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  • ddc:000  (810)
  • English  (810)
  • 101
    Publication Date: 2021-08-05
    Description: This paper reports on the fourth version of the Mixed Integer Programming Library. Since ({\sc miplib}) is to provide a concise set of challenging problems, it became necessary to purge instances that became too easy. We present an overview of the 27 new problems and statistical data for all 60 instances.
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  • 102
    Publication Date: 2021-01-22
    Description: \newcommand{\chordsharp}{Chord$^\##$} Data lookup is a fundamental problem in peer-to-peer systems: Given a key, find the node that stores the associated object. Chord and other P2P algorithms use distributed hash tables (DHTs) to distribute the keys and nodes evenly across a logical ring. Using an efficient routing strategy, DHTs provide a routing performance of $O (\log N)$ in networks of $N$ nodes. While the routing performance has been shown to be optimal, the uniform key distribution makes it impossible for DHTs to support range queries. For range queries, consecutive keys must be stored on lo gically neighboring nodes. In this paper, we present an enhancement of Chord that eliminates the hash function while keeping the same routing performance. The resulting algorithm, named \chordsharp{}, provides a richer function ality while maintaining the same complexity. In addition to Chord, \chordsharp{} adapts to load imbalance.
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  • 103
    Publication Date: 2019-01-29
    Description: This paper is concerned with the sensitivities of function space oriented interior point approximations in parameter dependent problems. For an abstract setting that covers control constrained optimal control problems, the convergence of interior point sensitivities to the sensitivities of the optimal solution is shown. Error bounds for $L_q$ norms are derived and illustrated with numerical examples.
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  • 104
    Publication Date: 2020-08-05
    Description: We present an approach to implement an auction of railway slots. Railway network, train driving characteristics, and safety requirements are described by a simplified, but still complex macroscopic model. In this environment, slots are modelled as combinations of scheduled track segments. The auction design builds on the iterative combinatorial auction. However, combinatorial bids are restricted to some types of slot bundles that realize positive synergies between slots. We present a bidding language that allows bidding for these slot bundles. An integer programming approach is proposed to solve the winner determination problem of our auction. Computational results for auction simulations in the Hannover-Fulda-Kassel area of the German railway network give evidence that auction approaches can induce a more efficient use of railway capacity.
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  • 105
    Publication Date: 2014-11-10
    Description: We study the complexity of two Inverse Shortest Paths (ISP) problems with integer arc lengths and the requirement for uniquely determined shortest paths. Given a collection of paths in a directed graph, the task is to find positive integer arc lengths such that the given paths are uniquely determined shortest paths between their respective terminals. The first problem seeks for arc lengths that minimize the length of the longest of the prescribed paths. In the second problem, the length of the longest arc is to be minimized. We show that it is $np-hard$ to approximate the minimal longest path length within a factor less than $8/7$ or the minimal longest arc length within a factor less than $9/8$. This answers the (previously) open question whether these problems are $np-hard$ or not. We also present a simple algorithm that achieves an $\mathcal{O}(|V|)$-approximation guarantee for both variants. Both ISP problems arise in the planning of telecommunication networks with shortest path routing protocols. Our results imply that it is $\mathcal{NP}$-hard to decide whether a given path set can be realized with a real shortest path routing protocol such as OSPF, IS-IS, or RIP.
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  • 106
    Publication Date: 2014-02-26
    Description: We perform a classification of integrable systems of mixed scalar and vector evolution equations with respect to higher symmetries. We consider polynomial systems that are homogeneous under a suitable weighting of variables. This paper deals with the KdV weighting, the Burgers (or potential KdV or modified KdV) weighting, the Ibragimov--Shabat weighting and two unfamiliar weightings. The case of other weightings will be studied in a subsequent paper. Making an ansatz for undetermined coefficients and using a computer package for solving bilinear algebraic systems, we give the complete lists of $2^{\mbox{\scriptsize nd }}$order systems with a $3^{\mbox{\scriptsize rd }}$order or a $4^{\mbox{\scriptsize th }}$order symmetry and $3^{\mbox{\scriptsize rd }}$order systems with a $5^{\mbox{\scriptsize th }}$order symmetry. For all but a few systems in the lists, we show that the system (or, at least a subsystem of it) admits either a Lax representation or a linearizing transformation. A thorough comparison with recent work of Foursov and Olver is made.
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  • 107
    Publication Date: 2014-02-26
    Description: The result after $N$ steps of an implicit Runge-Kutta time discretization of an inhomogeneous linear parabolic differential equation is computed, up to accuracy $\varepsilon$, by solving only $$O\Big(\log N\, \log \frac1\varepsilon \Big) $$ linear systems of equations. We derive, analyse, and numerically illustrate this fast algorithm.
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  • 108
    Publication Date: 2020-11-13
    Description: In this paper, we study wavelength assignment problems in multi-fiber WDM networks. We focus on the special case that all lightpaths have at most two links. This in particular holds in case the network topology is a star. As the links incident to a specific node in a meshed topology form a star subnetwork, results for stars are also of interest for general meshed topologies. We show that wavelength assignment with at most two links per lightpath can be modeled as a generalized edge coloring problem. By this relation, we show that for a network with an even number of fibers at all links and at most two links per lightpath, all lightpaths can be assigned a wavelength without conversion. Moreover, we derive a lower bound on the number of lightpaths to be converted for networks with arbitrary numbers of fibers at the links. A comparison with linear programming lower bounds reveals that the bounds coincide for problems with at most two links per lightpath. For meshed topologies, the cumulative lower bound over all star subnetworks equals the best known solution value for all realistic wavelength assignment instances available, by this proving optimality.
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  • 109
    Publication Date: 2014-11-21
    Description: We prove that the Random-Edge simplex algorithm requires an expected number of at most $13n/sqrt(d)$ pivot steps on any simple d-polytope with n vertices. This is the first nontrivial upper bound for general polytopes. We also describe a refined analysis that potentially yields much better bounds for specific classes of polytopes. As one application, we show that for combinatorial d-cubes, the trivial upper bound of $2^d$ on the performance of Random-Edge can asymptotically be improved by any desired polynomial factor in d.
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  • 110
    Publication Date: 2014-02-26
    Description: We present a new algorithm for fairing of space curves with respect spatial constraints based on a vector valued curvature function. Smoothing with the vector valued curvature function is superior to standard Frenet techniques since the individual scalar components can be modeled similar to curvature-based curve smoothing techniques in 2d. This paper describes a curve smoothing flow that satisfies strict spatial constraints and allows simultaneous control of both curvature functions.
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  • 111
    Publication Date: 2016-06-09
    Description: Scattering problems in integrated optics can be modeled in simple cases by the Helmholtz equation. The computational domain is truncated by a non-reflecting boundary condition. We investigate Schwarz algorithms with a sort of DtN operator, realized by the PML-method, at the interfaces of the sub-domains as an iterative solver.
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  • 112
    Publication Date: 2019-05-10
    Description: Adaptive numerical methods in space and time are introduced and studied for multiscale cardiac reaction-diffusion models in three dimensions. The evolution of a complete heartbeat, from the excitation to the recovery phase, is simulated with both the anisotropic Bidomain and Monodomain models, coupled with either a variant of the simple FitzHugh-Nagumo model or the more complex phase-I Luo-Rudy ionic model. The simulations are performed with the {\sc kardos} library, that employs adaptive finite elements in space and adaptive linearly implicit methods in time. The numerical results show that this adaptive method successfully solves these complex cardiac reaction-diffusion models on three-dimensional domains of moderate sizes. By automatically adapting the spatial meshes and time steps to the proper scales in each phase of the heartbeat, the method accurately resolves the evolution of the intra- and extra-cellular potentials, gating variables and ion concentrations during the excitation, plateau and recovery phases.
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  • 113
    Publication Date: 2021-02-01
    Description: Mathematical decision support for operative planning in water supply systems is highly desirable but leads to very difficult optimization problems. We propose a nonlinear programming approach that yields practically satisfactory operating schedules in acceptable computing time even for large networks. Based on a carefully designed model supporting gradient-based optimization algorithms, this approach employs a special initialization strategy for convergence acceleration, special minimum up and down time constraints together with pump aggregation to handle switching decisions, and several network reduction techniques for further speed-up. Results for selected application scenarios at Berliner Wasserbetriebe demonstrate the success of the approach.
