws, whereas the separation between all left and right claws did not show significance. Additionally, the procedure offers other benefits. It is easy to reproduce and creates sparse variance in the data, closures integrate smoothly into the total structures and the algorithm saves a significant amount of time.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-77744</identifier>
    <author>Yannic Ege</author>
    <submitter>Daniel Baum</submitter>
    <author>Christian Foth</author>
    <author>Daniel Baum</author>
    <author>Christian S. Wirkner</author>
    <author>Stefan Richter</author>
    <series>
      <title>ZIB-Report</title>
      <number>20-09</number>
    </series>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/7774/ZR-20-09.pdf</file>
  </doc>
  <doc>
    <id>7848</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2020-06-09</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">The Quality of Heuristic Functions for IDA*</title>
    <abstract language="eng">The aim of this thesis is to deepen our understand of how&#13;
IDA* heuristics influence the number of nodes expanded during&#13;
search.  To this end, we develop Korf's formula for the number&#13;
of expanded nodes into a heuristic quality η which&#13;
expresses the quality of a heuristic function as a constant factor&#13;
on the number of expanded nodes, independent of a particular problem&#13;
instance.&#13;
&#13;
We proceed to show how to compute η for some common kinds of&#13;
heuristics and how to estimate η by means of a random sample for&#13;
arbitrary heuristics.  Using the value of η for some concrete&#13;
examples, we then inspect for which parts of the search space the&#13;
values of h(v) are particularly critical to the performance of the&#13;
heuristic, allowing us to build better heuristics for future problems.&#13;
&#13;
This report originally appeared as a master thesis at Humboldt&#13;
University of Berlin.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-78489</identifier>
    <author>Robert Clausecker</author>
    <submitter>Robert Clausecker</submitter>
    <series>
      <title>ZIB-Report</title>
      <number>20-17</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>IDA* heuristic search sampling random walks</value>
    </subject>
    <collection role="ccs" number="">Graph and tree search strategies</collection>
    <collection role="ccs" number="">Heuristic methods</collection>
    <collection role="msc" number="05C81">Random walks on graphs</collection>
    <collection role="msc" number="60G50">Sums of independent random variables; random walks</collection>
    <collection role="msc" number="62D05">Sampling theory, sample surveys</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="persons" number="clausecker">Clausecker, Robert</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/7848/ZR-20-17.pdf</file>
  </doc>
  <doc>
    <id>5494</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2015-05-07</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Local Confluence Analysis for Amalgamated Graph Transformation: Long Version</title>
    <abstract language="eng">Amalgamated graph transformation allows to define schemes of rules&#13;
coinciding in common core activities and differing over additional parallel independent&#13;
activities. Consequently, a rule scheme is specified by a kernel rule and a set of extending multi-rules forming an interaction scheme. Amalgamated&#13;
transformations have been increasingly used in various modeling contexts.&#13;
&#13;
Critical Pair Analysis (CPA) can be used to show local confluence of graph transformation&#13;
systems. It is an open challenge to lift the CPA to amalgamated graph transformation systems, especially since infinite many pairs of amalgamated rules&#13;
occur in general. As a first step towards an efficient local confluence analysis of&#13;
amalgamated graph transformation systems, we show that the analysis of a finite&#13;
set of critical pairs suffices to prove local confluence.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-54943</identifier>
    <identifier type="doi">10.1007/978-3-319-21145-9_5</identifier>
    <enrichment key="SourceTitle">Appeared in: Graph Transformations. Proceedings of ICGT 2015. Springer LNCS 9151, p. 69-86</enrichment>
    <author>Gabriele Taentzer</author>
    <submitter>Ulrike Golas</submitter>
    <author>Ulrike Golas</author>
    <series>
      <title>ZIB-Report</title>
      <number>15-29</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>amalgamated graph transformation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>parallel independence</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>critical pair analysis</value>
    </subject>
    <collection role="ccs" number="F.">Theory of Computation</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5494/main TR.pdf</file>
  </doc>
  <doc>
    <id>5498</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2015-05-08</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Bag-Of-SFA-Symbols in Vector Space (BOSS VS)</title>
    <abstract language="eng">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.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-54984</identifier>
