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  • 2015-2019  (355)
  • 1920-1924
  • 2016  (355)
  • 201
    Publication Date: 2022-07-19
    Description: Purpose: To account for the impact of turbulence in blood damage modeling, a novel approach based on the generation of instantaneous flow fields from RANS simulations is proposed. Methods: Turbulent flow in a bileaflet mechanical heart valve was simulated using RANS-based (SST k-ω) flow solver using FLUENT 14.5. The calculated Reynolds shear stress (RSS) field is transformed into a set of divergence-free random vector fields representing turbulent velocity fluctuations using procedural noise functions. To consider the random path of the blood cells, instantaneous flow fields were computed for each time step by summation of RSS-based divergence-free random and mean velocity fields. Using those instantaneous flow fields, instantaneous pathlines and corresponding point-wise instantaneous shear stresses were calculated. For a comparison, averaged pathlines based on mean velocity field and respective viscous shear stresses together with RSS values were calculated. Finally, the blood damage index (hemolysis) was integrated along the averaged and instantaneous pathlines using a power law approach and then compared. Results: Using RSS in blood damage modeling without a correction factor overestimates damaging stress and thus the blood damage (hemolysis). Blood damage histograms based on both presented approaches differ. Conclusions: A novel approach to calculate blood damage without using RSS as a damaging parameter is established. The results of our numerical experiment support the hypothesis that the use of RSS as a damaging parameter should be avoided.
    Language: English
    Type: article , doc-type:article
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  • 202
    Publication Date: 2022-07-19
    Description: A method is developed for computing the local probability for the presence of a ridge in a Gaussian Random field.
    Language: English
    Type: bachelorthesis , doc-type:bachelorThesis
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  • 203
    Publication Date: 2022-07-19
    Description: We introduce techniques for the processing of motion and animations of non-rigid shapes. The idea is to regard animations of deformable objects as curves in shape space. Then, we use the geometric structure on shape space to transfer concepts from curve processing in Rn to the processing of motion of non-rigid shapes. Following this principle, we introduce a discrete geometric flow for curves in shape space. The flow iteratively replaces every shape with a weighted average shape of a local neighborhood and thereby globally decreases an energy whose minimizers are discrete geodesics in shape space. Based on the flow, we devise a novel smoothing filter for motions and animations of deformable shapes. By shortening the length in shape space of an animation, it systematically regularizes the deformations between consecutive frames of the animation. The scheme can be used for smoothing and noise removal, e.g., for reducing jittering artifacts in motion capture data. We introduce a reduced-order method for the computation of the flow. In addition to being efficient for the smoothing of curves, it is a novel scheme for computing geodesics in shape space. We use the scheme to construct non-linear Bézier curves by executing de Casteljau's algorithm in shape space.
    Language: English
    Type: article , doc-type:article
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  • 204
    Publication Date: 2022-07-19
    Language: English
    Type: article , doc-type:article
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  • 205
    Publication Date: 2022-07-19
    Description: In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.
