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  • 101
    Publication Date: 2022-09-21
    Description: The European energy system has been through a fundamental transformation since the Paris Agreement to reduce greenhouse gas emissions. The transition involves several energy-generating and consuming sectors emphasizing sector coupling. The increase in the share of renewable energy sources has revealed the need for flexibility in the electri city grid. Thus, holistic planning of pathways towards decarbonized energy systems also involves assessing the gas infrastructure to provide such a flexibility and support for the security of supply. In this paper, we propose a workflow to investigate such optimal energy transition pathways considering sector coupling. This workflow involves an integrated operational analysis of the electricity market, its transmission grid, and the gas grid in high spatio-temporal resolution. In a case study on a pan-European scale between 2020-2050, we show that carbon neutrality can be reached within feasible additional costs and in time. However, the manifestation of the potential pathways strongly depends on political and technological constraints. Sector coupling acts as an enabler of cross-border cooperation to achieve both, decarbonization and security of supply.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 102
    Publication Date: 2022-09-16
    Description: Geometric predicates are at the core of many algorithms, such as the construction of Delaunay triangulations, mesh processing and spatial relation tests. These algorithms have applications in scientific computing, geographic information systems and computer-aided design. With floating-point arithmetic, these geometric predicates can incur round-off errors that may lead to incorrect results and inconsistencies, causing computations to fail. This issue has been addressed using a combination of exact arithmetic for robustness and floating-point filters to mitigate the computational cost of exact computations. The implementation of exact computations and floating-point filters can be a difficult task, and code generation tools have been proposed to address this. We present a new C++ meta-programming framework for the generation of fast, robust predicates for arbitrary geometric predicates based on polynomial expressions. We combine and extend different approaches to filtering, branch reduction, and overflow avoidance that have previously been proposed. We show examples of how this approach produces correct results for data sets that could lead to incorrect predicate results with naive implementations. Our benchmark results demonstrate that our implementation surpasses state-of-the-art implementations.
    Language: English
    Type: article , doc-type:article
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  • 103
    Publication Date: 2022-09-16
    Description: The Robust Perron Cluster Analysis (PCCA+) has become a popular spectral clustering algorithm for coarse-graining transition matrices of nearly decomposable Markov chains with transition states. Originally developed for reversible Markov chains, the algorithm only worked for transition matrices with real eigenvalues. In this paper, we therefore extend the theoretical framework of PCCA+ to Markov chains with a complex eigen-decomposition. We show that by replacing a complex conjugate pair of eigenvectors by their real and imaginary components, a real representation of the same subspace is obtained, which is suitable for the cluster analysis. We show that our approach leads to the same results as the generalized PCCA+ (GenPCCA), which replaces the complex eigen-decomposition by a conceptually more difficult real Schur decomposition. We apply the method on non-reversible Markov chains, including circular chains,and demonstrate its efficiency compared to GenPCCA. The experiments are performed in the Matlab programming language and codes are provided.
    Language: German
    Type: article , doc-type:article
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  • 104
    Publication Date: 2022-09-16
    Description: Grasping, in both biological and engineered mechanisms, can be highly sensitive to the gripper and object morphology, as well as perception and motion planning. Here we circumvent the need for feedback or precise planning by using an array of fluidically-actuated slender hollow elastomeric filaments to actively entangle with objects that vary in geometric and topological complexity. The resulting stochastic interactions enable a unique soft and conformable grasping strategy across a range of target objects that vary in size, weight, and shape. We experimentally evaluate the grasping performance of our strategy, and use a computational framework for the collective mechanics of flexible filaments in contact with complex objects to explain our findings. Overall, our study highlights how active collective entanglement of a filament array via an uncontrolled, spatially distributed scheme provides new options for soft, adaptable grasping.
    Language: English
    Type: article , doc-type:article
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  • 105
    Publication Date: 2022-09-16
    Description: Alternative treatment methods for knee osteoarthritis (OA) are in demand, to delay the young (〈 50 Years) patient’s need for osteotomy or knee replacement. Novel interpositional knee spacers shape based on statistical shape model (SSM) approach and made of polyurethane (PU) were developed to present a minimally invasive method to treat medial OA in the knee. The implant should be supposed to reduce peak strains and pain, restore the stability of the knee, correct the malalignment of a varus knee and improve joint function and gait. Firstly, the spacers were tested in artificial knee models. It is assumed that by application of a spacer, a significant reduction in stress values and a significant increase in the contact area in the medial compartment of the knee will be registered. Biomechanical analysis of the effect of novel interpositional knee spacer implants on pressure distribution in 3D-printed knee model replicas: the primary purpose was the medial joint contact stress-related biomechanics. A secondary purpose was a better understanding of medial/lateral redistribution of joint loading. Six 3D printed knee models were reproduced from cadaveric leg computed tomography. Each of four spacer implants was tested in each knee geometry under realistic arthrokinematic dynamic loading conditions, to examine the pressure distribution in the knee joint. All spacers showed reduced mean stress values by 84–88% and peak stress values by 524–704% in the medial knee joint compartment compared to the non-spacer test condition. The contact area was enlarged by 462–627% as a result of the inserted spacers. Concerning the appreciable contact stress reduction and enlargement of the contact area in the medial knee joint compartment, the premises are in place for testing the implants directly on human knee cadavers to gain further insights into a possible tool for treating medial knee osteoarthritis.
    Language: English
    Type: article , doc-type:article
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  • 106
    Publication Date: 2022-09-16
    Description: Image segmentation is an active area of research for more than 30 years. Traditional image segmentation algorithms are problem-specific and limited in scope. On the other hand, machine learning offers an alternative paradigm where predefined features are combined into different classifiers, providing pixel-level classification and segmentation. However, machine learning only can not address the question as to which features are appropriate for a certain classification problem. This paper presents a project supported in part by the International Neuroinformatics Coordination Facility through the Google Summer of code. The project resulted in an automated image segmentation and classification platform, called Active Segmentation for ImageJ (AS/IJ). The platform integrates a set of filters computing differential geometrical invariants and combines them with machine learning approaches.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 107
    Publication Date: 2022-09-01
    Description: The analysis of brain networks is central to neurobiological research. In this context the following tasks often arise: (1) understand the cellular composition of a reconstructed neural tissue volume to determine the nodes of the brain network; (2) quantify connectivity features statistically; and (3) compare these to predictions of mathematical models. We present a framework for interactive, visually supported accomplishment of these tasks. Its central component, the stratification matrix viewer, allows users to visualize the distribution of cellular and/or connectional properties of neurons at different levels of aggregation. We demonstrate its use in four case studies analyzing neural network data from the rat barrel cortex and human temporal cortex.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 108
    Publication Date: 2022-09-01
    Description: During cell division, kinetochore microtubules (KMTs) provide a physical linkage between the chromosomes and the rest of the spindle. KMTs in mammalian cells are organized into bundles, so-called kinetochore-fibers (k-fibers), but the ultrastructure of these fibers is currently not well characterized. Here we show by large-scale electron tomography that each k-fiber in HeLa cells in metaphase is composed of approximately nine KMTs, only half of which reach the spindle pole. Our comprehensive reconstructions allowed us to analyze the three-dimensional (3D) morphology of k-fibers and their surrounding MTs in detail. We found that k-fibers exhibit remarkable variation in circumference and KMT density along their length, with the pole-proximal side showing a broadening. Extending our structural analysis then to other MTs in the spindle, we further observed that the association of KMTs with non-KMTs predominantly occurs in the spindle pole regions. Our 3D reconstructions have implications for KMT growth and k-fiber self-organization models as covered in a parallel publication applying complementary live-cell imaging in combination with biophysical modeling (Conway et al., 2022). Finally, we also introduce a new visualization tool allowing an interactive display of our 3D spindle data that will serve as a resource for further structural studies on mitosis in human cells.