    <author>Patrick Schäfer</author>
    <submitter>Patrick Schäfer</submitter>
    <series>
      <title>ZIB-Report</title>
      <number>15-30</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Time Series</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Classification</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Data Mining</value>
    </subject>
    <collection role="ccs" number="H.3.3">Information Search and Retrieval</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="persons" number="patrick.schaefer">Schäfer, Patrick</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5498/ZR-15-30.pdf</file>
  </doc>
  <doc>
    <id>5435</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2015-09-04</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials</title>
    <abstract language="eng">Current characterization methods of the so-called Bulk Heterojunction (BHJ), which is the main material of Organic Photovoltaic (OPV) solar cells, are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual characterization and exploration of local structure-performance correlations. We also propose a formula that correlates the structural features with the performance bottlenecks. Since research into BHJ materials is highly multidisciplinary, our framework enables a visual feedback strategy that allows scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characterizations. Furthermore, we show that our approach could substantially reduce the turnaround time.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-54353</identifier>
    <enrichment key="SourceTitle">Appeared in: Computer Graphics Forum, 34(3), pp. 401-410, 2015</enrichment>
    <author>Amal Aboulhassan</author>
    <submitter>Daniel Baum</submitter>
    <author>Daniel Baum</author>
    <author>Olga Wodo</author>
    <author>Baskar Ganapathysubramanian</author>
    <author>Aram Amassian</author>
    <author>Markus Hadwiger</author>
    <series>
      <title>ZIB-Report</title>
      <number>15-20</number>
    </series>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5435/ZR-15-20.pdf</file>
  </doc>
  <doc>
    <id>6323</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-10-04</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies</title>
    <abstract language="eng">The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-63239</identifier>
    <author>Amal Aboulhassan</author>
    <submitter>Daniel Baum</submitter>
    <author>Ronell Sicat</author>
    <author>Daniel Baum</author>
    <author>Olga Wodo</author>
    <author>Markus Hadwiger</author>
    <series>
      <title>ZIB-Report</title>
      <number>17-16</number>
    </series>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6323/ZR-17-16.pdf</file>
  </doc>
  <doc>
    <id>6418</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-05-29</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies</title>
    <abstract language="eng">Background&#13;
We assessed the novel MACC1 gene to further stratify stage II colon cancer&#13;
patients with proficient mismatch repair (pMMR).&#13;
Patients and methods&#13;
Four cohorts with 596 patients were analyzed: Charité 1 discovery cohort&#13;
was assayed for MACC1 mRNA expression and MMR in cryo-preserved&#13;
tumors. Charité 2 comparison cohort was used to translate MACC1 qRT-&#13;
PCR analyses to FFPE samples. In the BIOGRID 1 training cohort MACC1&#13;
mRNA levels were related to MACC1 protein levels from&#13;
immunohistochemistry in FFPE sections; also analyzed for MMR.&#13;
Chemotherapy-naïve pMMR patients were stratified by MACC1 mRNA and&#13;
protein expression to establish risk groups based on recurrence-free&#13;
survival (RFS). Risk stratification from BIOGRID 1 was confirmed in the&#13;
BIOGRID 2 validation cohort. Pooled BIOGRID datasets produced a best&#13;
effect-size estimate.&#13;
Results&#13;
In BIOGRID 1, using qRT-PCR and immunohistochemistry for MACC1&#13;
detection, pMMR/MACC1-low patients had a lower recurrence probability&#13;
versus pMMR/MACC1-high patients (5-year RFS of 92% and 67% versus&#13;
100% and 68%, respectively). In BIOGRID 2, longer RFS was confirmed&#13;
for pMMR/MACC1-low versus pMMR/MACC1-high patients (5-year RFS of&#13;
100% versus 90%, respectively). In the pooled dataset, 6.5% of patients&#13;
were pMMR/MACC1-low with no disease recurrence, resulting in a 17%&#13;
higher 5-year RFS (95% CI (12.6-21.3%)) versus pMMR/MACC1-high&#13;
patients (P=0.037). Outcomes were similar for pMMR/MACC1-low and&#13;
deficient MMR (dMMR) patients (5-year RFS of 100% and 96%,&#13;
respectively).&#13;
Conclusions&#13;
MACC1 expression stratifies colon cancer patients with unfavorable pMMR&#13;
status. Stage II colon cancer patients with pMMR/MACC1-low tumors have&#13;
a similar favorable prognosis to those with dMMR with potential&#13;
implications for the role of adjuvant therapy.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="doi">10.1093/annonc/mdx207</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-64184</identifier>
    <enrichment key="SourceTitle">Appeared in: Annals of Oncology</enrichment>
    <author>Ulrich-Peter Rohr</author>
    <submitter>Marc Osterland</submitter>
    <author>Pia Herrmann</author>