    Language: English
    Type: article , doc-type:article
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  • 206
    Publication Date: 2022-07-19
    Description: Many natural objects contain pores and cavities that are filled with the same material that also surrounds the object. When such objects are imaged using, for example, computed tomography, the pores and cavities cannot be distinguished from the surrounding material by considering gray values and texture properties of the image. In this case, morphological operations are often used to fill the inner region. This is efficient, if the pore and cavity structures are small compared to the overall size of the object and if the object’s shape is mainly convex. If this is not the case, the segmentation might be very difficult and may result in a lot of noise. We propose the usage of ambient occlusion for the segmentation of pores and cavities. One nice property of ambient occlusion is that it generates smooth scalar fields. Due to this smoothness property, a segmentation based on those fields will result in smooth boundaries at the pore and cavity openings. This is often desired, particularly when dealing with natural objects.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 207
    Publication Date: 2022-07-19
    Description: Statistical methods to design computer experiments usually rely on a Gaussian process (GP) surrogate model, and typically aim at selecting design points (combinations of algorithmic and model parameters) that minimize the average prediction variance, or maximize the prediction accuracy for the hyperparameters of the GP surrogate. In many applications, experiments have a tunable precision, in the sense that one software parameter controls the tradeoff between accuracy and computing time (e.g., mesh size in FEM simulations or number of Monte-Carlo samples). We formulate the problem of allocating a budget of computing time over a finite set of candidate points for the goals mentioned above. This is a continuous optimization problem, which is moreover convex whenever the tradeoff function accuracy vs. computing time is concave. On the other hand, using non-concave weight functions can help to identify sparse designs. In addition, using sparse kernel approximations drastically reduce the cost per iteration of the multiplicative weights updates that can be used to solve this problem.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 208
    Publication Date: 2022-07-19
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 209
    Publication Date: 2022-07-19
    Language: English
    Type: poster , doc-type:Other
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  • 210
    Publication Date: 2022-07-19
    Description: Traditionally, Lagrangian fields such as finite-time Lyapunov exponents (FTLE) are precomputed on a discrete grid and are ray casted afterwards. This, however, introduces both grid discretization errors and sampling errors during ray marching. In this work, we apply a progressive, view-dependent Monte Carlo-based approach for the visualization of such Lagrangian fields in time-dependent flows. Our ap- proach avoids grid discretization and ray marching errors completely, is consistent, and has a low memory consumption. The system provides noisy previews that con- verge over time to an accurate high-quality visualization. Compared to traditional approaches, the proposed system avoids explicitly predefined fieldline seeding structures, and uses a Monte Carlo sampling strategy named Woodcock tracking to distribute samples along the view ray. An acceleration of this sampling strategy requires local upper bounds for the FTLE values, which we progressively acquire during the rendering. Our approach is tailored for high-quality visualizations of complex FTLE fields and is guaranteed to faithfully represent detailed ridge surface structures as indicators for Lagrangian coherent structures (LCS). We demonstrate the effectiveness of our approach by using a set of analytic test cases and real-world numerical simulations.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 211
    Publication Date: 2022-07-19
    Description: Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish.
    Language: English
    Type: article , doc-type:article
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  • 212
    Publication Date: 2022-07-19
    Language: English
    Type: masterthesis , doc-type:masterThesis
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  • 213
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    Publication Date: 2022-07-19
    Language: English
    Type: bachelorthesis , doc-type:bachelorThesis
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  • 214
    Publication Date: 2022-07-19
    Description: When physical unfolding/unrolling of papyri is not possible or too dangerous for preserving the precious object, tomographic approaches may be the ap- propriate alternative. Requirements are the resolution and the contrast to distinguish writing and substrate. The steps to be performed are the following: (1) Select the object of interest (archaeological arguments, cultural back- ground of the object, etc.). (2) Find the proper physical procedure, especially with respect to contrast, take the tomographic data, e.g. by absorption x-ray tomography. (3) Apply mathematical unfolding transformations to the tomographic data, in order to obtain a 2d-planar reconstruction of text.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 215
    Publication Date: 2022-07-19
    Language: English
    Type: article , doc-type:article
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  • 216
    Publication Date: 2022-07-19
    Description: The reconstruction of an object's shape or surface from a set of 3D points is a common topic in materials and life sciences, computationally handled in computer graphics. Such points usually stem from optical or tactile 3D coordinate measuring equipment. Surface reconstruction also appears in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or the alignment of intra-operative navigation and preoperative planning data. In contrast to mere 3D point clouds, medical imaging yields contextual information on the 3D point data that can be used to adopt prior information on the shape that is to be reconstructed from the measurements. In this work we propose to use a statistical shape model (SSM) as a prior for surface reconstruction. The prior knowledge is represented by a point distribution model (PDM) that is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we reformulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given measurements are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are oriented according to the surface normals at the PDM points, a surface-based tting is accomplished. By estimating the parameters of the GMM in a maximum a posteriori manner, the reconstruction of the surface from the given measurements is achieved. Extensive experiments suggest that our proposed approach leads to superior surface reconstructions compared to Iterative Closest Point (ICP) methods.