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  • 114
    Publication Date: 2014-02-26
    Description: The theory of hierarchical Boolean satisfiability (SAT) solving proposed in this paper is based on a strict axiomatic system and introduces a new important notion of implicativity. The theory makes evident that increasing implicativity is the core of SAT-solving. We provide a theoretical basis for increasing the implicativity of a given SAT instance and for organizing SAT-solving in a hierarchical way. The theory opens a new domain of research: SAT-model construction. Now quite different mathematical models can be used within practical SAT-solvers. The theory covers many advanced techniques such as circuit-oriented SAT-solving, mixed BDD/CNF SAT-solving, merging gates, using pseudo-Boolean constraints, using state machines for representation of Boolean functions, arithmetic reasoning, and managing don t cares. We believe that hierarchical SAT-solving is a cardinal direction of research in practical SAT-solving.
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  • 115
    Publication Date: 2020-12-15
    Description: The \emph{fare planning problem} for public transport is to design a system of fares that maximize the revenue. We introduce a nonlinear optimization model to approach this problem. It is based on a d iscrete choice logit model that expresses demand as a function of the fares. We illustrate our approach by computing and comparing two different fare systems for the intercity network of the Netherlands.
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  • 116
    Publication Date: 2020-12-15
    Description: The line planning problem is one of the fundamental problems in strategic planning of public and rail transport. It consists in finding lines and corresponding frequencies in a network such that a giv en demand can be satisfied. There are two objectives. Passengers want to minimize travel times, the transport company wishes to minimize operating costs. We investigate three variants of a multi-commo dity flow model for line planning that differ with respect to passenger routings. The first model allows arbitrary routings, the second only unsplittable routings, and the third only shortest path rou tings with respect to the network. We compare these models theoretically and computationally on data for the city of Potsdam.
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  • 117
    Publication Date: 2022-03-14
    Description: The Feasibility Pump of Fischetti, Glover, Lodi, and Bertacco has proved to be a very successful heuristic for finding feasible solutions of mixed integer programs. The quality of the solutions in terms of the objective value, however, tends to be poor. This paper proposes a slight modification of the algorithm in order to find better solutions. Extensive computational results show the success of this variant: in 89 out of 121 MIP instances the modified version produces improved solutions in comparison to the original Feasibility Pump.
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  • 118
    Publication Date: 2014-02-26
    Description: In this letter we report on a numerical investigation of the Aoki phase in the case of finite temperature which continues our former study at zero temperature. We have performed simulations with Wilson fermions at $\beta=4.6$ using lattices with temporal extension $N_{\tau}=4$. In contrast to the zero temperature case, the existence of an Aoki phase can be confirmed for a small range in $\kappa$ at $\beta=4.6$, however, shifted slightly to lower $\kappa$. Despite fine-tuning $\kappa$ we could not separate the thermal transition line from the Aoki phase.
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  • 119
    Publication Date: 2021-02-01
    Description: The dynamics of pressurized water distribution networks are naturally modeled by differential algebraic equations (DAE). This paper investigates fundamental structural properties of such a DAE model under weak regularity assumptions. The usual partial derivative-based index-1 condition is shown to be necessary and sufficient for several index concepts, as well as sufficient for solvability in a strong sense. Using the physical properties of nonlinear network elements and the inherent saddle point structure of network hydraulics, we then derive purely topological index criteria based on the network graph and the choice of control variables. Several examples illustrate the theoretical results and explore different non-index-1 situations. A brief discussion of the implications for operative planning by discrete time DAE boundary value problems concludes the paper.
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  • 120
    Publication Date: 2020-02-11
    Description: Using the popular puzzle game of Sudoku, this article highlights some of the ideas and topics covered in ZR-04-58.
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  • 121
    Publication Date: 2021-03-16
    Description: Perfect graphs constitute a well-studied graph class with a rich structure, reflected by many characterizations with respect to different concepts. Perfect graphs are, for instance, precisely those graphs $G$ where the stable set polytope $STAB(G)$ coincides with the fractional stable set polytope $QSTAB(G)$. For all imperfect graphs $G$ it holds that $STAB(G) \subset QSTAB(G)$. It is, therefore, natural to use the difference between the two polytopes in order to decide how far an imperfect graph is away from being perfect; we discuss three different concepts, involving the facet set of $STAB( G)$, the disjunctive index of $QSTAB(G)$, and the dilation ratio of the two polytopes. Including only certain types of facets for $STAB(G)$, we obtain graphs that are in some sense close to perfect graphs, for example minimally immperfect graphs, and certain other classes of so-called rank-perfect graphs. The imperfection ratio has been introduced by (Gerke and McDiarmid, 2001) as the dilation ratio of $STAB(G)$ and $QSTAB(G)$, whereas (Aguilera et al., 2003) suggest to take the disjunctive index of $Q STAB(G)$ as the imperfection index of $G$. For both invariants there exist no general upper bounds, but there are bounds known for the imperfection ratio of several graph classes (Coulonges et al. 2005, Gerke and McDiarmid, 2001). Outgoing from a graph-theoretical interpretation of the imperfection index, we conclude that the imperfection index is NP-hard to compute and we prove that there exists no upper bound on the imperfect ion index for those graph classes with a known bounded imperfection ratio. Comparing the two invariants on those classes, it seems that the imperfection index measures imperfection much more roughly than the imperfection ratio; therefoe, discuss possible directions for refinements.
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  • 122
    Publication Date: 2020-11-13
    Description: Many online problems encountered in real-life involve a two-stage decision process: upon arrival of a new request, an irrevocable first-stage decision (the assignment of a specific resource to the request) must be made immediately, while in a second stage process, certain ``subinstances'' (that is, the instances of all requests assigned to a particular resource) can be solved to optimality (offline) later. We introduce the novel concept of an \emph{Online Target Date Assignment Problem} (\textsc{OnlineTDAP}) as a general framework for online problems with this nature. Requests for the \textsc{OnlineTDAP} become known at certain dates. An online algorithm has to assign a target date to each request, specifying on which date the request should be processed (e.\,g., an appointment with a customer for a washing machine repair). The cost at a target date is given by the \emph{downstream cost}, the optimal cost of processing all requests at that date w.\,r.\,t.\ some fixed downstream offline optimization problem (e.\,g., the cost of an optimal dispatch for service technicians). We provide general competitive algorithms for the \textsc{OnlineTDAP} independently of the particular downstream problem, when the overall objective is to minimize either the sum or the maximum of all downstream costs. As the first basic examples, we analyze the competitive ratios of our algorithms for the par ticular academic downstream problems of bin-packing, nonpreemptive scheduling on identical parallel machines, and routing a traveling salesman.
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  • 123
    Publication Date: 2014-02-26
    Description: The mathematical modeling of a special modular catalytic reactor kit leads to a system of partial differential equation in two space dimensions. As customary, this model contains unconfident physical parameters, which may be adapted to fit experimental data. To solve this nonlinear least squares problem we apply a damped Gauss-Newton method. A method of lines approach is used to evaluate the associated model equations. By an a priori spatial discretization a large DAE system is derived and integrated with an adaptive, linearly-implicit extrapolation method. For sensitivity evaluation we apply an internal numerical differentiation technique, which reuses linear algebra information from the model integration. In order not to interfere the control of the Gauss-Newton iteration these computations are done usually very accurately and, therefore, very costly. To overcome this difficulty, we discuss several accuracy adaptation strategies, e.g., a master-slave mode. Finally, we present some numerical experiments.
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  • 124
    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.
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  • 125
    Publication Date: 2014-02-26
    Description: We present an integer linear programming model for the design of multi-layer telecommunication networks. The formulation integrates hardware, capacity, routing, and grooming decisions in \emph{any} n umber of network layers. Practical hardware restrictions and cost can accurately be taken into account for technologies based on connection-oriented routing protocols.