    <author>Katharina Ilm</author>
    <author>Hai Zhang</author>
    <author>Sabine Lohmann</author>
    <author>Astrid Reiser</author>
    <author>Andrea Muranyi</author>
    <author>Janice Smith</author>
    <author>Susen Burock</author>
    <author>Marc Osterland</author>
    <author>Katherine Leith</author>
    <author>Shalini Singh</author>
    <author>Patrick Brunhoeber</author>
    <author>Rebecca Bowermaster</author>
    <author>Jeanne Tie</author>
    <author>Michael Christie</author>
    <author>Hui-Li Wong</author>
    <author>Paul Waring</author>
    <author>Kandavel Shanmugam</author>
    <author>Peter Gibbs</author>
    <author>Ulrike Stein</author>
    <series>
      <title>ZIB-Report</title>
      <number>17-28</number>
    </series>
    <collection role="msc" number="92-XX">BIOLOGY AND OTHER NATURAL SCIENCES</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6486</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-09-08</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A multi scale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics</title>
    <abstract language="eng">We investigate metastable dynamical systems subject to non-stationary forcing as they appear in molecular dynamics for systems driven by external fields. We show, that if the strength of the forcing is inversely proportional to the length of the slow metastable time scales of the unforced system, then the effective behavior of the forced system on slow time scales can be described by a low-dimensional reduced master equation. Our construction is explicit and uses the multiscale perturbation expansion method called two-timing, or method of multiple scales. The reduced master equation—a Markov state model—can be assembled by constructing two equilibrium Markov state models; one for the unforced system, and one for a slightly perturbed one.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-64868</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2018-08-15</enrichment>
    <enrichment key="SubmissionStatus">accepted for publication</enrichment>
    <author>Péter Koltai</author>
    <submitter>Paulina Bressel</submitter>
    <author>Christof Schütte</author>
    <series>
      <title>ZIB-Report</title>
      <number>17-49</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov state model</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>non-equilibrium molecular dynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>two timescale master equation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>non-stationary forcing</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>metastability</value>
    </subject>
    <collection role="msc" number="34E13">Multiple scale methods</collection>
    <collection role="msc" number="60J20">Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) [See also 90B30, 91D10, 91D35, 91E40]</collection>
    <collection role="msc" number="60J60">Diffusion processes [See also 58J65]</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6486/ZIB-Report_17-49.pdf</file>
  </doc>
  <doc>
    <id>6448</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-11-07</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Rational Solutions of Underdetermined Polynomial Equations</title>
    <abstract language="eng">In this paper we report on an application of computer algebra in which mathematical puzzles are generated of a type that had been widely used in mathematics contests by a large number of participants worldwide. &#13;
&#13;
The algorithmic aspect of our work provides a method to compute rational solutions of single polynomial equations that are typically large with 10^2 ... 10^5 terms and that are heavily underdetermined. &#13;
&#13;
It was possible to obtain this functionality by adding a number of new modules for a new type of splitting of equations to the existing package CRACK that is normally used to solve polynomial algebraic and differential systems of equations.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-64488</identifier>
    <author>Thomas Wolf</author>
    <submitter>Winfried Neun</submitter>
    <author>Chimaobi Amadi</author>
    <series>
      <title>ZIB-Report</title>
      <number>17-33</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>underdetermined polynomial systems, rational solutions, computer algebra, recreational mathematics</value>
    </subject>
    <collection role="msc" number="08-XX">GENERAL ALGEBRAIC SYSTEMS</collection>
    <collection role="msc" number="13-XX">COMMUTATIVE RINGS AND ALGEBRAS</collection>
    <collection role="msc" number="97-XX">MATHEMATICS EDUCATION</collection>
    <collection role="institutes" number="sis">Digital Data and Information for Society, Science, and Culture</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6448/ZR-17-33.pdf</file>
  </doc>
  <doc>
    <id>5700</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-01-11</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Variational Bayesian Inference and Model Selection for the Stochastic Block Model with Irrelevant Vertices</title>