    Language: English
    Type: article , doc-type:article
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  • 109
    Publication Date: 2022-09-01
    Description: Background: Despite recent advances in cellular cryo-electron tomography (CET), developing automated tools for macromolecule identification in submolecular resolution remains challenging due to the lack of annotated data and high structural complexities. To date, the extent of the deep learning methods constructed for this problem is limited to conventional Convolutional Neural Networks (CNNs). Identifying macromolecules of different types and sizes is a tedious and time-consuming task. In this paper, we employ a capsule-based architecture to automate the task of macro- molecule identification, that we refer to as 3D-UCaps. In particular, the architecture is composed of three components: feature extractor, capsule encoder, and CNN decoder. The feature extractor converts voxel intensities of input sub-tomograms to activities of local features. The encoder is a 3D Capsule Network (CapsNet) that takes local features to generate a low-dimensional representation of the input. Then, a 3D CNN decoder reconstructs the sub-tomograms from the given representation by upsampling. Results: We performed binary and multi-class localization and identification tasks on synthetic and experimental data. We observed that the 3D-UNet and the 3D-UCaps had an F1−score mostly above 60% and 70%, respectively, on the test data. In both network architectures, we observed degradation of at least 40% in the F1-score when identifying very small particles (PDB entry 3GL1) compared to a large particle (PDB entry 4D8Q). In the multi-class identification task of experimental data, 3D-UCaps had an F1-score of 91% on the test data in contrast to 64% of the 3D-UNet. The better F1-score of 3D-UCaps compared to 3D-UNet is obtained by a higher precision score. We speculate this to be due to the capsule network employed in the encoder. To study the effect of the CapsNet-based encoder architecture further, we performed an ablation study and perceived that the F1-score is boosted as network depth is increased which is in contrast to the previously reported results for the 3D-UNet. To present a reproducible work, source code, trained models, data as well as visualization results are made publicly available. Conclusion: Quantitative and qualitative results show that 3D-UCaps successfully perform various downstream tasks including identification and localization of macro- molecules and can at least compete with CNN architectures for this task. Given that the capsule layers extract both the existence probability and the orientation of the molecules, this architecture has the potential to lead to representations of the data that are better interpretable than those of 3D-UNet.
    Language: English
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  • 110
    Publication Date: 2022-08-25
    Language: English
    Type: article , doc-type:article
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  • 111
    Publication Date: 2022-08-25
    Language: English
    Type: article , doc-type:article
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  • 112
    Publication Date: 2022-08-24
    Description: Biological armors derive their mechanical integrity in part from their geometric architectures, often involving tessellations: individual structural elements tiled together to form surface shells. The carapace of boxfish, for example, is comprised of mineralized polygonal plates, called scutes, arranged in a complex geometric pattern and nearly completely encasing the body. In contrast to artificial armors, the boxfish exoskeleton grows with the fish; the relationship between the tessellation and the gross structure of the armor is therefore critical to sustained protection throughout growth. To clarify whether or how the boxfish tessellation is maintained or altered with age, we quantify architectural aspects of the tessellated carapace of the longhorn cowfish Lactoria cornuta through ontogeny (across nearly an order of magnitude in standard length) and in a high-throughput fashion, using high-resolution microCT data and segmentation algorithms to characterize the hundreds of scutes that cover each individual. We show that carapace growth is canalized with little variability across individuals: rather than continually adding scutes to enlarge the carapace surface, the number of scutes is surprisingly constant, with scutes increasing in volume, thickness, and especially width with age. As cowfish and their scutes grow, scutes become comparatively thinner, with the scutes at the edges (weak points in a boxy architecture) being some of the thickest and most reinforced in younger animals and thinning most slowly across ontogeny. In contrast, smaller scutes with more variable curvature were found in the limited areas of more complex topology (e.g. around fin insertions, mouth, and anus). Measurements of Gaussian and mean curvature illustrate that cowfish are essentially tessellated boxes throughout life: predominantly zero curvature surfaces comprised of mostly flat scutes, and with scutes with sharp bends used sparingly to form box edges. Since growth of a curved, tiled surface with a fixed number of tiles would require tile restructuring to accommodate the surface’s changing radius of curvature, our results therefore illustrate a previously unappreciated advantage of the odd boxfish morphology: by having predominantly flat surfaces, it is the box-like body form that in fact permits a relatively straightforward growth system of this tessellated architecture (i.e. where material is added to scute edges). Our characterization of the ontogeny and maintenance of the carapace tessellation provides insights into the potentially conflicting mechanical, geometric and developmental constraints of this species, but also perspectives into natural strategies for constructing mutable tiled architectures.
    Language: English
    Type: article , doc-type:article
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  • 113
    Publication Date: 2022-08-29
    Description: The electric conductivity of cardiac tissue determines excitation propagation and is important for quantifying ischemia and scar tissue and for building personalized models. Estimating conductivity distributions from endocardial mapping data is a challenging inverse problem due to the computational complexity of the monodomain equation, which describes the cardiac excitation. For computing a maximum posterior estimate, we investigate different optimization approaches based on adjoint gradient computation: steepest descent, limited memory BFGS, and recursive multilevel trust region methods, which are using mesh hierarchies or heterogeneous model hierarchies. We compare overall performance, asymptotic convergence rate, and pre-asymptotic progress on selected examples in order to assess the benefit of our multifidelity acceleration.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 114
    Publication Date: 2022-08-29
    Language: English
    Type: article , doc-type:article
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  • 115
    Publication Date: 2022-08-29
    Description: Recently developed Concentric Tube Continuum Robots (CTCRs) are widely exploited in, for example in minimally invasive surgeries which involve navigating inside narrow body cavities close to sensitive regions. These CTCRs can be controlled by extending and rotating the tubes in order to reach a target point or perform some task. The robot must deviate as little as possible from this narrow space and avoid damaging neighbouring tissue. We consider \emph{open-loop} optimal control of CTCRs parameterized over pseudo-time, primarily aiming at minimizing the robot's working volume during its motion. External loads acting on the system like tip loads or contact with tissues are not considered here. We also discussed the inclusion of tip's orientation in the optimal framework to perform some tasks. We recall a quaternion-based formulation of the robot configuration, discuss discretization, develop optimization objectives addressing different criteria, and investigate their impact on robot path planning for several numerical examples. This optimal framework can be applied to any backbone based continuum robots.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 116
    Publication Date: 2022-08-29
    Description: In light of the energy transition production planning of future decarbonized energy systems lead to very large and complex optimization problems. A widely used modeling paradigm for modeling and solving such problems is mathematical programming. While there are various scientific energy system models and modeling tools, most of them do not provide the necessary level of detail or the modeling flexibility to be applicable for industrial usage. Industrial modeling tools, on the other hand, provide a high level of detail and modeling flexibility. However, those models often exhibit a size and complexity that restricts their scope to a time horizon of several months, severely complicating long-term planning. As a remedy, we propose a model class that is detailed enough for real-world usage but still compact enough for long-term planning. The model class is based on a generalized unit commitment problem on a network with investment decisions. The focus lies on the topological dependency of different energy production and transportation units.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 117
    Publication Date: 2022-09-08
    Description: Our ability to grasp and understand complex phenomena is essentially based on recognizing structures and relating these to each other. For example, any meteorological description of a weather condition and explanation of its evolution recurs to meteorological structures, such as convection and circulation structures, cloud fields and rain fronts. All of these are spatiotemporal structures, defined by time-dependent patterns in the underlying fields. Typically, such a structure is defined by a verbal description that corresponds to the more or less uniform, often somewhat vague mental images of the experts. However, a precise, formal definition of the structures or, more generally, concepts is often desirable, e.g., to enable automated data analysis or the development of phenomenological models. Here, we present a systematic approach and an interactive tool to obtain formal definitions of spatiotemporal structures. The tool enables experts to evaluate and compare different structure definitions on the basis of data sets with time-dependent fields that contain the respective structure. Since structure definitions are typically parameterized, an essential part is to identify parameter ranges that lead to desired structures in all time steps. In addition, it is important to allow a quantitative assessment of the resulting structures simultaneously. We demonstrate the use of the tool by applying it to two meteorological examples: finding structure definitions for vortex cores and center lines of temporarily evolving tropical cyclones. Ideally, structure definitions should be objective and applicable to as many data sets as possible. However, finding such definitions, e.g., for the common atmospheric structures in meteorology, can only be a long-term goal. The proposed procedure, together with the presented tool, is just a first systematic approach aiming at facilitating this long and arduous way.