    Language: English
    Type: article , doc-type:article
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  • 217
    Publication Date: 2022-07-19
    Description: The endoskeleton of sharks and rays (elasmobranchs) is comprised of a cartilaginous core, covered by thousands of mineralized tiles, called tesserae. Characterizing the relationship between tesseral morphometrics, skeletal growth and mechanics is challenging because tesserae are small (a few hundred micrometers wide), anchored to the surrounding tissue in complex three-dimensional ways, and occur in huge numbers. We integrate material property, histology, electron microscopy and synchrotron and laboratory µCT scans of skeletal elements from an ontogenetic series of round stingray Urobatis halleri, to gain insights into the generation and maintenance of a natural tessellated system. Using a custom-made semiautomatic segmentation algorithm, we present the first quantitative and 3d description of tesserae across whole skeletal elements. The tessellation is not interlocking or regular, with tesserae showing a great range of shapes, sizes and number of neighbors. This is partly region-dependent: for example, thick, columnar tesserae are arranged in series along convex edges with small radius of curvature (RoC), whereas more brick- or disc-shaped tesserae are found in planar/flatter areas. Comparison of the tessellation across ontogeny, shows that in younger animals, the forming tesseral network is less densely packed, appearing as a covering of separate, poorly mineralized islands that grow together with age to form a complete surface. Some gaps in the tessellation are localized to specific regions in all samples, indicating they are real features, perhaps either regions of delayed mineralization or of tendon insertion. We will use the structure of elasmobranch skeletons as a road map for understanding shark and ray skeletal mechanics, but also to extract fundamental engineering principles for tiled composite materials.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 218
    Publication Date: 2022-07-19
    Description: We propose a novel Riemannian framework for statistical analysis of shapes that is able to account for the nonlinearity in shape variation. By adopting a physical perspective, we introduce a differential representation that puts the local geometric variability into focus. We model these differential coordinates as elements of a Lie group thereby endowing our shape space with a non-Euclidian structure. A key advantage of our framework is that statistics in a manifold shape space become numerically tractable improving performance by several orders of magnitude over state-of-the-art. We show that our Riemannian model is well suited for the identification of intra-population variability as well as inter-population differences. In particular, we demonstrate the superiority of the proposed model in experiments on specificity and generalization ability. We further derive a statistical shape descriptor that outperforms the standard Euclidian approach in terms of shape-based classification of morphological disorders.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 219
    Publication Date: 2022-07-19
    Description: In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 220
    Publication Date: 2022-07-19
    Description: Statistical shape models (SSM) describe the shape variability contained in a given population. They are able to describe large populations of complex shapes with few degrees of freedom. This makes them a useful tool for a variety of tasks that arise in computer-aided madicine. In this chapter we are going to explain the basic methodology of SSMs and present a variety of examples, where SSMs have been successfully applied.
    Language: English
    Type: bookpart , doc-type:bookPart
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  • 221
    Publication Date: 2022-07-19
    Description: Models of cortical dynamics often assume a homogeneous connectivity structure. However, we show that heterogeneous input connectivity can prevent the dynamic balance between excitation and inhibition, a hallmark of cortical dynamics, and yield unrealistically sparse and temporally regular firing. Anatomically based estimates of the connectivity of layer 4 (L4) rat barrel cortex and numerical simulations of this circuit indicate that the local network possesses substantial heterogeneity in input connectivity, sufficient to disrupt excitation-inhibition balance. We show that homeostatic plasticity in inhibitory synapses can align the functional connectivity to compensate for structural heterogeneity. Alternatively, spike-frequency adaptation can give rise to a novel state in which local firing rates adjust dynamically so that adaptation currents and synaptic inputs are balanced. This theory is supported by simulations of L4 barrel cortex during spontaneous and stimulus-evoked conditions. Our study shows how synaptic and cellular mechanisms yield fluctuation-driven dynamics despite structural heterogeneity in cortical circuits.