    <abstract language="eng">Real World networks often exhibit a significant number of vertices which are sparsely and irregularly connected to other vertices in the network. For clustering theses networks with a model based algorithm, we propose the Stochastic Block Model with Irrelevant Vertices (SBMIV) for weighted net- works. We propose an original Variational Bayesian Expectation Maximiza- tion inference algorithm for the SBMIV which is an advanced version of our Blockloading algorithm for the Stochastic Block Model. We introduce a model selection criterion for the number of clusters of the SBMIV which is based on the lower variational bound of the model likelihood. We propose a fully Bayesian inference process, based on plausible informative priors, which is independent of other algorithms for preprocessing start values for the cluster assignment of vertices. Our inference methods allow for a multi level identification of irrelevant vertices which are hard to cluster reliably ac- cording to the SBM. We demonstrate that our methods improve on the normal Stochastic Block model by applying it to to Earthquake Networks which are an example of networks with a large number of sparsely and irregularly con- nected vertices.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-57003</identifier>
    <author>Christian Tobias Willenbockel</author>
    <submitter>Erlinda Körnig</submitter>
    <author>Christof Schütte</author>
    <series>
      <title>ZIB-Report</title>
      <number>16-01</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Clustering</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Variational Bayes EM</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Model Selection,</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Stochastic Block Model</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Networks</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>unsupervised classification</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Noise</value>
    </subject>
    <collection role="msc" number="62H12">Estimation</collection>
    <collection role="msc" number="62H30">Classification and discrimination; cluster analysis [See also 68T10]</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5700/ZIB-Report_16-01.pdf</file>
  </doc>
  <doc>
    <id>5801</id>
    <completedYear/>
    <publishedYear>2010</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition>10-12</edition>
    <issue/>
    <volume>2010</volume>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Challenges in Atomistic-to-Continuum Coupling</title>
    <abstract language="eng">This paper is concerned with the design, analysis, and implementation of concurrent coupling approaches where different (atomic and continuous) models are used simultaneously within a single simulation process. Thereby, several problems or pitfalls can happen, for example, the reflection of molecular movements at the “boundary” between the atomic and continuum regions which leads to an unphysical increase in energy in the atomic model. We investigate the problems with the aim of giving an introduction into this field and preventing errors for scientists starting their research towards multiscale methods.</abstract>
    <parentTitle language="eng">ZIB Report</parentTitle>
    <identifier type="doi">10.1155/2015/834517</identifier>
    <enrichment key="PreprintUrn">Preprint</enrichment>
    <author>Konstantin Fackeldey</author>
    <submitter>Konstantin Fackeldey</submitter>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="projects" number="no-project">no-project</collection>
  </doc>
  <doc>
    <id>5786</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition>145</edition>
    <issue/>
    <volume>174103</volume>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-03-16</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">On metastability and Markov state models for non-stationary molecular dynamics</title>
    <abstract language="eng">We utilize the theory of coherent sets to build Markov state models for non- equilibrium molecular dynamical systems. Unlike for systems in equilibrium, “meta- stable” sets in the non-equilibrium case may move as time evolves. We formalize this concept by relying on the theory of coherent sets, based on this we derive finite-time non-stationary Markov state models, and illustrate the concept and its main differences to equilibrium Markov state modeling on simple, one-dimensional examples.</abstract>
    <parentTitle language="eng">The Journal of Chemical Physics</parentTitle>
    <subTitle language="deu">2016 Editor's Choice of The Journal of Chemical Physics</subTitle>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-57869</identifier>
    <identifier type="doi">10.1063/1.4966157</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="SourceTitle">Appeared in: The Journal of Chemical Physics 145 (2016)</enrichment>
    <author>Peter Koltai</author>
    <submitter>Erlinda Koernig</submitter>
    <author>Giovanni Ciccotti</author>
    <author>Christof Schütte</author>
    <series>
      <title>ZIB-Report</title>
      <number>16-11</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>coherent set,</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov state model</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>non-equilibrium molecular dynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>metastability</value>