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  • 126
    Publication Date: 2014-02-26
    Description: We introduce FreeLence, a lossless single-rate connectivity compression algorithm for triangle surface meshes. Based upon a geometry-driven traversal scheme we present two novel and simple concepts: free-valence connectivity encoding and entropy coding based on geometric context. Together these techniques yield significantly smaller rates for connectivity compression than current state of the art approaches - valence-based algorithms and Angle- Analyzer, with an average of $36\%$ improvement over the former and an average of $18\%$ over the latter on benchmark 3D models, combined with the ability to well adapt to the regularity of meshes. We also prove that our algorithm exhibits a smaller worst case entropy for a class of "'well-behaved"' triangle meshes than valence-driven connectivity encoding approaches.
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  • 127
    Publication Date: 2020-02-11
    Description: In this article, we present a mathematical model and an algorithm to support one of the central strategic planning decisions of network operators: How to organize a large number of locations into a hierarchical network? We propose a solution approach that is based on mixed-integer programming and Lagrangian relaxation techniques. As major advantage, our approach provides not only solutions but also worst-case quality guarantees. Real-world scenarios with more than 750 locations have been solved within 30 minutes to less than 1\% off optimality.
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  • 128
    Publication Date: 2020-02-11
    Description: This paper is concerned with UMTS radio network design. Our task is to reconfigure antennas and the related cells as to improve network quality. In contrast to second generation GSM networks, \emph{interference} plays a paramount role when designing third generation radio networks. A known compact formulation for assessing the interference characteristics of a radio network as coupling relations between cells based on user snapshots is generalized to statistical average load. This enables us to overcome the notorious difficulties of snapshot-based network optimization approaches. We recall a mixed-integer programming model for the network design problem that is based on user snapshots and contrast it with a new network design model based on the average coupling formulation. Exemplarily focusing on the important problem of optimizing antenna tilts, we give computational results for a fast local search algorithm and the application of a MIP solver to both models. These results demonstrate that our new average-based approaches outperform state-of-the-art snapshot models for UMTS radio network optimization.
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  • 129
    Publication Date: 2021-08-05
    Description: Constraint Programs and Mixed Integer Programs are closely related optimization problems originating from different scientific areas. Today's state-of-the-art algorithms of both fields have several strategies in common, in particular the branch-and-bound process to recursively divide the problem into smaller sub problems. On the other hand, the main techniques to process each sub problem are different, and it was observed that they have complementary strenghts. We propose a programming framework {\sffamily SCIP} that integrates techniques from both fields in order to exploit the strenghts of both, Constraint Programming and Mixed Integer Programming. In contrast to other proposals of recent years to combine both fields, {\sffamily SCIP} does not focus on easy implementation and rapid prototyping, but is tailored towards expert users in need of full, in-depth control and high performance.
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  • 130
    Publication Date: 2018-12-06
    Description: In this paper we describe the semantic analysis of differential equations given in the ubiquitous semi-structured formats MathML and OpenMath. The analysis is integrated in a deployed Web indexing framework. Starting from basic classifications for differential equations the proposed system architecture is amenable to extensions for further reconstruction of mathematical content on the Web. The syntactic analysis of mathematical formulae given in the considered formats must overcome ambiguities that stem from the fact that formula particles may have different encodings, which are in principle completely arbitrary. However, it turns out that the syntactic analysis can be done straightforward given some natural heuristic assumptions.
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  • 131
    Publication Date: 2014-02-26
    Description: A new method for noise removal of arbitrary surfaces meshes is presented which focuses on the preservation and sharpening of non-linear geometric features such as curved surface regions and feature lines. Our method uses a prescribed mean curvature flow (PMC) for simplicial surfaces which is based on three new contributions: 1. the definition and efficient calculation of a discrete shape operator and principal curvature properties on simplicial surfaces that is fully consistent with the well-known discrete mean curvature formula, 2. an anisotropic discrete mean curvature vector that combines the advantages of the mean curvature normal with the special anisotropic behaviour along feature lines of a surface, and 3. an anisotropic prescribed mean curvature flow which converges to surfaces with an estimated mean curvature distribution and with preserved non-linear features. Additionally, the PMC flow prevents boundary shrinkage at constrained and free boundary segments.
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  • 132
    Publication Date: 2019-01-29
    Description: A primal-dual interior point method for optimal control problems with PDE constraints is considered. The algorithm is directly applied to the infinite dimensional problem. Existence and convergence of the central path are analyzed. Numerical results from an inexact continuation method applied to a model problem are shown.
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  • 133
    Publication Date: 2014-02-26
    Description: In this paper, we present a novel approach to the congestion control and resource allocation problem of elastic and real-time traffic in telecommunication networks. With the concept of utility functions, where each source uses a utility function to evaluate the benefit from achieving a transmission rate, we interpret the resource allocation problem as a global optimization problem. The solution to this problem is characterized by a new fairness criterion, \e{utility proportional fairness}. We argue that it is an application level performance measure, i.e. the utility that should be shared fairly among users. As a result of our analysis, we obtain congestion control laws at links and sources that are globally stable and provide a utility proportional fair resource allocation in equilibrium. We show that a utility proportional fair resource allocation also ensures utility max-min fairness for all users sharing a single path in the network. As a special case of our framework, we incorporate utility max-min fairness for the entire network. To implement our approach, neither per-flow state at the routers nor explicit feedback beside ECN (Explicit Congestion Notification) from the routers to the end-systems is required.
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  • 134
    Publication Date: 2014-02-26
    Description: The problem of clustering data can be formulated as a graph partitioning problem. Spectral methods for obtaining optimal solutions have reveceived a lot of attention recently. We describe Perron Cluster Cluster Analysis (PCCA) and, for the first time, establish a connection to spectral graph partitioning. We show that in our approach a clustering can be efficiently computed using a simple linear map of the eigenvector data. To deal with the prevalent problem of noisy and possibly overlapping data we introduce the min Chi indicator which helps in selecting the number of clusters and confirming the existence of a partition of the data. This gives a non-probabilistic alternative to statistical mixture-models. We close with showing favorable results on the analysis of gene expressi on data for two different cancer types.
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  • 135
    Publication Date: 2014-02-26
    Description: In this paper, we study the conflict-free assignment of wavelengths to lightpaths in an optical network with the opportunity to place wavelength converters. To benchmark heuristics for the problem, we develop integer programming formulations and study their properties. Moreover, we study the computational performance of the column generation algorithm for solving the linear relaxation of the most promising formulation. In many cases, a non-zero lower bound on the number of required converters is generated this way. For several instances, we in fact prove optimality since the lower bound equals the best known solution value.
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  • 136
    Publication Date: 2021-02-01
    Description: Operative planning in gas distribution networks leads to large-scale mixed-integer optimization problems involving a hyperbolic PDE defined on a graph. We consider the NLP obtained under prescribed combinatorial decisions---or as relaxation in a branch and bound framework, addressing in particular the KKT systems arising in primal-dual interior methods. We propose a custom solution algorithm using sparse local projections, based on the KKT systems' structual properties induced by the discretized gas flow equations in combination with the underlying network topology. The numerical efficiency and accuracy of the algorithm are investigated, and detailed computational comparisons with a control space method and with the multifrontal solver MA27 are provided.
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  • 137
    Publication Date: 2021-02-01
    Description: The topic of this paper is minimum cost operative planning of pressurized water supply networks over a finite horizon and under reliable demand forecast. Since this is a very hard problem, it is desirable to employ sophisticated mathematical algorithms, which in turn calls for carefully designed models with suitable properties. The paper develops a nonlinear mixed integer model and a nonlinear programming model with favorable properties for gradient-based optimization methods, based on smooth component models for the network elements. In combination with further nonlinear programming techniques (to be reported elsewhere), practically satisfactory near-optimum solutions even for large networks can be generated in acceptable time using standard optimization software on a PC workstation. Such an optimization system is in operation at Berliner Wasserbetriebe.
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  • 138
    Publication Date: 2020-12-15
    Description: Morse matchings capture the essential structural information of discrete Morse functions. We show that computing optimal Morse matchings is NP-hard and give an integer programming formulation for the problem. Then we present polyhedral results for the corresponding polytope and report on computational results.
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  • 139
    Publication Date: 2014-02-26
    Description: In this paper, we study the minimum converter wavelength assignment problem in optical networks. To benchmark the quality of solutions obtained by heuristics, we derive an integer programming formula tion by generalizing the formulation of Mehrotra and Trick (1996) for the vertex coloring problem. To handle the exponential number of variables, we propose a column generation approach. Computational experiments show that the value of the linear relaxation states a good lower bound and can often prove optimality of the best solution generated heuristically.