    Language: English
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  • 222
    Publication Date: 2022-07-19
    Description: Deformable model-based approaches to 3D image segmentation have been shown to be highly successful. Such methodology requires an appearance model that drives the deformation of a geometric model to the image data. Appearance models are usually either created heuristically or through supervised learning. Heuristic methods have been shown to work effectively in many applications but are hard to transfer from one application (imaging modality/anatomical structure) to another. On the contrary, supervised learning approaches can learn patterns from a collection of annotated training data. In this work, we show that the supervised joint dictionary learning technique is capable of overcoming the traditional drawbacks of the heuristic approaches. Our evaluation based on two different applications (liver/CT and knee/MR) reveals that our approach generates appearance models, which can be used effectively and efficiently in a deformable model-based segmentation framework.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 223
    Publication Date: 2022-07-19
    Description: Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.
    Language: English
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  • 224
    Publication Date: 2022-07-19
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 225
    Publication Date: 2022-07-19
    Description: To improve existing weather prediction and reanalysis capabilities, high-resolution and multi-modal climate data becomes an increasingly important topic. The advent of increasingly dense numerical simulation of atmospheric phenomena, provides new means to better understand dynamic processes and to visualize structural flow patterns that remain hidden otherwise. In the presented illustrations we demonstrate an advanced technique to visualize multiple scales of dense flow fields and Lagrangian patterns therein, simulated by state-of-the-art simulation models for each scale. They provide a deeper insight into the structural differences and patterns that occur on each scale and highlight the complexity of flow phenomena in our atmosphere.
    Language: English
    Type: poster , doc-type:Other
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  • 226
    Publication Date: 2022-07-19
    Description: Background: Fossil ticks are extremely rare, whereby Ixodes succineus Weidner, 1964 from Eocene (ca. 44-49 Ma) Baltic amber is one of the oldest examples of a living hard tick genus (Ixodida: Ixodidae). Previous work suggested it was most closely related to the modern and widespread European sheep tick Ixodes ricinus (Linneaus, 1758). Results: Restudy using phase contrast synchrotron x-ray tomography yielded images of exceptional quality. These confirm the fossil's referral to Ixodes Latreille, 1795, but the characters resolved here suggest instead affinities with the Asian subgenus Partipalpiger Hoogstraal et al., 1973 and its single living (and medically significant) species Ixodes ovatus Neumann, 1899. We redescribe the amber fossil here as Ixodes (Partipalpiger) succineus. Conclusions: Our data suggest that Ixodes ricinus is unlikely to be directly derived from Weidner's amber species, but instead reveals that the Partipalpiger lineage was originally more widely distributed across the northern hemisphere. The closeness of Ixodes (P.) succineus to a living vector of a wide range of pathogens offers the potential to correlate its spatial and temporal position (northern Europe, nearly 50 million years ago) with the estimated origination dates of various tick-borne diseases.
    Language: English
    Type: article , doc-type:article
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  • 227
    Publication Date: 2022-07-19
    Description: Surgical robots are an important component for delivering advanced paradigm shifting technology such as image guided surgery and navigation. However, for robotic systems to be readily adopted into the operating room they must be easy and convenient to control and facilitate a smooth surgical workflow. In minimally invasive surgery, the laparoscope may be held by a robot but controlling and moving the laparoscope remains challenging. It is disruptive to the workflow for the surgeon to put down the tools to move the robot in particular for solo surgery approaches. This paper proposes a novel approach for naturally controlling the robot mounted laparoscope’s position by detecting a surgical grasping tool and recognizing if its state is open or close. This approach does not require markers or fiducials and uses a machine learning framework for tool and state recognition which exploits naturally occurring visual cues. Furthermore a virtual user interface on the laparoscopic image is proposed that uses the surgical tool as a pointing device to overcome common problems in depth perception. Instrument detection and state recognition are evaluated on in-vivo and ex-vivo porcine datasets. To demonstrate the practical surgical application and real time performance the system is validated in a simulated surgical environment.