    </subject>
    <collection role="msc" number="60J20">Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) [See also 90B30, 91D10, 91D35, 91E40]</collection>
    <collection role="msc" number="60J35">Transition functions, generators and resolvents [See also 47D03, 47D07]</collection>
    <collection role="msc" number="60J60">Diffusion processes [See also 58J65]</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="projects" number="MODAL-MedLab">MODAL-MedLab</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="projects" number="MODAL-Gesamt">MODAL-Gesamt</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5786/ZIB_16-11_new.pdf</file>
  </doc>
  <doc>
    <id>6558</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-11-13</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Notes on the Construction of Pattern Databases</title>
    <abstract language="eng">This report aims to explain and extend pattern databases as a tool in finding optimal solutions to combination puzzles. Using sliding tile puzzles as an example, an overview over techniques to construct and use pattern databases is given, analysed, and extended. As novel results, zero aware additive pattern databases and PDB catalogues are introduced. This report originally appeared as a bachelor thesis at Humboldt University of Berlin under the title Notes on the Construction of Tablebases.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-65586</identifier>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Robert Clausecker</author>
    <submitter>Robert Clausecker</submitter>
    <series>
      <title>ZIB-Report</title>
      <number>17-59</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>pattern-database 15-puzzle 24-puzzle ida* heuristic-search pdb-catalogue zpdb</value>
    </subject>
    <collection role="ccs" number="">Graph and tree search strategies</collection>
    <collection role="ccs" number="">Heuristic methods</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="persons" number="clausecker">Clausecker, Robert</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6558/zibba.pdf</file>
  </doc>
  <doc>
    <id>8446</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2021-10-22</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Spontaneous trail formation in populations of auto-chemotactic walkers</title>
    <abstract language="eng">We study the formation of trails in populations of self-propelled agents that make oriented deposits of pheromones and also sense such deposits to which they then respond with gradual changes of their direction of motion. Based on extensive off-lattice computer simulations aiming at the scale of insects, e.g., ants, we identify a number of emerging stationary patterns and obtain qualitatively the non-equilibrium \add{state} diagram of the model, spanned by the strength of the agent--pheromone interaction and the number density of the population. In particular, we demonstrate the spontaneous formation of persistent, macroscopic trails, and highlight some behaviour that is consistent with a dynamic phase transition. This includes a characterisation of the mass of system-spanning trails as a potential order parameter. We also propose a dynamic model for a few macroscopic observables, including the sub-population size of trail-following agents, which captures the early phase of trail formation.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-84466</identifier>
    <enrichment key="opus.source">publish</enrichment>
    <author>Zahra Mokhtari</author>
    <submitter>Felix Höfling</submitter>
    <author>Robert I. A. Patterson</author>
    <author>Felix Höfling</author>
    <series>
      <title>ZIB-Report</title>
      <number>21-36</number>
    </series>
    <collection role="pacs" number="80.00.00">INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY</collection>
    <collection role="msc" number="82-XX">STATISTICAL MECHANICS, STRUCTURE OF MATTER</collection>
    <collection role="institutes" number="vas">Distributed Algorithms and Supercomputing</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="persons" number="hoefling">Höfling, Felix</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/8446/ZR-21-36.pdf</file>
  </doc>
  <doc>
    <id>6075</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
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    <publishedDate>2016-01-11</publishedDate>
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    <title language="eng">The Graph Segmentation Problem</title>
    <abstract language="eng">We investigate a graph theoretical problem arising in the automatic billing of a network toll. Given a network and a family of user paths, we study the graph segmentation problem (GSP) to cover parts of the user paths by a set of disjoint segments. The GSP is shown to be NP-hard but for special cases it can be solved in polynomial time. We also show that the marginal utility of a segment is bounded. Computational results for real-world instances show that in practice the problem is more amenable than the theoretic bounds suggest.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-60750</identifier>