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  • 140
    Publication Date: 2014-11-10
    Description: The parameter contraction degeneracy -- the maximum minimum degree over all minors of a graph -- is a treewidth lower bound and was first defined in (Bodlaender, Koster, Wolle, 2004). In experiments it was shown that this lower bound improves upon other treewidth lower bounds. In this note, we examine some relationships between the contraction degeneracy and connected components of a graph, block s of a graph and the genus of a graph. We also look at chordal graphs, and we study an upper bound on the contraction degeneracy and another lower bound for treewidth. A data structure that can be used for algorithms computing the degeneracy and similar parameters, is also described.
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  • 141
    Publication Date: 2014-11-10
    Description: The Maximum Cardinality Search algorithm visits the vertices of a graph in some order, such that at each step, an unvisited vertex that has the largest number of visited neighbors becomes visited. An MCS-ordering of a graph is an ordering of the vertices that can be generated by the Maximum Cardinality Search algorithm. The visited degree of a vertex $v$ in an MCS-ordering is the number of neighbors of $v$ that are before $v$ in the ordering. The visited degree of an MCS-ordering $\psi$ of $G$ is the maximum visited degree over all vertices $v$ in $\psi$. The maximum visited degree over all MCS-orderings of graph $G$ is called its {\em maximum visited degree}. Lucena (2003) showed that the treewidth of a graph $G$ is at least its maximum visited degree. We show that the maximum visited degree is of size $O(\log n)$ for planar graphs, and give examples of planar graphs $G$ with maximum visited degree $k$ with $O(k!)$ vertices, for all $k\in \Bbb{N}$. Given a graph $G$, it is NP-complete to determine if its maximum visited degree is at least $k$, for any fixed $k\geq 7$. Also, this problem does not have a polynomial time approximation algorithm with constant ratio, unless P=NP. Variants of the problem are also shown to be NP-complete. We also propose and experimentally analyses some heuristics for the problem. Several tiebreakers for the MCS algorithm are proposed and evaluated. We also give heuristics that give upper bounds on the value of the maximum visited degree of a graph, which appear to give results close to optimal on many graphs from real life applications.
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  • 142
    Publication Date: 2014-02-26
    Description: A new and time efficient model to evaluate the free energy of solvation has been developed. The solvation free energy is separated into an electrostatic term, a hydrogen bond term, and a rest-term, combining both entropic and van der Waals effects. The electrostatic contribution is evaluated with a simplified boundary element method using the partial charges of the MMFF94 force field. The number of hydrogen bonds and the solvent excluded surface area over the surface atoms are used in a linear model to estimate the non-electrostatic contribution. This model is applied to a set of 213 small and mostly organic molecules, yielding an rmsd of 0.87kcal/mol and a correlation with experimental data of r=0.951. The model is applied as a supplementary component of the free energy of binding to estimate binding constants of protein ligand complexes. The intermolecular interaction energy is evaluated by using the MMFF94 force field.
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  • 143
    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.
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  • 144
    Publication Date: 2014-02-26
    Description: Molecular dynamics simulations of possible ligands for proteins yield large amounts of data in the form of trajectories which are further processed in order to find metastable conformations. These conformations can then be used for docking between ligand and protein. Around this core computation procedure lots of other data have to be managed. It should also be possible for external users not involved in program development to perform computations. As a paradigm for other fields where a similar constitution of program usage and data processing is found we present a software architecture for data generation, access and management. Requirements for this system include: Ease of use, graphical user interface, persistent storage of data concerning molecules, users, programs, program parameters, metadata, and results. A mere storage in the file system would render a quick overview of data more or less impossible. On the other hand, storing large amounts of binary data in a database doesn't yield any advantage concerning speed of access. Therefore, a hybrid approach combining file system and database is appropriate. The system should be easily extensible by inserting new applications which can be controlled and whose results can be collected and stored. The software system described here consists of different components, the presentation layer (graphical user interface), the business logic, the persistence layer (relational database plus file system), and an interface to the compute cluster (batch system for parallel processing). We will discuss the alternatives and take a closer look at the components.
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  • 145
    Publication Date: 2020-03-09
    Description: We propose an approach for transforming the sampling of a molecular conformation distribution into an analytical model based on Hidden Markov Models. The model describes the sampled shape density as a mixture of multivariate unimodal densities. Thus, it delivers an interpretation of the sampled density as a set of typical shapes that appear with different probabilities and are characterized by their geometry, their variability and transition probabilities between the shapes. The gained model is used to identify atom groups of constant shape that are connected by metastable torsion angles. Based on this description an alignment for the original sampling is computed. As it takes into account the different shapes contained in the sampled set, this alignment allows to compute reasonable average shapes and meaningful shape density plots. Furthermore, it enables us to visualize typical conformations.
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  • 146
    Publication Date: 2020-02-11
    Description: We present publicly available data sets related to research on wireless networks. The scenarios contain a wide range of data and are detailed in all aspects. To our knowledge, this is the most realistic, comprehensive, and detailed \emph{public} data collection on mobile networking. We indicate example uses of this data collection in applications related tu UMTS.
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  • 147
    Publication Date: 2020-12-15
    Description: The \emph{line planning problem} is one of the fundamental problems in strategic planning of public and rail transport. It consists of finding lines and corresponding frequencies in a public transport network such that a given travel demand can be satisfied. There are (at least) two objectives. The transport company wishes to minimize its operating cost; the passengers request short travel times. We propose two new multi-commodity flow models for line planning. Their main features, in comparison to existing models, are that the passenger paths can be freely routed and that the lines are generated dynamically.
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  • 148
    Publication Date: 2014-02-26
    Description: The aim of this paper is to give a survey of the known results concerning centrally symmetric polytopes, spheres, and manifolds. We further enumerate nearly neighborly centrally symmetric spheres and centrally symmetric products of spheres with dihedral or cyclic symmetry on few vertices, and we present an infinite series of vertex-transitive nearly neighborly centrally symmetric 3-spheres.
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  • 149
    Publication Date: 2019-05-10
    Description: We focus on the role of anisotropic elasticity in the simulation of the load distribution in a human mandible due to a lateral bite on the leftmost premolar. Based on experimental evidence, we adopt ``local''" orthotropy of the elastic properties of the bone tissue. Since the trajectories of anisotropic elasticity are not accessible from Computer Tomographic (CT) data, they will be reconstructed from (i) the organ's geometry and (ii) from coherent structures which can be recognized from the spatial distribution of the CT values. A sensitivity analysis comprising various 3D FE simulations reveals the relevance of elastic anisotropy for the load carrying behavior of a human mandible: Comparison of the load distributions in isotropic and anisotropic simulations indicates that anisotropy seems to ``spare''" the mandible from loading. Moreover, a maximum degree of anisotropy leads to kind of an load minimization of the mandible, expressed by a minimum of different norms of local strain, evaluated throughout the organ. Thus, we may suggest that anisotropy is not only relevant, but also in some sense ``optimal''.
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  • 150
    Publication Date: 2019-05-10
    Description: The paper extends affine conjugate Newton methods from convex to nonconvex minimization, with particular emphasis on PDE problems originating from compressible hyperelasticity. Based on well-known schemes from finite dimensional nonlinear optimization, three different algorithmic variants are worked out in a function space setting, which permits an adaptive multilevel finite element implementation. These algorithms are tested on two well-known 3D test problems and a real-life example from surgical operation planning.
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  • 151
    Publication Date: 2014-02-26
    Description: We present formulae for the corner points of the multidimensional Hausdorff and Dale Polytopes and show how these results can be used to improve linear programming models for computing e.\,g.\ moments of exit distribution of diffusion processes. Specifically, we compute the mean exit time of twodimensional Brownian motion from the unit square and the unit triangle, as well as higher moments of the exit time of time space Brownian motion from a triangle.