    Language: English
    Type: article , doc-type:article
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  • 118
    Publication Date: 2022-09-12
    Language: English
    Type: article , doc-type:article
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  • 119
    Publication Date: 2022-09-12
    Description: The segmentation of cavities in three-dimensional images of arbitrary objects is a difficult problem since the cavities are usually connected to the outside of the object without any difference in image intensity. Hence, the information whether a voxel belongs to a cavity or the outside needs to be derived from the ambient space. If a voxel is enclosed by object material, it is very likely that this voxel belongs to a cavity. However, there are dense structures where a voxel might still belong to the outside even though it is surrounded to a large degree by the object. This is, for example, the case for coral colonies. Therefore, additional information needs to be considered to distinguish between those cases. In this paper, we introduce the notion of ambient curvature, present an efficient way to compute it, and use it to segment coral polyp cavities by integrating it into the ambient occlusion framework. Moreover, we combine the ambient curvature with other ambient information in a Gaussian mixture model, trained from a few user scribbles, resulting in a significantly improved cavity segmentation. We showcase the superiority of our approach using four coral colonies of very different morphological types. While in this paper we restrict ourselves to coral data, we believe that the concept of ambient curvature is also useful for other data. Furthermore, our approach is not restricted to curvature but can be easily extended to exploit any properties given on an object's surface, thereby adjusting it to specific applications.
    Language: English
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  • 120
    Publication Date: 2022-09-14
    Description: 3D shapes provide substantially more information than 2D images. However, the acquisition of 3D shapes is sometimes very difficult or even impossible in comparison with acquiring 2D images, making it necessary to derive the 3D shape from 2D images. Although this is, in general, a mathematically ill-posed problem, it might be solved by constraining the problem formulation using prior information. Here, we present a new approach based on Kendall’s shape space to reconstruct 3D shapes from single monocular 2D images. The work is motivated by an application to study the feeding behavior of the basking shark, an endangered species whose massive size and mobility render 3D shape data nearly impossible to obtain, hampering understanding of their feeding behaviors and ecology. 2D images of these animals in feeding position, however, are readily available. We compare our approach with state-of-the-art shape-based approaches both on human stick models and on shark head skeletons. Using a small set of training shapes, we show that the Kendall shape space approach is substantially more robust than previous methods and always results in plausible shapes. This is essential for the motivating application in which specimens are rare and therefore only few training shapes are available.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 121
    Publication Date: 2022-09-13
    Language: English
    Type: article , doc-type:article
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  • 122
    Publication Date: 2022-09-13
    Description: Version 4.0 of the Message Passing Interface standard introduced the concept of Partitioned Communication which adds support for multiple contributions to a communication buffer. Although initially targeted at multithreaded MPI applications, Partitioned Communication currently receives attraction in the context of accelerators, especially GPUs. In this publication it is demonstrated that this communication concept can also be implemented for SYCL-programmed FPGAs. This includes a discussion of the design space and the presentation of a prototypical implementation. Experimental results show that a lightweight implementation on top of an existing MPI library is possible. In addition, the presented approach also reveals issues in both the SYCL and the MPI standard which need to be addresses for improved support of the intended communication style.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 123
    Publication Date: 2022-09-15
    Description: Reconstructing anatomical shapes from sparse or partial measurements relies on prior knowledge of shape variations that occur within a given population. Such shape priors are learned from example shapes, obtained by segmenting volumetric medical images. For existing models, the resolution of a learned shape prior is limited to the resolution of the training data. However, in clinical practice, volumetric images are often acquired with highly anisotropic voxel sizes, e.g. to reduce image acquisition time in MRI or radiation exposure in CT imaging. The missing shape information between the slices prohibits existing methods to learn a high-resolution shape prior. We introduce a method for high-resolution shape reconstruction from sparse measurements without relying on high-resolution ground truth for training. Our method is based on neural implicit shape representations and learns a continuous shape prior only from highly anisotropic segmentations. Furthermore, it is able to learn from shapes with a varying field of view and can reconstruct from various sparse input configurations. We demonstrate its effectiveness on two anatomical structures: vertebra and femur, and successfully reconstruct high-resolution shapes from sparse segmentations, using as few as three orthogonal slices.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 124
    Publication Date: 2022-09-20
    Description: In this note, we apply Transition Path Theory (TPT) from Markov chains to shed light on the problem of Iceland-Scotland Overflow Water (ISOW) equatorward export. A recent analysis of observed trajectories of submerged floats demanded revision of the traditional abyssal circulation theory, which postulates that ISOW should steadily flow along a deep boundary current (DBC) around the subpolar North Atlantic prior to exiting it. The TPT analyses carried out here allow to focus the attention on the portions of flow from the origin of ISOW to the region where ISOW exits the subpolar North Atlantic and suggest that insufficient sampling may be biasing the aforementioned demand. The analyses, appropriately adapted to represent a continuous input of ISOW, are carried out on three time-homogeneous Markov chains modeling the ISOW flow. One is constructed using a high number of simulated trajectories homogeneously covering the flow domain. The other two use much fewer trajectories which heterogeneously cover the domain. The trajectories in the latter two chains are observed trajectories or simulated trajectories subsampled at the observed frequency. While the densely sampled chain supports a well-defined DBC, the more heterogeneously sampled chains do not, irrespective of whether observed or simulated trajectories are used. Studying the sampling sensitivity of the Markov chains, we can give recommendations for enlarging the existing float dataset to improve the significance of conclusions about time-asymptotic aspects of the ISOW circulation.