    <enrichment key="SourceTitle">INOC 2017 – 8th International Network Optimization Conference</enrichment>
    <author>Stephan Schwartz</author>
    <submitter>Stephan Schwartz</submitter>
    <author>Ralf Borndörfer</author>
    <author>Gerald Bartz</author>
    <series>
      <title>ZIB-Report</title>
      <number>16-53</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>toll billing</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>graph segmentation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>combinatorial optimization</value>
    </subject>
    <collection role="msc" number="90-XX">OPERATIONS RESEARCH, MATHEMATICAL PROGRAMMING</collection>
    <collection role="institutes" number="optimization">Mathematical Optimization</collection>
    <collection role="institutes" number="traffic">Mathematics of Transportation and Logistics</collection>
    <collection role="persons" number="borndoerfer">Borndörfer, Ralf</collection>
    <collection role="persons" number="schwartz">Schwartz, Stephan</collection>
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    <publishedDate>2015-12-15</publishedDate>
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    <title language="eng">New Conjectures For Union-Closed Families</title>
    <abstract language="eng">The Frankl conjecture, also known as the union-closed sets conjecture, states that there exists an element in at least half of the sets of any (non-empty) union-closed family. From an optimization point of view, one could instead prove that 2a is an upper bound to the number of sets in a union-closed family with n elements where each element is in at most a sets, where a and n are non-negative integers. Formulating these problems as integer programs we observe that computed optimal values do not vary with n. We formalize these observations as conjectures, and show that they are not equivalent to the Frankl conjecture while still having&#13;
wide-reaching implications if proven true. Finally, we partially prove the new conjectures and discuss possible approaches to solve them completely.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-56804</identifier>
    <author>Jonad Pulaj</author>
    <submitter>Jonad Pulaj</submitter>
    <author>Annie Raymond</author>
    <author>Dirk Theis</author>
    <series>
      <title>ZIB-Report</title>
      <number>15-57</number>
    </series>
    <collection role="institutes" number="optimization">Mathematical Optimization</collection>
    <collection role="institutes" number="tele">Mathematics of Telecommunication</collection>
    <collection role="persons" number="pulaj">Pulaj, Jonad</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="aopt">Applied Optimization</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5680/ZIB.pdf</file>
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    <completedDate>--</completedDate>
    <publishedDate>2017-10-06</publishedDate>
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    <title language="eng">Variational characterization of free energy: Theory and algorithms</title>
    <abstract language="eng">The article surveys and extends variational formulations of the thermodynamic free&#13;
energy and discusses their information-theoretic content from the perspective of mathematical statistics. We revisit the well-known Jarzynski equality for  nonequilibrium free energy sampling within the framework of importance sampling and Girsanov change-of-measure transformations. The implications of the different variational formulations for designing efficient stochastic optimization and nonequilibrium simulation algorithms for computing free energies are discussed and illustrated.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-65045</identifier>
    <author>Carsten Hartmann</author>
    <submitter>Paulina Bressel</submitter>
    <author>Lorenz Richter</author>
    <author>Christof Schütte</author>
    <author>Wei Zhang</author>
    <series>
      <title>ZIB-Report</title>
      <number>17-52</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Importance sampling</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Donsker-Varadhan principle</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>thermodynamic free energy</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>nonequilibrium molecular dynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>stochastic approximation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>cross-entropy method</value>
    </subject>
    <collection role="msc" number="37A60">Dynamical systems in statistical mechanics [See also 82Cxx]</collection>
    <collection role="msc" number="60J60">Diffusion processes [See also 58J65]</collection>
    <collection role="msc" number="82C05">Classical dynamic and nonequilibrium statistical mechanics (general)</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="persons" number="zhang">Zhang, Wei</collection>
    <collection role="institutes" number="MSoCP">Modeling and Simulation of Complex Processes</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6504/ZIB-Report_17-52.pdf</file>
  </doc>
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