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  • 152
    Publication Date: 2014-11-10
    Description: Normal graphs are defined in terms of cross-intersecting set families: a graph is normal if it admits a clique cover $\cal Q$ and a stable set cover $\cal S$ s.t.~every clique in $\cal Q$ intersects every stable set in $\cal S$. Normal graphs can be considered as closure of perfect graphs by means of co-normal products (Körner 1973) and graph entropy (Czisz\'ar et al. 1990). Perfect graphs have been recently characterized as those graphs without odd holes and odd antiholes as induced subgraphs (Strong Perfect Graph Theorem, Chudnovsky et al. 2002). Körner and de Simone observed that $C_5$, $C_7$, and $\overline C_7$ are minimal not normal and conjectured, as generalization of the Strong Perfect Graph Theorem, that every $C_5$, $C_7$, $\overline C_7$- free graph is normal (Normal Graph Conjecture, Körner and de Simone 1999). We prove this conjecture for a first class of graphs that generalize both odd holes and odd antiholes, the circulants, by characterizing all the normal circulants.
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  • 153
    Publication Date: 2014-02-26
    Description: It is known that the suspension of a simplicial complex can be realized with only one additional point. Suitable iterations of this construction generate highly symmetric simplicial complexes with a various interesting combinatorial and topological properties. In particular, infinitely many non-PL spheres as well as contactible simplicial complexes with a vertex-transitive group of automorphisms cab be contained in this way.
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  • 154
    Publication Date: 2020-03-10
    Description: This paper presents an automatic approach for segmentation of the liver from computer tomography (CT) images based on a 3D statistical shape model. Segmentation of the liver is an important prerequisite in liver surgery planning. One of the major challenges in building a 3D shape model from a training set of segmented instances of an object is the determination of the correspondence between different surfaces. We propose to use a geometric approach that is based on minimizing the distortion of the correspondence mapping between two different surfaces. For the adaption of the shape model to the image data a profile model based on the grey value appearance of the liver and its surrounding tissues in contrast enhanced CT data was developed. The robustness of this method results from a previous nonlinear diffusion filtering of the image data. Special focus is turned to the quantitative evaluation of the segmentation process. Several different error measures are discussed and implemented in a study involving more than 30 livers.
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  • 155
    Publication Date: 2021-08-05
    Description: Mixed integer programs are commonly solved with linear programming based branch-and-bound algorithms. The success of the algorithm strongly depends on the strategy used to select the variable to branch on. We present a new generalization called {\sl reliability branching} of today's state-of-the-art {\sl strong branching} and {\sl pseudocost branching} strategies for linear programming based branch-and-bound algorithms. After reviewing commonly used branching strategies and performing extensive computational studies we compare different parameter settings and show the superiority of our proposed newstrategy.
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  • 156
    Publication Date: 2020-03-09
    Description: This article proposes a Lagrangean relaxation approach to solve integrated duty and vehicle scheduling problems arising in public transport. The approach is based on the proximal bundle method for the solution of concave decomposable functions, which is adapted for the approximate evaluation of the vehicle and duty scheduling components. The primal and dual information generated by the bundle method is used to guide a branch-and-bound type algorithm. Computational results for large-scale real-world integrated vehicle and duty scheduling problems with up to 1,500 timetabled trips are reported. Compared with the results of a classical sequential approach and with reference solutions, integrated scheduling offers remarkable potentials in savings and drivers' satisfaction.
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  • 157
    Publication Date: 2019-05-10
    Description: Structural mechanics simulation of bony organs is of general medical and biomechanical interest, because of the interdependence of the inner architecture of bone and its functional loading already stated by Wolff in 1892. This work is part of a detailed research project concerning the human mandible. By adaptive finite element techniques, stress/strain profiles occurring in the bony structure under biting were simulated. Estimates of the discretization errors, local grid refinement, and multilevel techniques guarantee the reliability and efficiency of the method. In general, our simulation requires a representation of the organ's geometry, an appropriate material description, and the load case due to teeth, muscle, or joint forces. In this paper, we want to focus on the influence of the masticatory system. Our goal is to capture the physiological situation as far as possible. By means of visualization techniques developed by the group, we are able to extract individual muscle fibres from computed tomography data. By a special algorithm, the fibres are expanded to fanlike (esp. for the musc. temporalis) coherent vector fields similar to the anatomical reality. The activity of the fibres can be adapted according to compartmentalisation of the muscles as measured by electromyological experiments. A refined sensitivity analysis proved remarkable impact of the presented approach on the simulation results.
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  • 158
    Publication Date: 2021-02-01
    Description: Operative planning in gas networks with prescribed binary decisions yields large scale nonlinear programs defined on graphs. We study the structure of the KKT systems arising in interior methods and present a customized direct solution algorithm. Computational results indicate that the algorithm is suitable for optimization in small and medium-sized gas networks.
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  • 159
    Publication Date: 2014-02-26
    Description: We investigate a special class of quadratic Hamiltonians on $so(4)$ and $so(3,1)$ and describe Hamiltonians that have additional polynomial integrals. One of the main results is a new integrable case with an integral of sixth degree.
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  • 160
    Publication Date: 2020-11-16
    Description: We present a graph theoretical model for scheduling trains on a single unidirectional track between two stations. The set of departures of all possible train types at all possible (discrete) points of time is turned into an undirected graph $\Gneu$ by joining two nodes if the corresponding departures are in conflict. This graph $\Gneu$ has no odd antiholes and no $k$-holes for any integer $k\geq 5$. In particular, any finite, node induced subgraph of $\Gneu$ is perfect. For any integer $r\geq 2$ we construct minimal headways for $r$ train types so that the resulting graph $\Gneu$ has $2r$-antiholes and $4$-holes at the same time. Hence, $\Gneu$ is neither a chordal graph nor the complement of a chordal graph, in general. At the end we analyse the maximal cliques in $G$.
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  • 161
    Publication Date: 2021-02-01
    Description: Unnecessarily conservative behavior of standard process control techniques can be avoided by stochastic programming models when the distribution of random disturbances is known. In an earlier study we have investigated such an approach for tank level constraints of a distillation process. Here we address techniques that have accelerated the numerical solution of the large and expensive stochastic programs by a factor of six, and then present a refined optimization model for the same application.
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  • 162
    Publication Date: 2014-02-26
    Description: We investigate the impact of hop-limited routing paths on the total cost of a telecommunication network. For different survivability settings (dedicated protection, link and path restoration), the optimal network cost without restrictions on the admissible path set is compared to the results obtained with two strategies to impose hop limits on routing paths. In a thorough computational study on optimal solutions for nine real-world based problem instances, we show that hop limits should be avoided if the technology allows it and network cost is a major planning issue. In this case, column generation should be employed to deal with all routing paths. If hop-limits are required, these should be defined for each demand individually and as large as possible.
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  • 163
    Publication Date: 2020-11-13
    Description: Under high load, the automated dispatching of service vehicles for the German Automobile Association (ADAC) must reoptimize a dispatch for 100--150 vehicles and 400 requests in about ten seconds to near optimality. In the presence of service contractors, this can be achieved by the column generation algorithm ZIBDIP. In metropolitan areas, however, service contractors cannot be dispatched automatically because they may decline. The problem: a model without contractors yields larger optimality gaps within ten seconds. One way-out are simplified reoptimization models. These compute a short-term dispatch containing only some of the requests: unknown future requests will influence future service anyway. The simpler the models the better the gaps, but also the larger the model error. What is more significant: reoptimization gap or reoptimization model error? We answer this question in simulations on real-world ADAC data: only the new model ZIBDIP{\footnotesize dummy} can keep up with ZIBDIP.
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  • 164
    Publication Date: 2020-11-13
    Description: Edge contraction is shown to be a useful mechanism to improve lower bound heuristics for treewidth. A successful lower bound for treewidth is the degeneracy: the maximum over all subgraphs of the minimum degree. The degeneracy is polynomial time computable. We introduce the notion of contraction degeneracy: the maximum over all minors of the minimum degree. We show that the contraction degeneracy problem is NP-complete, even for bipartite graphs, but for fixed $k$, it is polynomial time decidable if a given graph $G$ has contraction degeneracy at least $k$. Heuristics for computing the contraction degeneracy are proposed and evaluated. It is shown that these can lead in practice to considerable improvements of the lower bound for treewidth, but can perform arbitrarily bad on some examples. A study is also made for the combination of contraction with Lucena's lower bound based on Maximum Cardinality Search (Lucena, 2003). Finally, heuristics for the treewidth are proposed and! evaluated that combine contraction with a treewidth lower bound technique by Clautiaux et al (2003).
