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  • Opus Repository ZIB  (151)
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  • 1
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    Finding All Maximal Cliques of a Family of Induced Subgraphs (2004)
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    Publication Date: 2020-03-06
    Description: Many real world problems can be mapped onto graphs and solved with well-established efficient algorithms studied in graph theory. One such problem is to find large sets of points satisfying some mutual relationship. This problem can be transformed to the problem of finding all cliques of an undirected graph by mapping each point onto a vertex of the graph and connecting any two vertices by an edge whose corresponding points satisfy our desired relationship. Clique detection has been widely studied and there exist efficient algorithms. In this paper we study a related problem, where all points have a set of binary attributes, each of which is either 0 or 1. This is only a small limitation, since all discrete properties can be mapped onto binary attributes. In our case, we want to find large sets of points not only satisfying some mutual relationship; but, in addition, all points of a set also need to have at least one common attribute with value 1. The problem we described can be mapped onto a set of induced subgraphs, where each subgraph represents a single attribute. For attribute $i$, its associated subgraph contains those vertices corresponding to the points with attribute $i$ set to 1. We introduce the notion of a maximal clique of a family, $\mathcal{G}$, of induced subgraphs of an undirected graph, and show that determining all maximal cliques of $\mathcal{G}$ solves our problem. Furthermore, we present an efficient algorithm to compute all maximal cliques of $\mathcal{G}$. The algorithm we propose is an extension of the widely used Bron-Kerbosch algorithm.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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  • 2
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    Multiple Semi-flexible 3D Superposition of Drug-sized Molecules (2004)
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    Publication Date: 2020-03-06
    Description: In this paper we describe a new algorithm for multiple semi-flexible superpositioning of drug-sized molecules. The algorithm identifies structural similarities of two or more molecules. When comparing a set of molecules on the basis of their three-dimensional structures, one is faced with two main problems. (1) Molecular structures are not fixed but flexible, i.e., a molecule adopts different forms. To address this problem, we consider a set of conformers per molecule. As conformers we use representatives of conformational ensembles, generated by the program ZIBMol. (2) The degree of similarity may vary considerably among the molecules. This problem is addressed by searching for similar substructures present in arbitrary subsets of the given set of molecules. The algorithm requires to preselect a reference molecule. All molecules are compared to this reference molecule. For this pairwise comparison we use a two-step approach. Clique detection on the correspondence graph of the molecular structures is used to generate start transformations, which are then iteratively improved to compute large common substructures. The results of the pairwise comparisons are efficiently merged using binary matching trees. All common substructures that were found, whether they are common to all or only a few molecules, are ranked according to different criteria, such as number of molecules containing the substructure, size of substructure, and geometric fit. For evaluating the geometric fit, we extend a known scoring function by introducing weights which allow to favor potential pharmacophore points. Despite considering the full atomic information for identifying multiple structural similarities, our algorithm is quite fast. Thus it is well suited as an interactive tool for the exploration of structural similarities of drug-sized molecules.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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  • 3
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    Optimal Operation of Transient Gas Transport Networks
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    Publication Date: 2022-01-18
    Description: In this paper, we describe an algorithmic framework for the optimal operation of transient gas transport networks consisting of a hierarchical MILP formulation together with a sequential linear programming inspired post-processing routine. Its implementation is part of the KOMPASS decision support system, which is currently used in an industrial setting. Real-world gas transport networks are controlled by operating complex pipeline intersection areas, which comprise multiple compressor units, regulators, and valves. In the following, we introduce the concept of network stations to model them. Thereby, we represent the technical capabilities of a station by hand-tailored artificial arcs and add them to network. Furthermore, we choose from a predefined set of flow directions for each network station and time step, which determines where the gas enters and leaves the station. Additionally, we have to select a supported simple state, which consists of two subsets of artificial arcs: Arcs that must and arcs that cannot be used. The goal is to determine a stable control of the network satisfying all supplies and demands. The pipeline intersections, that are represented by the network stations, were initially built centuries ago. Subsequently, due to updates, changes, and extensions, they evolved into highly complex and involved topologies. To extract their basic properties and to model them using computer-readable and optimizable descriptions took several years of effort. To support the dispatchers in controlling the network, we need to compute a continuously updated list of recommended measures. Our motivation for the model presented here is to make fast decisions on important transient global control parameters, i.e., how to route the flow and where to compress the gas. Detailed continuous and discrete technical control measures realizing them, which take all hardware details into account, are determined in a subsequent step. In this paper, we present computational results from the KOMPASS project using detailed real-world data.