    Language: English
    Type: article , doc-type:article
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  • 228
    Publication Date: 2022-07-19
    Description: A comprehensive framework for detection and characterization of partial intrinsic symmetry over 3D shapes is proposed. To identify prominent symmetric regions which overlap in space and vary in form, the proposed framework is decoupled into a Correspondence Space Voting (CSV) procedure followed by a Transformation Space Mapping (TSM) procedure. In the CSV procedure, significant symmetries are first detected by identifying surface point pairs on the input shape that exhibit local similarity in terms of their intrinsic geometry while simultaneously maintaining an intrinsic distance structure at a global level. To allow detection of potentially overlapping symmetric shape regions, a global intrinsic distance-based voting scheme is employed to ensure the inclusion of only those point pairs that exhibit significant intrinsic symmetry. In the TSM procedure, the Functional Map framework is employed to generate the final map of symmetries between point pairs. The TSM procedure ensures the retrieval of the underlying dense correspondence map throughout the 3D shape that follows a particular symmetry. The TSM procedure is also shown to result in the formulation of a metric symmetry space where each point in the space represents a specific symmetry transformation and the distance between points represents the complexity between the corresponding transformations. Experimental results show that the proposed framework can successfully analyze complex 3D shapes that possess rich symmetries.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 229
    Publication Date: 2022-07-19
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 230
    Publication Date: 2022-07-19
    Description: The evolution of complexly folded septa in ammonoids has long been a controversial topic. Explanations of the function of these folded septa can be divided into physiological and mechanical hypotheses with the mechanical functions tending to find widespread support. The complexity of the cephalopod shell has made it difficult to directly test the mechanical properties of these structures without oversimplification of the septal morphology or extraction of a small sub-domain. However, the power of modern finite element analysis now permits direct testing of mechanical hypothesis on complete, empirical models of the shells taken from computed tomographic data. Here we compare, for the first time using empirical models, the capability of the shells of extant Nautilus pompilius, Spirula spirula, and the extinct ammonite Cadoceras sp. to withstand hydrostatic pressure and point loads. Results show hydrostatic pressure imparts highest stress on the final septum with the rest of the shell showing minimal compression. S. spirula shows the lowest stress under hydrostatic pressure while N. pompilius shows the highest stress. Cadoceras sp. shows the development of high stress along the attachment of the septal saddles with the shell wall. Stress due to point loads decreases when the point force is directed along the suture as opposed to the unsupported chamber wall. Cadoceras sp. shows the greatest decrease in stress between the point loads compared to all other models. Greater amplitude of septal flutes corresponds with greater stress due to hydrostatic pressure; however, greater amplitude decreases the stress magnitude of point loads directed along the suture. In our models, sutural complexity does not predict greater resistance to hydrostatic pressure but it does seem to increase resistance to point loads, such as would be from predators. This result permits discussion of palaeoecological reconstructions on the basis of septal morphology. We further suggest that the ratio used to characterize septal morphology in the septal strength index and in calculations of tensile strength of nacre are likely insufficient. A better understanding of the material properties of cephalopod nacre may allow the estimation of maximum depth limits of shelled cephalopods through finite element analysis.