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  • 165
    Publication Date: 2019-01-29
    Description: A primal interior point method for control constrained optimal control problems with PDE constraints is considered. Pointwise elimination of the control leads to a homotopy in the remaining state and dual variables, which is addressed by a short step pathfollowing method. The algorithm is applied to the continuous, infinite dimensional problem, where discretization is performed only in the innermost loop when solving linear equations. The a priori elimination of the least regular control permits to obtain the required accuracy with comparable coarse meshes. Convergence of the method and discretization errors are studied, and the method is illustrated at two numerical examples.
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  • 166
    Publication Date: 2020-02-11
    Description: In this article, strategical infrastructure planning problems in the design of large-scale telecommunication networks are discussed based on experiences from three projects with industrial partners: The access network planning of the German Gigabit-Wissenschaftsnetz (G-WiN) for DFN (Verein zur Förderung eines Deutschen Forschungsnetzes e.V.), the mobile network switching center location planning project for E-Plus Mobilfunk, and the fixed network switching center location planning project for TELEKOM AUSTRIA. We introduce a mathematical model for a hierarchical multi-commodity capacitated facility location problem, present adaptions of this basic model to the specific requirements within the different projects and discuss the individual peculiarities and model decisions made. Eventually, we present and discuss computational results of three associated case studies, illustrating '"how we did the job`` with mathematical methods.
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  • 167
    Publication Date: 2014-11-10
    Description: Every lower bound for treewidth can be extended by taking the maximum of the lower bound over all subgraphs or minors. This extension is shown to be a very vital idea for improving treewidth lower bounds. In this paper, we investigate a total of nine graph parameters, providing lower bounds for treewidth. The parameters have in common that they all are the vertex-degree of some vertex in a subgra ph or minor of the input graph. We show relations between these graph parameters and study their computational complexity. To allow a practical comparison of the bounds, we developed heuristic algorithms for those parameters that are NP-hard to compute. Computational experiments show that combining the treewidth lower bounds with minors can considerably improve the lower bounds.
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  • 168
    Publication Date: 2019-01-29
    Description: The paper addresses primal interior point method for state constrained PDE optimal control problems. By a Lavrentiev regularization, the state constraint is transformed to a mixed control-state constraint with bounded Lagrange multiplier. Existence and convergence of the central path are established, and linear convergence of a short-step pathfollowing method is shown. The behaviour of the regularizations are demonstrated by numerical examples.
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  • 169
    Publication Date: 2014-02-26
    Description: In [7,8,12] homogenization techniques are applied to derive an anisotropic variant of the bio-heat transfer equation as asymptotic result of boundary value problems providing a microscopic description for microvascular tissue. In view of a future application on treatment planning in hyperthermia, we investigate here the homogenization limit for a coupling model, which takes additionally into account the influence of convective heat transfer in medium size blood vessels. This leads to second order elliptic boundary value problems with nonlocal boundary conditions on parts of the boundary. Moreover, we present asymptotic estimates for first order correctors.
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  • 170
    Publication Date: 2014-02-26
    Description: Our main result is that every $n$-dimensional polytope can be described by at most $2n-1$ polynomial inequalities and, moreover, these polynomials can explicitly be constructed. For an $n$-dimensional pointed polyhedral cone we prove the bound $2n-2$ and for arbitrary polyhedra we get a constructible representation by $2n$ polynomial inequalities.
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  • 171
    Publication Date: 2014-11-10
    Description: Graphs with circular symmetry, called webs, are relevant w.r.t. describing the stable set polytopes of two larger graph classes, quasi-line graphs and claw-free graphs. Providing a decent linear description of the stable set polytopes of claw-free graphs is a long-standing problem. However, even the problem of finding all facets of stable set polytopes of webs is open. So far, it is only known that stable set polytopes of webs with clique number $\leq 3$ have rank facets only while there are examples with clique number $〉4$ having non-rank facets.
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  • 172
    Publication Date: 2014-02-26
    Description: The bio-heat transfer equation is a macroscopic model for describing the heat transfer in microvascular tissue. In [{\sl Deuflhard, Hochmuth 2002}] the authors applied homogenization techniques to derive the bio-heat transfer equation as asymptotic result of boundary value problems which provide a microscopic description for microvascular tissue. Here those results are generalized to a geometrical setting where the regions of blood are allowed to be connected. Moreover, asymptotic corrector results are derived.
    Keywords: ddc:000
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  • 173
    Publication Date: 2014-11-10
    Description: Stable multi-sets are an evident generalization of the well-known stable sets. As integer programs, they constitute a general structure which allows for a wide applicability of the results. Moreover, the study of stable multi-sets provides new insights to well-known properties of stable sets. In this paper, we continue our investigations started in [{\sl Koster and Zymolka 2002}] and present results of three types: on the relation to other combinatorial problems, on the polyhedral structure of the stable multi-set polytope, and on the computational impact of the polyhedral results. First of all, we embed stable multi-sets in a framework of generalized set packing problems and point out several relations. The second part discusses properties of the stable multi-set polytope. We show that the vertices of the linear relaxation are half integer and have a special structure. Moreover, we strengthen the conditions for cycle inequalities to be facet defining, show that the separation problem for these inequalities is polynomial time solvable, and discuss the impact of chords in cycles. The last result allows to interpret cliques as cycles with many chords. The paper is completed with a computational study to the practical importance of the cycle inequalities. The computations show that the performance of state-of-the-art integer programming solvers can be improved significantly by including these inequalities.
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  • 174
    Publication Date: 2014-02-26
    Description: In this paper, first solutions of the dust moment equations developed in [{\sl Woitke & Helling 2002}] for the description of dust formation and precipitation in brown dwarf and giant gas planet atmospheres are presented. We consider the special case of a static brown dwarf atmosphere, where dust particles continuously nucleate from the gas phase, grow by the accretion of molecules, settle gravitationally and re-evaporate thermally. Applying a kinetic description of the relevant microphysical and chemical processes for TiO$_2$-grains, the model makes predictions about the large-scale stratification of dust in the atmosphere, the depletion of molecules from the gas phase, the supersaturation of the gas in the atmosphere as well as the mean size and the mass fraction of dust grains as function of depth. Our results suggest that the nucleation occu in the upper atmosphere where the gas is cool, strongly depleted, but nevertheless highly supersaturated ($S\!\gg\!1$). These particles settle gravitationally and populate the warmer layers below, where the in-situ formation (nucleation) is ineffective or even not possible. During their descent, the particles grow up to radii $\approx\!0.3\,\mu{\rm m}\,...\,150\,\mu{\rm m}$, depending gas around the cloud base. The particles finally sink into layers which are sufficiently hot to cause their thermal evaporation. Hence, an effective transport mechanism for condensable elements exi considered solid/liquid material. In the stationary case studied here, this downward directed element transport by precipitating dust grains is balanced by an upward directed flux of condensable elements from the deep interior of the star via convective mixing (no dust without mixing). We find a self-regulation mechanism which leads to an approximate phase equilibrium ($S\!\approx\!1$) around the cloud base. The mass fraction of dust present in the atmosphere results be to approximately given by the mass fraction of condensable elements in the gas being mixed up.
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  • 175
    Publication Date: 2020-03-09
    Description: Analysis of phenomena that simultaneously occur on quite different spatial and temporal scales require adaptive, hierarchical schemes to reduce computational and storage demands. For data represented as grid functions, the key are adaptive, hierarchical, time-dependent grids that resolve spatio-temporal details without too much redundancy. Here, so-called AMR grids gain increasing popularity. For visualization and feature identification/tracking, the underlying continuous function has to be faithfully reconstructed by spatial and temporal interpolation. Well designed interpolation methods yield better results and help to reduce the amount of data to be stored. We address the problem of temporal interpolation of AMR grid data, e.g.\ for creation of smooth animations or feature tracking. Intermediate grid hierarchies are generated by merging the cells on all refinement levels that are present in the key frames considered. Utilizing a clustering algorithm a structure of nested grids is induced on the resulting collection of cells. The grid functions are mapped to the intermediate hierarchy, thus allowing application of appropriate interpolation techniques.