    Language: English
    Type: article , doc-type:article
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  • 125
    Publication Date: 2022-09-20
    Language: English
    Type: article , doc-type:article
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  • 126
    Publication Date: 2022-09-19
    Description: Air freight is usually shipped in standardized unit load devices (ULDs). The planning process for the consolidation of transit cargo from inbound flights or locally emerging shipments into ULDs for outbound flights is called build-up scheduling. More specifically, outbound ULDs must be assigned a time and a workstation subject to both workstation capacity constraints and the availability of shipments which in turn depends on break-down decisions for incoming ULDs. ULDs scheduled for the same outbound flight should be built up in temporal and spatial proximity. This serves both to minimize overhead in transportation times and to allow workers to move freight between ULDs. We propose to address this requirement by processing ULDs for the same outbound flight in batches. For the above build-up scheduling problem, we introduce a multi-commodity network design model. Outbound flights are modeled as commodities; transit cargo is represented by cargo flow volume and unpack and batch decisions are represented as design variables. The model is solved with a standard MIP solver on a set of benchmark data. For instances with a limited number of resource conflicts, near-optimal solutions are found in under two hours for a whole week of operations.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 127
    Publication Date: 2022-09-19
    Description: We consider the price-optimal earliest arrival problem in public transit (POEAP) in which we aim to calculate the Pareto-front of journeys with respect to ticket price and arrival time in a public transportation network. Public transit fare structures are often a combination of various fare strategies such as, e.g., distance-based fares, zone-based fares or flat fares. The rules that determine the actual ticket price are often very complex. Accordingly, fare structures are notoriously difficult to model as it is in general not sufficient to simply assign costs to arcs in a routing graph. Research into POEAP is scarce and usually either relies on heuristics or only considers restrictive fare models that are too limited to cover the full scope of most real-world applications. We therefore introduce conditional fare networks (CFNs), the first framework for representing a large number of real-world fare structures. We show that by relaxing label domination criteria, CFNs can be used as a building block in label-setting multi-objective shortest path algorithms. By the nature of their extensive modeling capabilities, optimizing over CFNs is NP-hard. However, we demonstrate that adapting the multi-criteria RAPTOR (MCRAP) algorithm for CFNs yields an algorithm capable of solving POEAP to optimality in less than 400 ms on average on a real-world data set. By restricting the size of the Pareto-set, running times are further reduced to below 10 ms.
    Language: English
    Type: article , doc-type:article
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  • 128
    Publication Date: 2022-09-19
    Description: Die Handreichung soll Mitarbeiter:innen von kulturellen Einrichtungen bei der Digitalisierung von Audio- und Videomaterial unterstützten. Diese Einführung richtet sich besonders an Personen, die nicht mit dem Thema vertraut sind. Nach einer Einführung in die Geschichte von Ton- und Bildsignalen werden verschiedene Medientypen vorgestellt und der Umgang mit ihnen um eine Digitalisierung zu beginnen. Die Digitalisierung wird im Zusammenhang mit wichtigen Grundbegriffen und Parametern vorgestellt. Abgeschlossen wird die Handreichung durch Hinweise zur Qualitätsprüfung und Archivierung.
    Keywords: Digitalisierung ; Datenkompression ; Container 〈Informatik〉 ; Codec ; Tonsignal ; Bildsignal ; Bitrate ; Bildauflösung ; Bildformat ; Archiv ; Langzeitarchivierung ; Abtastung ; Restaurierung ; Archivierung
    Language: German
    Type: other , doc-type:Other
    Format: application/pdf
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  • 129
    Book
    Book
    Cambridge :MIT Press,
    Title: Probabilistic Machine Learning : An Introduction
    Author: Murphy, Kevin
    Publisher: Cambridge :MIT Press,
    Year of publication: 2022
    Pages: 944 Seiten
    ISBN: 978-0-262-04682-4
    Type of Medium: Book
    Language: German
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  • 130
    Title: Discovering modern C++ : an intensive course for scientists, engineers, and programmers
    Author: Gottschling, Peter
    Edition: 2nd edition
    Year of publication: 2022
    Pages: 576 Seiten
    Series Statement: C++ in-depth series
    ISBN: 978-0-13-667764-2
    Type of Medium: Book
    Language: English
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  • 131
    Book
    Book
    Shelter Island, NY :Manning Publications,
    Title: Deep learning with Python /
    Author: Chollet, François
    Edition: Second edition
    Publisher: Shelter Island, NY :Manning Publications,
    Year of publication: 2022
    Pages: 400 Seiten
    ISBN: 978-1-61729-686-4
    Type of Medium: Book
    Language: English
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  • 132
    Publication Date: 2022-03-14
    Language: English
    Type: masterthesis , doc-type:masterThesis
    Format: application/pdf
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  • 133
    Publication Date: 2021-10-19
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 134
    Publication Date: 2022-02-17
    Description: The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.
    Language: English
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  • 135
    Publication Date: 2022-01-18
    Description: Propagation of linear constraints has become a crucial sub-routine in modern Mixed-Integer Programming (MIP) solvers. In practice, iterative algorithms with tolerance-based stopping criteria are used to avoid problems with slow or infinite convergence. However, these heuristic stopping criteria can pose difficulties for fairly comparing the efficiency of different implementations of iterative propagation algorithms in a real-world setting. Most significantly, the presence of unbounded variable domains in the problem formulation makes it difficult to quantify the relative size of reductions performed on them. In this work, we develop a method to measure -- independently of the algorithmic design -- the progress that a given iterative propagation procedure has made at a given point in time during its execution. Our measure makes it possible to study and better compare the behavior of bounds propagation algorithms for linear constraints. We apply the new measure to answer two questions of practical relevance: (i) We investigate to what extent heuristic stopping criteria can lead to premature termination on real-world MIP instances. (ii) We compare a GPU-parallel propagation algorithm against a sequential state-of-the-art implementation and show that the parallel version is even more competitive in a real-world setting than originally reported.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 136
    Publication Date: 2022-01-05
    Description: Image segmentation still represents an active area of research since no universal solution can be identified. Traditional image segmentation algorithms are problem-specific and limited in scope. On the other hand, machine learning offers an alternative paradigm where predefined features are combined into different classifiers, providing pixel-level classification and segmentation. However, machine learning only can not address the question as to which features are appropriate for a certain classification problem. The article presents an automated image segmentation and classification platform, called Active Segmentation, which is based on ImageJ. The platform integrates expert domain knowledge, providing partial ground truth, with geometrical feature extraction based on multi-scale signal processing combined with machine learning. The approach in image segmentation is exemplified on the ISBI 2012 image segmentation challenge data set. As a second application we demonstrate whole image classification functionality based on the same principles. The approach is exemplified using the HeLa and HEp-2 data sets. Obtained results indicate that feature space enrichment properly balanced with feature selection functionality can achieve performance comparable to deep learning approaches. In summary, differential geometry can substantially improve the outcome of machine learning since it can enrich the underlying feature space with new geometrical invariant objects.