    Language: English
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  • 231
    Publication Date: 2022-07-19
    Description: Neural circuit mapping is generating datasets of 10,000s of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types including searching neurons against transgene expression patterns. Finally we show that NBLAST is effective with data from other invertebrates and zebrafish.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 232
    Publication Date: 2022-07-19
    Description: We introduce techniques for the processing of motion and animations of non-rigid shapes. The idea is to regard animations of deformable objects as curves in shape space. Then, we use the geometric structure on shape space to transfer concepts from curve processing in R^n to the processing of motion of non-rigid shapes. Following this principle, we introduce a discrete geometric flow for curves in shape space. The flow iteratively replaces every shape with a weighted average shape of a local neighborhood and thereby globally decreases an energy whose minimizers are discrete geodesics in shape space. Based on the flow, we devise a novel smoothing filter for motions and animations of deformable shapes. By shortening the length in shape space of an animation, it systematically regularizes the deformations between consecutive frames of the animation. The scheme can be used for smoothing and noise removal, e.g., for reducing jittering artifacts in motion capture data. We introduce a reduced-order method for the computation of the flow. In addition to being efficient for the smoothing of curves, it is a novel scheme for computing geodesics in shape space. We use the scheme to construct non-linear “Bézier curves” by executing de Casteljau’s algorithm in shape space.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 233
    Publication Date: 2022-07-19
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 234
    Publication Date: 2022-07-19
    Description: Visualization and Analysis of atomic compositions is essential to understand the structure and functionality of molecules. There exist versatile areas of applications, from fundamental researches in biophysics and materials science to drug development in pharmaceutics. For most applications, the hard-sphere model is the most often used molecular model. Although the model is a quite simple approximation of reality, it enables investigating important physical properties in a purely geometrical manner. Furthermore, large data sets with thousands up to millions of atoms can be visualized and analyzed. In addition to an adequate and efficient visualization of the data, the extraction of important structures plays a major role. For the investigation of biomolecules, such as proteins, especially the analysis of cavities and their dynamics is of high interest. Substrates can bind in cavities, thereby inducing changes in the function of the protein. Another example is the transport of substrates through membrane proteins by the dynamics of the cavities. For both, the visualization as well as the analysis of cavities, the following contributions will be presented in this thesis: 1. The rendering of smooth molecular surfaces for the analysis of cavities is accelerated and visually improved, which allows showing dynamic proteins. On the other hand, techniques are proposed to interactively render large static biological structures and inorganic materials up to atomic resolution for the first time. 2. A Voronoi-based method is presented to extract molecular cavities. The procedure comes with a high geometrical accuracy by a comparatively fast computation time. Additionally, new methods are presented to visualize and highlight the cavities within the molecular structure. In a further step, the techniques are extended for dynamic molecular data to trace cavities over time and visualize topological changes. 3. To further improve the accuracy of the approaches mentioned above, a new molecular surface model is presented that shows the accessibility of a substrate. For the first time, the structure and dynamics of the substrate as hard-sphere model is considered for the accessibility computation. In addition to the definition of the surface, an efficient algorithm for its computation is proposed, which additionally allows extracting cavities. The presented algorithms are demonstrated on different molecular data sets. The data sets are either the result of physical or biological experiments or molecular dynamics simulations.
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
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  • 235
  • 236
    Publication Date: 2023-01-06
    Description: We present an overview of the current status of the European collaborative project PAEON. The challenge of PAEON is to provide specialists in reproduc- tive medicine with a computerised model of the menstrual cycle under normal and various pathological conditions, which will allow them to get further in- sight in fertility dynamics. This model also enables the simulation of treatment protocols, which were used within in vitro fertilization. By the definition of virtual patients through biologically admissible parametrizations our approach allows not only the evaluation of a given treatment strategy in silico, but also the design and optimization of such protocols. Once a protocol is formalized in the virtual hospital, the success can be controlled by a treatment execution monitor, which works then as a clinical decision support system. All these tools will be combined in a virtual hospital environment, enabling the access to the PAEON services through the web.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 237
    Publication Date: 2023-01-06
    Description: An der internationalen Open-Access-Woche 2016 vom 24.-28. Oktober war der KOBV erstmalig mit einem Online „Publishing Event“ beteiligt. An fünf aufeinanderfolgenden Tagen erschien täglich eine Sonderausgabe des KOBV-Newsletters zu ausgewählten Open-Access-Themen. Die einzelnen Beiträge sind in dieser Sonderedition als Online-Reader zusammengestellt. Der aktuelle Diskussionsstand zum jeweiligen Thema wird von Expertinnen und Experten in kurzen Übersichtsartikeln vorgestellt und mit Praxistipps ergänzt. Zielgruppe sind vor allem Bibliothekare und Bibliothekarinnen, die sich einen schnellen Überblick zu Open Access verschaffen wollen.