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  • 176
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    Publication Date: 2020-03-09
    Description: An improved general-purpose technique for the visualization of symmetric positive definite tensor fields of rank two is described. It is based on a splatting technique that is built from tiny transparent glyph primitives which are capable to incorporate the full directional information content of a tensor. The result is an information-rich image that allows to read off the preferred directions in a tensor field at each point of a three-dimensional volume or two-dimensional surface. It is useful for analyzing slices or volumes of a three-dimensional tensor field and can be overlayed with standard volume rendering or color mapping. The application of the rendering technique is demonstrated on general relativistic data and the diffusion tensor field of a human brain.
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  • 177
    Publication Date: 2014-11-10
    Description: Graphs with circular symmetry, called webs, are relevant for describing the stable set polytopes of two larger graph classes, quasi-line graphs [{\sl Giles and Trotter 1981, Oriolo 2001}] and claw-free graphs [{\sl Galluccio and Sassano 1997, Giles and Trotter 1981}]. Providing a decent linear description of the stable set polytopes of claw-free graphs is a long-standing problem [{\sl Grötschel, Lov\'asz, and Schrijver 1988}]. However, even the problem of finding all facets of stable set polytopes of webs is open. So far, it is only known that stable set polytopes of webs with clique number $\leq 3$ have rank facets only [{\sl Dahl 1999, Trotter 1975}] while there are examples with clique number $\geq 4$ having non-rank facets [{\sl e.g. Liebling et al. 2003, Oriolo 2001, P\^echer and Wagler 2003}]. In this paper, we provide a construction for non-rank facets of stable set polytopes of webs. We use this construction to prove, for several fixed values of $\omega$ including all odd values at least 5, that there are only finitely many webs with clique number $\omega$ whose stable set polytopes admit rank facets only.
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  • 178
    Publication Date: 2020-11-13
    Description: We present an algorithm that constructs parametrizations of boundary and interface surfaces automatically. Starting with high-resolution triangulated surfaces describing the computational domains, we iteratively simplify the surfaces yielding a coarse approximation of the boundaries with the same topological type. While simplifying we construct a function that is defined on the coarse surface and whose image is the original surface. This function allows access to the correct shape and surface normals of the original surface as well as to any kind of data defined on it. Such information can be used by geometric multigrid solvers doing adaptive mesh refinement. Our algorithm runs stable on all types of input surfaces, including those that describe domains consisting of several materials. We have used our method with success in different fields and we discuss examples from structural mechanics and biomechanics.
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  • 179
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    Publication Date: 2020-08-05
    Description: This article investigates a certain class of combinatorial packing problems and some polyhedral relations between such problems and the set packing problem.
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  • 180
    Publication Date: 2014-02-26
    Description: We construct non-constructible simplicial $d$-spheres with $d+10$ vertices and non-constructible, non-realizable simplicial $d$-balls with $d+9$ vertices for $d\geq 3$.
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  • 181
    Publication Date: 2014-11-11
    Description: We consider the problem of designing a network that employs a non-bifurcated shortest path routing protocol. The network's nodes and the set of potential links are given together with a set of forecasted end-to-end traffic demands. All relevant hardware components installable at links or nodes are considered. The goal is to simultaneously choose the network's topology, to decide which hardware components to install on which links and nodes, and to find appropriate routing weights such that the overall network cost is minimized. In this paper, we present a mathematical optimization model for this problem and an algorithmic solution approach based on a Lagrangian relaxation. Computational results achieved with this approach for several real-world network planning problems are reported.
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  • 182
    Publication Date: 2014-02-26
    Description: We investigate the impact of link and path restoration on the cost of telecommunication networks. The surprising result is the following: the cost of an optimal network configuration is almost independent of the restoration concept if (i) the installation of network elements (ADMs, DXCs, or routers) and interface cards, (ii) link capacities, and (iii) working and restoration routings are simultaneously optimized. We present a mixed-integer programming model which integrates all these decisions. Using a branch-and-cut algorithm (with column generation to deal with all potential routing paths), we solve structurally different real-world problem instances and show that the cost of optimal solutions is almost independent of the used restoration concept. In addition, we optimize spare capacities for given shortest working paths which are predetermined with respect to different link metrics. In comparison to simultaneous optimization of working and restoration routings, it turns out that this approach does not allow to obtain predictably good results.
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  • 183
    Publication Date: 2020-11-13
    Description: In the dial-a-ride-problem (DARP) objects have to be moved between given sources and destinations in a transportation network by means of a server. The goal is to find a shortest transportation for the server. We study the DARP when the underlying transportation network forms a caterpillar. This special case is strongly NP-hard in the worst case. We prove that in a probabilistic setting there exists a polynomial time algorithm which almost surely finds an optimal solution. Moreover, with high probability the optimality of the solution found can be certified efficiently. We also examine the complexity of the DARP in a semi-random setting and in the unweighted case.
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  • 184
    Publication Date: 2019-01-29
    Description: The paper presents a new affine invariant theory on asymptotic mesh independence of Newton's method in nonlinear PDEs. Compared to earlier attempts, the new approach is both much simpler and more natural from the algorithmic point of view. The theory is exemplified at collocation methods for ODE boundary value problems and at finite element methods for elliptic PDE problems.
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  • 185
    Publication Date: 2014-02-26
    Description: In this paper we introduce the notion of smoothed competitive analysis of online algorithms. Smoothed analysis has been proposed by [{\sl Spielman and Teng} STOC 2001] to explain the behaviour of algorithms that work well in practice while performing very poorly from a worst case analysis point of view. We apply this notion to analyze the Multi-Level Feedback (MLF) algorithm to minimize the total flow time on a sequence of jobs released over time when the processing time of a job is only known at time of completion. The initial processing times are integers in the range $[1,2^K]$. We use a partial bit randomization model, where the initial processing times are smoothened by changing the $k$ least significant bits under a quite general class of probability distributions. We show that MLF admits a smoothed competitive ratio of $O(max((2^k/\sigma)^3, (2^k/\sigma)^2 2^K-k))$, where $\sigma$ denotes the standard deviation of the distribution. In particular, we obtain a competitive ratio of $O(2^K-k)$ if $\sigma = \Theta(2^k)$. %The analysis holds for an oblivious as well as for a stronger adaptive %adversary. We also prove an $\Omega(2^{K-k})$ lower bound for any deterministic algorithm that is run on processing times smoothened according to the partial bit randomization model. For various other smoothening models, including the additive symmetric smoothening model used by [{\sl Spielman and Teng}], we give a higher lower bound of $\Omega(2^K)$. A direct consequence of our result is also the first average case analysis of MLF. We show a constant expected ratio of the total flow time of MLF to the optimum under several distributions including the uniform distribution.
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  • 186
    Publication Date: 2014-11-11
    Description: For the general G/G/1 processor sharing (PS) system a sample path result for the sojourn times in a busy period is proved, which yields a relation between the sojourn times under PS and FCFS discipline. In particular, the result provides a formula for the mean sojourn time in G/D/1-PS in terms of the mean sojourn time in the corresponding G/D/1-FCFS, generalizing known results for GI/M/1 and M/GI/1. Extensions of the formula provide the basis for a two-moment approximation of the mean sojourn time in G/GI/1-PS in terms of a related G/D/1-FCFS.
    Keywords: ddc:000
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  • 187
    Publication Date: 2014-02-26
    Description: The paper surveys recent progress in the mathematical modelling and simulation of essential molecular dynamics. Particular emphasis is put on computational drug design wherein time scales of $msec$ up to $min$ play the dominant role. Classical long-term molecular dynamics computations, however, would run into ill-conditioned initial value problems already after time spans of only $psec=10^{-12} sec$. Therefore, in order to obtain results for times of pharmaceutical interest, a combined deterministic-stochastic model is needed. The concept advocated in this paper is the direct identification of metastable conformations together with their life times and their transition patterns. It can be interpreted as a {\em transfer operator} approach corresponding to some underlying hybrid Monte Carlo process, wherein short-term trajectories enter. Once this operator has been discretized, which is a hard problem of its own, a stochastic matrix arises. This matrix is then treated by {\em Perron cluster analysis}, a recently developed cluster analysis method involving the numerical solution of an eigenproblem for a Perron cluster of eigenvalues. In order to avoid the 'curse of dimension', the construction of appropriate boxes for the spatial discretization of the Markov operator requires careful consideration. As a biomolecular example we present a rather recent SARS protease inhibitor.