    Language: English
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  • 137
    Publication Date: 2022-03-11
    Description: The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 8.0 of the SCIP Optimization Suite. Major updates in SCIP include improvements in symmetry handling and decomposition algorithms, new cutting planes, a new plugin type for cut selection, and a complete rework of the way nonlinear constraints are handled. Additionally, SCIP 8.0 now supports interfaces for Julia as well as Matlab. Further, UG now includes a unified framework to parallelize all solvers, a utility to analyze computational experiments has been added to GCG, dual solutions can be postsolved by PaPILO, new heuristics and presolving methods were added to SCIP-SDP, and additional problem classes and major performance improvements are available in SCIP-Jack.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 138
    Publication Date: 2022-01-19
    Description: Die Bestimmung optimaler Treiberfunktionen von Lautsprechern mit frequenzabhängiger Richtcharakteristik ist ein schlecht gestelltes Optimierungsproblem. Zu dessen Lösung haben die Autoren in vorangegangenen Beiträgen eine adjungierten-basierte Methode zur Optimierung von Lautsprecher-Arrays im Zeitbereich vorgestellt [5, 6, 8]. Diese ermöglicht unter anderem die Berücksichtigung von Berandungen und Umgebungseffekten wie Wind, war jedoch bisher auf monopol-artige Quellen beschränkt. Um diese Einschränkung zu beheben, haben die Autoren einen adjungierten-basierten Zeitbereichsansatz mit Finiten-Differenzen (FDTD) zur Synthese komplexer synthetischer Schallquellen durch diskrete, gitter-basierte Monopole vorgestellt [4, 9]. In diesem Beitrag demonstrieren die Autoren die entsprechende Modellierung eines realen Zweiwege-Monitors (A). Zudem wird gezeigt, wie sich die Vielzahl der zur Synthese verwendeten Monopole in eine Lautsprecher-Treiberfunktion überführen lassen (B).
    Language: German
    Type: proceedings , doc-type:Other
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  • 139
    Publication Date: 2022-03-11
    Language: English
    Type: bachelorthesis , doc-type:bachelorThesis
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  • 140
    Publication Date: 2022-02-01
    Description: In this paper, we introduce the Targeted Multiobjective Dijkstra Algorithm (T-MDA), a label setting algorithm for the One-to-One Multiobjective Shortest Path (MOSP) Problem. The T-MDA is based on the recently published Multiobjective Dijkstra Algorithm (MDA) and equips it with A*-like techniques. The resulting speedup is comparable to the speedup that the original A* algorithm achieves for Dijkstra's algorithm. Unlike other methods from the literature, which rely on special properties of the biobjective case, the T-MDA works for any dimension. To the best of our knowledge, it gives rise to the first efficient implementation that can deal with large scale instances with more than two objectives. A version tuned for the biobjective case, the T-BDA, outperforms state-of-the-art methods on almost every instance of a standard benchmark testbed that is not solvable in fractions of a second.
    Language: English
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  • 141
    Publication Date: 2022-01-31
    Language: English
    Type: other , doc-type:Other
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  • 142
    Publication Date: 2022-02-03
    Language: English
    Type: article , doc-type:article
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  • 143
    Publication Date: 2022-02-04
    Description: Standard correspondence analysis (CA) is a visualisation method to show the relationship between two categorical variables on a simplified figure (usually of two-dimensions). This method represents each variable separately, in different spaces, but combines the results on the same figure for interpretation. Consequently, the distance between two categories of different variables is not interpretable and this complicates the interpretation. Additionally, the plausibility of the interpretation depends on the amount of information traded for the simplifications. In this work, we present Tensor CA, a method that circumvents these issues. In our method, we represent the two variables in the same space and this enables us to accurately control the amount of information used to produce the results. We then provide a method to produce a two-dimensional figure in which the euclidean distances, both within and between the variables, are interpretable and indicate measures of independence, similarity, and association. We then use Tensor CA to extract new knowledge from historical linguistic data (ancient Egyptian).
    Language: English
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  • 144
    Publication Date: 2022-02-15
    Description: This article considers non-stationary incompressible linear fluid equations in a moving domain. We demonstrate the existence and uniqueness of an appropriate weak formulation of the problem by making use of the theory of time-dependent Bochner spaces. It is not possible to directly apply established evolving Hilbert space theory due to the incompressibility constraint. After we have established the well-posedness, we derive and analyse a time discretisation of the system.
    Language: English
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  • 145
    Publication Date: 2021-12-23
    Language: English
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  • 146
    Publication Date: 2021-10-28
    Language: English
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  • 147
    Publication Date: 2021-07-06
    Description: Solving partial differential equations on unstructured grids is a cornerstone of engineering and scientific computing. Nowadays, heterogeneous parallel platforms with CPUs, GPUs, and FPGAs enable energy-efficient and computationally demanding simulations. We developed the HighPerMeshes C++-embedded Domain-Specific Language (DSL) for bridging the abstraction gap between the mathematical and algorithmic formulation of mesh-based algorithms for PDE problems on the one hand and an increasing number of heterogeneous platforms with their different parallel programming and runtime models on the other hand. Thus, the HighPerMeshes DSL aims at higher productivity in the code development process for multiple target platforms. We introduce the concepts as well as the basic structure of the HighPer-Meshes DSL, and demonstrate its usage with three examples, a Poisson and monodomain problem, respectively, solved by the continuous finite element method, and the discontinuous Galerkin method for Maxwell’s equation. The mapping of the abstract algorithmic description onto parallel hardware, including distributed memory compute clusters is presented. Finally, the achievable performance and scalability are demonstrated for a typical example problem on a multi-core CPU cluster.
    Language: English
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  • 148
    Publication Date: 2022-03-14
    Description: We report on the selection process leading to the sixth version of the Mixed Integer Programming Library. Selected from an initial pool of over 5,000 instances, the new MIPLIB 2017 collection consists of 1,065 instances. A subset of 240 instances was specially selected for benchmarking solver performance. For the first time, the compilation of these sets was done using a data-driven selection process supported by the solution of a sequence of mixed integer optimization problems, which encoded requirements on diversity and balancedness with respect to instance features and performance data.
    Language: English
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  • 149
    Publication Date: 2021-10-28
    Language: English
    Type: article , doc-type:article
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  • 150
    Publication Date: 2021-11-30
    Description: We used transition path theory (TPT) to infer "reactive" pathways of floating marine debris trajectories. The TPT analysis was applied on a pollution-aware time-homogeneous Markov chain model constructed from trajectories produced by satellite-tracked undrogued buoys from the NOAA Global Drifter Program. The latter involved coping with the openness of the system in physical space, which further required an adaptation of the standard TPT setting. Directly connecting pollution sources along coastlines with garbage patches of varied strengths, the unveiled reactive pollution routes represent alternative targets for ocean cleanup efforts. Among our specific findings we highlight: constraining a highly probable pollution source for the Great Pacific Garbage Patch; characterizing the weakness of the Indian Ocean gyre as a trap for plastic waste; and unveiling a tendency of the subtropical gyres to export garbage toward the coastlines rather than to other gyres in the event of anomalously intense winds.