    Language: English
    Type: article , doc-type:article
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  • 4
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    From Natural Gas towards Hydrogen - A Feasibility Study on Current Transport Network Infrastructure and its Technical Control (2020)
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    Publication Date: 2020-11-24
    Description: This study examines the usability of a real-world, large-scale natural gas transport infrastructure for hydrogen transport. We investigate whether a converted network can transport the amounts of hydrogen necessary to satisfy current energy demands. After introducing an optimization model for the robust transient control of hydrogen networks, we conduct computational experiments based on real-world demand scenarios. Using a representative network, we demonstrate that replacing each turbo compressor unit by four parallel hydrogen compressors, each of them comprising multiple serial compression stages, and imposing stricter rules regarding the balancing of in- and outflow suffices to realize transport in a majority of scenarios. However, due to the reduced linepack there is an increased need for technical and non-technical measures leading to a more dynamic network control. Furthermore, the amount of energy needed for compression increases by 364% on average.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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    OPUS
  • 5
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    Length-Constrained Cycle Partition with an Application to UAV Routing (2020)
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    Publication Date: 2020-11-24
    Description: In this article, we discuss the Length-Constrained Cycle Partition Problem (LCCP). Besides edge weights, the undirected graph in LCCP features an individual critical weight value for each vertex. A cycle partition, i.e., a vertex disjoint cycle cover, is a feasible solution if the length of each cycle is not greater than the critical weight of each of the vertices in the cycle. The goal is to find a feasible partition with the minimum number of cycles. In this article, we discuss theoretical properties, preprocessing techniques, and two mixed-integer programming models (MIP) for LCCP both inspired by formulations for the closely related Travelling Salesperson Problem (TSP). Further, we introduce conflict hypergraphs, whose cliques yield valid constraints for the MIP models. We conclude with a report on computational experiments conducted on (A)TSPLIB-based instances. As an example, we use a routing problem in which a fleet of uncrewed aerial vehicles (UAVs) patrols a set of areas.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 6
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    On the Complexity of Computing Maximum and Minimum Min‐Cost‐Flows (2021)
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    Publication Date: 2022-01-18
    Description: Consider a flow network, i.e., a directed graph where each arc has a nonnegative capacity value and an associated length, together with nonempty supply intervals for the sources and nonempty demand intervals for the sinks. The Maximum Min-Cost-Flow Problem (MaxMCF) is to find fixed supply and demand values within these intervals such that the optimal objective value of the induced Min-Cost-Flow Problem (MCF) is maximized. In this paper, we show that MaxMCF as well as its uncapacitated variant, the Maximum Transportation Problem (MaxTP), are NP-hard. Further, we prove that MaxMCF is APX-hard if a connectedness-condition regarding the sources and the sinks of the flow network is dropped. Finally, we show how the Minimum Min-Cost-Flow Problem (MinMCF) can be solved in polynomial time.
    Language: English
    Type: article , doc-type:article
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  • 7
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    Automated segmentation of insect anatomy from micro-CT images using deep learning (2021)
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    Publication Date: 2022-03-11
    Language: English
    Type: article , doc-type:article
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  • 8
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    An Optimization Approach for the Transient Control of Hydrogen Transport Networks (2021)
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    Publication Date: 2021-02-11
    Language: English
    Type: article , doc-type:article
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  • 9
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    Segmentation of abdominal chordotonal organs based on semithin serial sections in the Rhododendron leafhopper Graphocephala fennahi (Cicadomorpha: Cicadellidae) (2021)
    Details
    Publication Date: 2022-03-11
    Description: For mating, leafhoppers (Cicadellidae) use substrate-borne vibrational signals to communicate. We provide the first complete description of the abdominal chordotonal organs that enable the perception of these signals. This supplementary data provides the aligned stack of 450 semithin serial sections of the first and second abdominal segment of an adult male Rhododendron leafhopper (Graphocephala fennahi). Further, this supplementary data comprises the segmentation files of five chordotonal organs, the exoskeleton, the segmental nerves and the spiracles of the first and the second abdominal segment. Due to time limitations, the structures of only one half of the body were segmented. The specimen was caught by hand net in September 2018 in Berlin-Tiergarten, Germany. Samples were embedded in Araldite® 502 resin and cut transversally in 1 μm thick sections using a Leica ultramicrotome and a DIATOME Histo Jumbo 6.0 mm diamond knife. Sections were placed on microscopic slides and stained with methylene blue/azur II. The images were taken by means of a 3DHISTECH PANNORAMIC SCAN II slide scanner in the Institute of Pathology Charité in Berlin-Mitte, Germany. Images with a voxel size of 0.273809 μm x 0.273809 μm x 1 μm where obtained. The images were converted from MRXS-files to TIFF-files with the 3DHistech software Slide Converter 2.3. Using Photoshop, the images were cropped to the same canvas size and artefacts were removed. All further steps, such as alignment and segmentation, were done with the software Amira. In order to facilitate the further processing of the dataset, the voxels where resampled to a size of 0.547619 μm x 0.547619 μm x 1 μm.
    Language: English
    Type: researchdata , doc-type:ResearchData
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  • 10
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    Bounding the final rank during a round robin tournament with integer programming (2020)
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    Publication Date: 2021-04-20
    Description: This article is mainly motivated by the urge to answer two kinds of questions regarding the Bundesliga, which is Germany’s primary football (soccer) division having the highest average stadium attendance worldwide: “At any point in the season, what is the lowest final rank a certain team can achieve?” and “At any point in the season, what is the highest final rank a certain team can achieve?”. Although we focus on the Bundesliga in particular, the integer programming formulations we introduce to answer these questions can easily be adapted to a variety of other league systems and tournaments.
    Language: English
    Type: article , doc-type:article
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