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  • 188
    Publication Date: 2021-02-01
    Description: The operative planning problem in natural gas distribution networks is addressed. An optimization model focusing on the governing PDE and other nonlinear aspects is presented together with a suitable discretization for transient optimization in large networks by SQP methods. Computational results for a range of related dynamic test problems demonstrate the viability of the approach.
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  • 189
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    Publication Date: 2014-02-26
    Description: This article presents a new computational approach to the three-dimensional (3D) modeling of ribonucleic acid (RNA) sequences with unknown spatial structure. The main concept is a mapping of the query sequence onto the 3D structures of a suitable template RNA molecule. This technique called \textit{threading} has originally been developed for the modeling of protein 3D structures. The application to RNA systems bridges the information gap between the growing mass of RNA sequence data and the relatively limited number of available 3D structures. The new RNA threading method is demonstrated on a tRNA model system because sufficient representative 3D structures have experimentally been elucidated and deposited in the public databases. Nevertheless, the method is in principle transferable on all other RNA species. Algorithms are developed that decompose these template structures into their secondary structure elements and gather this information in a specific template database. The best template is chosen with public alignment and secondary structure prediction tools which are integrated in the RNA modeling module. The structural information gathered from the template and the best alignment is combined to establish a comprehensive 3D model of the query sequence. A range of complete tRNA structures has successfully been modeled with the RNA threading method. The prototype module visualizes the models and provides convenient access to the proposed 3D structures. Therefore, the method could give new insight into a variety of RNA systems which in the recent years have become increasingly important as potential new pharmaceutical agents.
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  • 190
    Publication Date: 2014-02-26
    Description: Collection of abstracts of the Korean-German Bilateral Symposium on Scientific Computing, Berlin January 15/16, 2004
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  • 191
    Publication Date: 2020-08-05
    Description: Point-to-Multipoint systems are one kind of radio systems supplying wireless access to voice/data communication networks. Such systems have to be run using a certain frequency spectrum, which typically causes capacity problems. Hence it is, on the one hand, necessary to reuse frequencies but, on the other hand, no interference must be caused thereby. This leads to the bandwidth allocation problem, a special case of so-called chromatic scheduling problems. Both problems are NP-hard, and there exist no polynomial time approximation algorithms with a guaranteed quality. One kind of algorithms which turned out to be successful for many other combinatorial optimization problems uses cutting plane methods. In order to apply such methods, knowledge on the associated polytopes is required. The present paper contributes to this issue, exploring basic properties of chromatic scheduling polytopes and several classes of facet-defining inequalities.
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  • 192
    Publication Date: 2020-02-11
    Description: The UMTS radio network planning problem poses the challenge of designing a cost-effective network that provides users with sufficient coverage and capacity. We describe an optimization model for this problem that is based on comprehensive planning data of the EU project MOMENTUM. We present heuristic mathematical methods for this realistic model, including computational results.
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  • 193
    Publication Date: 2014-02-26
    Description: Relaying -- allowing multiple wireless hops -- is a protocol extension for cellular networks conceived to improve data throughput. Its benefits have only been quantified for small example networks. For assessing its general potential, we define a complex resource allocation\slash{}scheduling problem. Several mathematical models are presented for this problem; while a time-expanded MIP approach turns out intractable, a sophisticated column generation scheme leads to good computational results. We thereby show that for selected cases relaying can increase data throughput by 30\% on the average.
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  • 194
    Publication Date: 2014-02-26
    Description: Finding conflict-free wavelength assignments with a minimum number of required conversions for a routing of the lightpaths is one of the important tasks within the design of all-optical networks. We consider this problem in multi-fiber networks with different types of WDM systems. We give a detailed description of the problem and derive its theoretical complexity. For practical application, we propose several sequential algorithms to compute appropriate wavelength assignments. We also perform computational experiments to evaluate their performance. For the iterative algorithms, we identify characteristic patterns of progression. Two of these algorithms qualify for application in practice.
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  • 195
    Publication Date: 2014-09-30
    Description: A recently developed algorithm allows Rigid Body Docking of ligands to proteins, regardless of the accessibility and location of the binding site. The Docking procedure is divided into three subsequent optimization phases, two of which utilize rigid body dynamics. The last one is applied with the ligand already positioned inside the binding pocket and accounts for full flexibility. Initially, a combination of geometrical and force-field based methods is used as a Coarse Docking strategy, considering only Lennard-Jones interactions between the target and pharmaceutically relevant atoms or functional groups. The protein is subjected to a Hot Spot Analysis, which reveals points of high affinity in the protein environment towards these groups. The hot spots are distributed into different subsets according to their group affiliation. The ligand is described as a complementary point set, consisting of the same subsets. Both sets are matched in $\mathrm{I\!R}^{3}$, by superimposing members of the same subsets. In the first instance, steric inhibition is nearly neglected, preventing the system's trajectory from trapping in local minima and thus from finding false positive solutions. Hence the exact location of the binding site can be determined fast and reliably without any additional information. Subsequently, errors resulting from approximations are minimized via finetuning, this time considering both Lennard-Jones and Coulomb forces. Finally, the potential energy of the whole complex is minimized. In a first evaluation, results are rated by a reduced scoring function considering only noncovalent interaction energies. Exemplary Screening results will be given for specific ligands.
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  • 196
    Publication Date: 2014-02-26
    Description: We suggest a new model for the design of telecommunication networks which integrates decisions about the topology, configuration of the switching hardware, link dimensioning, and protected routing of communication demands. Applying the branch-and-cut-algorithm implemented in our network planning and optimization tool DISCNET, we demonstrate that real-world based network planning instances of such an enhanced model can be solved.
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  • 197
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    Publication Date: 2014-02-26
    Description: The problem of clustering data can often be transformed into the problem of finding a hidden block diagonal structure in a stochastic matrix. Deuflhard et al. have proposed an algorithm that state s the number $k$ of clusters and uses the sign structure of $k$ eigenvectors of the stochastic matrix to solve the cluster problem. Recently Weber and Galliat discovered that this system of eigenvectors can easily be transformed into a system of $k$ membership functions or soft characteristic functions describing the clusters. In this article we explain the corresponding cluster algorithm and point out the underlying theory. By means of numerical examples we explain how the grade of membership can be interpreted.
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  • 198
    Publication Date: 2014-02-26
    Description: The KOBV Informationsportal aims to be a universal gateway to the sources of information hosted by the partner libraries from the Berlin-Brandenburg area. Due to the large number of these sources, an intuitive navigation is an essential component of the portal. The navigation-component should preserve the partner libraries? independence and overcome their administrative and technical differences. This paper proposes a collection-level navigation with four dimensions: the sources? subject areas (e.g. the first two levels of DDC), the sources? type (e.g. e-journals, databases, OPACs, etc.), the sources? location (e.g. Berlin, Brandenburg) / the library that hosts that source and the sources? accessing state (e.g. free, restricted, etc.).
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
    Library Location Call Number Volume/Issue/Year Availability
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  • 199
    Publication Date: 2014-02-26
    Description: Our main result is that every n-dimensional polytope can be described by at most (2n-1) polynomial inequalities and, moreover, these polynomials can explicitly be constructed. For an n-dimensional pointed polyhedral cone we prove the bound 2n-2 and for arbitrary polyhedra we get a constructible representation by 2n polynomial inequalities.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
    Library Location Call Number Volume/Issue/Year Availability
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  • 200
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    Publication Date: 2020-02-11
    Description: The NETLIB has now served for 18 years as a repository of LP problem instances. From the beginning to the present day there was some uncertainness about the precise values of the optimal solutions. We implemented a program using exact rational arithmetic to compute proofs for the feasibility and optimality of an LP solution. This paper reports the \emph{exact} optimal objective values for all NETLIB problems.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
    Library Location Call Number Volume/Issue/Year Availability
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