    Language: English
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  • 151
    Publication Date: 2021-09-28
    Description: In this article, we introduce the Maximum Diversity Assortment Selection Problem (MDASP), which is a generalization of the two-dimensional Knapsack Problem (2D-KP). Given a set of rectangles and a rectangular container, the goal of 2D-KP is to determine a subset of rectangles that can be placed in the container without overlapping, i.e., a feasible assortment, such that a maximum area is covered. MDASP is to determine a set of feasible assortments, each of them covering a certain minimum threshold of the container, such that the diversity among them is maximized. Thereby, diversity is defined as the minimum or average normalized Hamming distance of all assortment pairs. MDASP was the topic of the 11th AIMMS-MOPTA Competition in 2019. The methods described in this article and the resulting computational results won the contest. In the following, we give a definition of the problem, introduce a mathematical model and solution approaches, determine upper bounds on the diversity, and conclude with computational experiments conducted on test instances derived from the 2D-KP literature.
    Language: English
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  • 152
    Publication Date: 2021-11-30
    Description: This article addresses the problem of estimating the Koopman generator of a Markov process. The direct computation of the infinitesimal generator is not easy because of the discretization of the state space, in particular because of the trade-off inherent in the choice of the best lag time to study the process. Short lag times implies a strong discretization of the state space and a consequent loss of Markovianity. Large lag times bypass events on fast timescales. We propose a method to approximate the generator with the computation of the Newton polynomial extrapolation. This technique is a multistep approach which uses as its input Koopman transfer operators evaluated for a series of lag times. Thus, the estimated infinitesimal generator combines information from different time resolutions and does not bias only fast- or slow-decaying dynamics. We show that the multi-scale Newton method can improve the estimation of the generator in comparison to the computation using finite difference or matrix logarithm methods.
    Language: English
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  • 153
    Publication Date: 2021-03-09
    Description: Understanding the fluctuations by which phenomenological evolution equations with thermodynamic structure can be enhanced is the key to a general framework of nonequilibrium statistical mechanics. These fluctuations provide an idealized representation of microscopic details. We consider fluctuation-enhanced equations associated with Markov processes and elaborate the general recipes for evaluating dynamic material properties, which characterize force-flux constitutive laws, by statistical mechanics. Markov processes with continuous trajectories are conveniently characterized by stochastic differential equations and lead to Green–Kubo-type formulas for dynamic material properties. Markov processes with discontinuous jumps include transitions over energy barriers with the rates calculated by Kramers. We describe a unified approach to Markovian fluctuations and demonstrate how the appropriate type of fluctuations (continuous versus discontinuous) is reflected in the mathematical structure of the phenomenological equations.
    Language: English
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  • 154
    Publication Date: 2021-03-09
    Description: For a given thermodynamic system, and a given choice of coarse-grained state variables, the knowledge of a force-flux constitutive law is the basis for any nonequilibrium modeling. In the first paper of this series we established how, by a generalization of the classical fluctuation-dissipation theorem (FDT), the structure of a constitutive law is directly related to the distribution of the fluctuations of the state variables. When these fluctuations can be expressed in terms of diffusion processes, one may use Green–Kubo-type coarse-graining schemes to find the constitutive laws. In this paper we propose a coarse-graining method that is valid when the fluctuations are described by means of general Markov processes, which include diffusions as a special case. We prove the success of the method by numerically computing the constitutive law for a simple chemical reaction A⇄B. Furthermore, we show that, for such a system, one cannot find a consistent constitutive law by any Green–Kubo-like scheme.
    Language: English
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  • 155
    Publication Date: 2021-06-29
    Description: Aims. Detection and quantification of myocardial scars are helpful both for diagnosis of heart diseases and for building personalized simulation models. Scar tissue is generally charac­terized by a different conduction of electrical excitation. We aim at estimating conductivity-related parameters from endocardial mapping data, in particular the conductivity tensor. Solving this inverse problem requires computationally expensive monodomain simulations on fine discretizations. Therefore, we aim at accelerating the estimation using a multilevel method combining electrophysiology models of different complexity, namely the mono­domain and the eikonal model. Methods. Distributed parameter estimation is performed by minimizing the misfit between simulated and measured electrical activity on the endocardial surface, subject to the mono­domain model and regularization, leading to a constrained optimization problem. We formulate this optimization problem, including the modeling of scar tissue and different regularizations, and design an efficient iterative solver. We consider monodomain grid hierarchies and monodomain-eikonal model hierarchies in a recursive multilevel trust-region method. Results. From several numerical examples, both the efficiency of the method and the estimation quality, depending on the data, are investigated. The multilevel solver is significantly faster than a comparable single level solver. Endocardial mapping data of realistic density appears to be just sufficient to provide quantitatively reasonable estimates of location, size, and shape of scars close to the endocardial surface. Conclusion. In several situations, scar reconstruction based on eikonal and monodomain models differ significantly, suggesting the use of the more accurate but more expensive monodomain model for this purpose. Still, eikonal models can be utilized to accelerate the computations considerably, enabling the use of complex electrophysiology models for estimating myocardial scars from endocardial mapping data.
    Language: English
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  • 156
    Publication Date: 2021-09-30
    Description: In dieser Arbeit wird ein graphenbasiertes Modell zur Einbindung von Preissystemen des öffentlichen Nahverkehrs in Routing-Algorithmen vorgestellt. Jeder Knoten des Graphen repräsentiert einen abstrakten Preiszustand einer Route und ist an einen tatsächlichen Preis gekoppelt. Damit sind sehr einfache und konzise Beschreibungen von Tarifstrukturen möglich, diesich algorithmisch behandeln lassen. Durch das zeitgleiche Tracken eines Pfades im Routinggraphen im Ticketgraphen kann schon während einer Routenberechnung der Preis bestimmt werden. Dies ermöglicht die Berechnung von preisoptimalen Routen. An den Tarifsystemen der Verkehrsverbünde MDV (Mitteldeutscher Verkehrsverbund) und VBB (Verkehrsverbund Berlin-Brandenburg) wird die Konstruktion des Modells detailliert erläutert.
    Language: German
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  • 157
    Publication Date: 2021-11-30
    Description: This paper revolves around a subtle distinction between two concepts: passing to the limit in a family of gradient systems, on one hand, and deriving effective kinetic relations on the other. The two concepts are strongly related, and in many examples they even appear to be the same. Our main contributions are to show that they are different, to show that well-known techniques developed for the former may give incorrect results for the latter, and to introduce new tools to remedy this. The approach is based on the Energy-Dissipation Principle that provides a variational formulation to gradient-flow equations that allows one to apply techniques from Γ-convergence of functional on states and functionals on trajectories.
    Language: English
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  • 158
    Publication Date: 2022-03-11
    Language: English
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  • 159
    Publication Date: 2022-03-17
    Description: It is well known that the interface between two regions of an incompressible ideal fluid flow moving in a relative motion is necessarily destabilized, regardless of the velocity difference's strength. This phenomenon is the so-called Kelvin-Helmholtz instability (KHI). However, a large number of works demonstrated a surprising result that the instability is suppressed for shallow water flows; the interface is stabilized if the Froude number, defined by the velocity difference's ratio to the gravity wave's speed, is sufficiently large. In a limited way, these authors have been used the shallow-water equations without the higher-order effect of the dispersive terms. Thus, this investigation aims to examine these higher-order dispersive effects to analyze the interface stability problem of tangential-velocity discontinuity in shallow-water flows. In particular, we use the Green-Naghdi equations to introduce the dispersive terms related to the depth and the depth-averaged horizontal velocities of the fluid. We show that the interface stability depends on the Froude number (i.e., the velocity difference's strength) and the water depth. A critical value of the Froude number to stabilize the interface is smaller than the case of no dispersive terms, and the flow in a deeper region is more stable than in a shallower one. We also consider the distribution of kinetic and potential energy to clarify a feature characteristic of a large class of instabilities in shallow water flow. The instability of flows is caused by the decrease in the kinetic energy during the perturbation of waves. This phenomenon is known as negative energy modes and plays a vital role in applying the model to industrial equipment. A conclusion is that the equipartition of energies occurs if and only if the velocity difference is zero and the water depth is shallow enough to ignore the dispersive terms.
    Language: English
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  • 160
    Publication Date: 2021-12-09
    Description: We report our progress on the project for solving larger scale quadratic assignment problems (QAPs). Our main approach to solve large scale NP-hard combinatorial optimization problems such as QAPs is a parallel branch-and-bound method efficiently implemented on a powerful computer system using the Ubiquity Generator(UG) framework that can utilize more than 100,000 cores. Lower bounding procedures incorporated in the branch-and-bound method play a crucial role in solving the problems. For a strong lower bounding procedure, we employ the Lagrangian doubly nonnegative (DNN) relaxation and the Newton-bracketing method developed by the authors’ group. In this report, we describe some basic tools used in the project including the lower bounding procedure and branching rules, and present some preliminary numerical results. Our next target problem is QAPs with dimension at least 50, as we have succeeded to solve tai30a and sko42 from QAPLIB for the first time.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 161
    Publication Date: 2021-03-05
    Description: We discuss the properties of the distributions of energies of minima obtained by gradient descent in complex energy landscapes. We find strikingly similar phenomenology across several prototypical models. We particularly focus on the distribution of energies of minima in the analytically well-understood p-spin-interaction spin-glass model. We numerically find non-Gaussian distributions that resemble the Tracy-Widom distributions often found in problems of random correlated variables, and nontrivial finite-size scaling. Based on this, we propose a picture of gradient-descent dynamics that highlights the importance of a first-passage process in the eigenvalues of the Hessian. This picture provides a concrete link to problems in which the Tracy-Widom distribution is established. Aspects of this first-passage view of gradient-descent dynamics are generic for nonconvex complex landscapes, rationalizing the commonality that we find across models.
    Language: English
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  • 162
    Publication Date: 2022-03-11
    Description: The Portable Computing Language (PoCL) is a vendor independent open-source OpenCL implementation that aims to support a variety of compute devices in a single platform. Evaluating PoCL versus the Intel OpenCL implementation reveals significant performance drawbacks of PoCL on Intel CPUs – which run 92 % of the TOP500 list. Using a selection of benchmarks, we identify and analyse performance issues in PoCL with a focus on scheduling and vectorisation. We propose a new CPU device-driver based on Intel Threading Building Blocks (TBB), and evaluate LLVM with respect to automatic compiler vectorisation across work-items in PoCL. Using the TBB driver, it is possible to narrow the gap to Intel OpenCL and even outperform it by a factor of up to 1.3× in our proxy application benchmark with a manual vectorisation strategy.
    Language: English
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  • 163
    Publication Date: 2021-05-06
    Language: English
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  • 164
    Publication Date: 2021-11-02
    Description: This is a list of codes generated from ancient egyptian texts. The codes are used for a correspondence analysis (CA). Codes and CA software are available from the linked webpage.
    Language: English
    Type: researchdata , doc-type:ResearchData
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  • 165
    Publication Date: 2021-12-08
    Description: In practice, transient gas transport problems frequently have to be solved for large-scale gas networks. Gas network optimization problems typically belong to the class of Mixed-Integer Nonlinear Programming Problems (MINLP). However current state-of-the-art MINLP solvers are not yet mature enough to solve large-scale real-world instances. Therefore, an established approach in practice is to solve the problems with respect to a coarser representation of the network and thereby reducing the size of the underlying model. Two well-known aggregation methods that effectively reduce the network size are parallel and serial pipe merges. However, these methods have only been studied in stationary gas transport problems so far. This paper closes this gap and presents parallel and serial pipe merging methods in the context of transient gas transport. To this end, we introduce the concept of equivalent and heuristic subnetwork replacements. For the heuristic methods, we conduct a huge empirical evaluation based on real-world data taken from one of the largest gas networks in Europe. It turns out that both, parallel and serial pipe merging can be considered as appropriate aggregation methods for real-world transient gas flow problems.
    Language: English
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  • 166
    Publication Date: 2021-11-25
    Description: The aim of this paper is to provide a comprehensive overview of the MICCAI 2020 AutoImplant Challenge. The approaches and publications submitted and accepted within the challenge will be summarized and reported, highlighting common algorithmic trends and algorithmic diversity. Furthermore, the evaluation results will be presented, compared and discussed in regard to the challenge aim: seeking for low cost, fast and fully automated solutions for cranial implant design. Based on feedback from collaborating neurosurgeons, this paper concludes by stating open issues and post-challenge requirements for intra-operative use.
    Language: English
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  • 167
    Publication Date: 2022-02-07
    Description: We present a heuristic based on linear programming (LP) for the integrated tour and crew roster planning of toll enforcement inspectors. Their task is to enforce the proper paying of a distance-based toll on German motorways. This leads to an integrated tour planning and duty rostering problem; it is called Toll Enforcement Problem (TEP). We tackle the TEP by a standard multi-commodity flow model with some extensions in order to incorporate the control tours. The heuristic consists of two variants. The first, called Price & Branch, is a column generation approach to solve the model’s LP relaxation by pricing tour and roster arc variables. Then, we compute an integer feasible solution by restricting to all variables that were priced. The second is a coarse-to-fine approach. Its basic idea is projecting variables to an aggregated variable space, which is much smaller. The aim is to spend as much algorithmic effort in this coarse model as possible. For both heuristic procedures we will show that feasible solutions of high quality can be computed even for large scale industrial instances.
    Language: English
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  • 168
    Publication Date: 2021-04-30
    Description: This report presents a method to integrate highly flexible technology models for distributed energy resources such as electric vehicles, power-to-heat systems, or home battery systems into a Lagrangian relaxation of the pan-European day-ahead electricity market (EULR). These flexible technology models are highly sensitive to the changes of Lagrangian multipliers within the iterative Lagrangian relaxation process, leading to volatile behavior. Furthermore, they show a high concurrency in their market behavior due to their technical homogeneity. Therefore, the method proposed in this report is an extension of the existing EULR modeling approach to improve the model's convergence. The methodological extension comprises a convex combination of iteration solutions for the Lagrangian relaxation subproblems similar to Dantzig-Wolfe decomposition. An exemplary case study shows the effectiveness of this extended approach.
    Language: English
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  • 169
    Publication Date: 2022-01-18
    Description: Consider a flow network, i.e., a directed graph where each arc has a nonnegative capacity value and an associated length, together with nonempty supply intervals for the sources and nonempty demand intervals for the sinks. The Maximum Min-Cost-Flow Problem (MaxMCF) is to find fixed supply and demand values within these intervals such that the optimal objective value of the induced Min-Cost-Flow Problem (MCF) is maximized. In this paper, we show that MaxMCF as well as its uncapacitated variant, the Maximum Transportation Problem (MaxTP), are NP-hard. Further, we prove that MaxMCF is APX-hard if a connectedness-condition regarding the sources and the sinks of the flow network is dropped. Finally, we show how the Minimum Min-Cost-Flow Problem (MinMCF) can be solved in polynomial time.
    Language: English
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  • 170
    Publication Date: 2021-12-01
    Description: The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the inclusion of experimental constraints. Here, we add support of PLANTS to VirtualFlow (VirtualFlow Ants), which adds a valuable method for primary virtual screenings and rescoring procedures. Furthermore, we have added support of ligand libraries in the MOL2 format, as well as on the fly conversion of ligand libraries which are in the PDBQT format to the MOL2 format to endow VirtualFlow Ants with an increased flexibility regarding the ligand libraries. The on the fly conversion is carried out with Open Babel and the program SPORES. We applied VirtualFlow Ants to a test system involving KEAP1 on the Google Cloud up to 128,000 CPUs, and the observed scaling behavior is approximately linear. Furthermore, we have adjusted several central docking parameters of PLANTS (such as the speed parameter or the number of ants) and screened 10 million compounds for each of the 10 resulting docking scenarios. We analyzed their docking scores and average docking times, which are key factors in virtual screenings. The possibility of carrying out ultra-large virtual screening with PLANTS via VirtualFlow Ants opens new avenues in computational drug discovery.
    Language: English
    Type: article , doc-type:article
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  • 171
    Publication Date: 2022-03-11
    Language: English
    Type: article , doc-type:article
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  • 172
    Publication Date: 2021-08-09
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 173
    Publication Date: 2021-11-30
    Description: Objectives The clinical parameter “morning stiffness” is widely used to assess the status of rheumatoid arthritis (RA), but its accurate quantitative assessment in a clinical setting has not yet been successful. This lack of individual quantification limits both personalized medication and efficacy evaluation in the treatment of RA. Methods We have developed a novel technology to assess passive resistance of the metacarpophalangeal (MCP) III joint (stiffness) and its Passive Range of Motion (PRoM). Within this pilot study, nineteen female postmenopausal RA patients and nine healthy controls were examined in the evening as well as in the morning of the following day. To verify the specificity of the biomechanical quantification, eleven patients with RA were assessed both prior to and ∼3 h after glucocorticoid therapy. Results While the healthy controls showed only minor changes between afternoon and morning, in RA patients mean±SD PRoM decreased significantly by 18 ± 22% and stiffness increased significantly by 20 ± 18% in the morning compared with the previous afternoon. We found a significant positive correlation between RA activity and biomechanical measures. Glucocorticoids significantly increased mean PRoM by 16 ± 11% and reduced mean stiffness by 23 ± 22%. Conclusion This technology allowed mechanical stiffness to be quantified in MCP joints, and has demonstrated high sensitivity in respect to disease status as well as medication effect in RA patients. Such non-invasive, low risk, and rapid assessment of biomechanical joint stiffness opens a novel avenue for judging therapy efficacy in patients with RA, and potentially also in other non-RA inflammatory joint diseases.
    Language: English
    Type: article , doc-type:article
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  • 174
    Publication Date: 2022-02-14
    Description: Secure energy transport is considered as highly relevant for the basic infrastructure of nowadays society and economy. To satisfy increasing demands and to handle more diverse transport situations, operators of energy networks regularly expand the capacity of their network by building new network elements, known as the expansion planning problem. A key constraint function in expansion planning problems is a nonlinear and nonconvex potential loss function. In order to improve the algorithmic performance of state-of-the-art MINLP solvers, this paper presents an algebraic description for the convex envelope of this function. Through a thorough computational study, we show that this tighter relaxation tremendously improve the performance of the MINLP solver SCIP on a large test set of practically relevant instances for the expansion planning problem. In particular, the results show that our achievements lead to an improvement of the solver performance for a development version by up to 58%.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 175
    Publication Date: 2021-09-27
    Description: Building upon earlier research, we revisit a bilevel formulation of service design and pricing for freight networks, with the aim of investigating its algorithmic aspects. The model adds substantial computational challenges to the existing literature, as it deals with general integer network design variables. An iterative heuristic algorithm is introduced, based on the concepts of inverse optimization and neighbourhood search. The procedure alternates between two versions of restricted formulations of the model while inducing promising changes into the service assignments. The approach has proven a high performance for all of the considered real-world instances. Its efficiency rests on its ability to deliver results within a close proximity to those obtained by the exact solver in terms of quality, yet within a significantly smaller amount of time, and to land feasible solutions for the large-sized instances that could not be previously solved. In line with the sustainable transport goals, a deeper observation of the transport management side highlights the strategy of the algorithm favouring freight consolidation and achieving high load factors.
    Language: English
    Type: article , doc-type:article
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  • 176
    Publication Date: 2022-02-02
    Description: The traditional linear regression model that assumes normal residuals is applied extensively in engineering and science. However, the normality assumption of the model residuals is often ineffective. This drawback can be overcome by using a generalized normal regression model that assumes a non-normal response. In this paper, we propose regression models based on generalizations of the normal distribution. The proposed regression models can be used effectively in modeling data with a highly skewed response. Furthermore, we study in some details the structural properties of the proposed generalizations of the normal distribution. The maximum likelihood method is used for estimating the parameters of the proposed method. The performance of the maximum likelihood estimators in estimating the distributional parameters is assessed through a small simulation study. Applications to two real datasets are given to illustrate the flexibility and the usefulness of the proposed distributions and their regression models.
    Language: English
    Type: article , doc-type:article
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  • 177
    Publication Date: 2022-03-11
    Description: The benefits of cutting planes based on the perspective function are well known for many specific classes of mixed-integer nonlinear programs with on/off structures. However, we are not aware of any empirical studies that evaluate their applicability and computational impact over large, heterogeneous test sets in general-purpose solvers. This paper provides a detailed computational study of perspective cuts within a linear programming based branch-and-cut solver for general mixed-integer nonlinear programs. Within this study, we extend the applicability of perspective cuts from convex to non-convex nonlinearities. This generalization is achieved by applying a perspective strengthening to valid linear inequalities which separate solutions of linear relaxations. The resulting method can be applied to any constraint where all variables appearing in nonlinear terms are semi-continuous and depend on at least one common indicator variable. Our computational experiments show that adding perspective cuts for convex constraints yields a consistent improvement of performance, and adding perspective cuts for nonconvex constraints reduces branch-and-bound tree sizes and strengthens the root node relaxation, but has no significant impact on the overall mean time.
    Language: English
    Type: article , doc-type:article
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  • 178
    Publication Date: 2021-12-22
    Description: Two different approaches to parameter estimation (PE) in the context of polymerization are introduced, refined, combined, and applied. The first is classical PE where one is interested in finding parameters which minimize the distance between the output of a chemical model and experimental data. The second is Bayesian PE allowing for quantifying parameter uncertainty caused by experimental measurement error and model imperfection. Based on detailed descriptions of motivation, theoretical background, and methodological aspects for both approaches, their relation are outlined. The main aim of this article is to show how the two approaches complement each other and can be used together to generate strong information gain regarding the model and its parameters. Both approaches and their interplay in application to polymerization reaction systems are illustrated. This is the first part in a two-article series on parameter estimation for polymer reaction kinetics with a focus on theory and methodology while in the second part a more complex example will be considered.
    Language: English
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