    Language: German
    Type: other , doc-type:Other
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  • 238
    Publication Date: 2022-12-12
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 239
    Publication Date: 2022-12-12
    Description: Effective vectorization is becoming increasingly important for high performance and energy efficiency on processors with wide SIMD units. Compilers often require programmers to identify opportunities for vectorization, using directives to disprove data dependences. The OpenMP 4.x SIMD directives strive to provide portability. We investigate the ability of current compilers (GNU, Clang, and Intel) to generate SIMD code for microbenchmarks that cover common patterns in scientific codes and for two kernels from the VASP and the MOM5/ERGOM application. We explore coding strategies for improving SIMD performance across different compilers and platforms (Intel® Xeon® processor and Intel® Xeon Phi™ (co)processor). We compare OpenMP* 4.x SIMD vectorization with and without vector data types against SIMD intrinsics and C++ SIMD types. Our experiments show that in many cases portable performance can be achieved. All microbenchmarks are available as open source as a reference for programmers and compiler experts to enhance SIMD code generation.
    Language: English
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  • 240
    Publication Date: 2022-12-12
    Description: A classical technique to vectorize code that contains control flow is a control-flow to data-flow conversion. In that approach statements are augmented with masks that denote whether a given vector lane participates in the statement’s execution or idles. If the scheduling of work to vector lanes is performed statically, then some of the vector lanes will run idle in case of control flow divergences or varying work intensities across the loop iterations. With an increasing number of vector lanes, the likelihood of divergences or heavily unbalanced work assignments increases and static scheduling leads to a poor resource utilization. In this paper, we investigate different approaches to dynamic SIMD vector lane scheduling using the Mandelbrot set algorithm as a test case. To overcome the limitations of static scheduling, idle vector lanes are assigned work items dynamically, thereby minimizing per-lane idle cycles. Our evaluation on the Knights Corner and Knights Landing platform shows, that our approaches can lead to considerable performance gains over a static work assignment. By using the AVX-512 vector compress and expand instruction, we are able to further improve the scheduling.
    Language: English
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  • 241
    Publication Date: 2022-12-12
    Description: The effectiveness of ahead-of-time compiler optimization heavily depends on the amount of available information at compile time. Input-specific information that is only available at runtime cannot be used, although it often determines loop counts, branching predicates and paths, as well as memory-access patterns. It can also be crucial for generating efficient SIMD-vectorized code. This is especially relevant for the many-core architectures paving the way to exascale computing, which are more sensitive to code-optimization. We explore the design-space for using input-specific information at compile-time and present KART, a C++ library solution that allows developers to compile, link, and execute code (e.g., C, C++ , Fortran) at application runtime. Besides mere runtime compilation of performance-critical code, KART can be used to instantiate the same code multiple times using different inputs, compilers, and options. Other techniques like auto-tuning and code-generation can be integrated into a KART-enabled application instead of being scripted around it. We evaluate runtimes and compilation costs for different synthetic kernels, and show the effectiveness for two real-world applications, HEOM and a WSM6 proxy.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 242
    Publication Date: 2023-02-06
    Description: The project DeepGreen aims to realise better usage of green open access publication rights with regard to Alliance Licenses in Germany (https://www.nationallizenzen.de/open-access). Together with publishers who offer Alliance Licenses and authorized libraries, the project group intends to develop a prototype of a nearly fully automated workflow that covers the delivery of data from the publishers, including the article full texts, as well as the process of loading data into the institutional repositories of licensees. Further information about the project can be found within ZIB-Report 15-58, urn:nbn:de:0297-zib-56799. In order to become acquainted with publishers’ processes for exchanging documents and metadata, the project group developed a questionnaire for an online survey. The publishing of this questionnaire is intended to demonstrate relevant aspects of the issue (e. g. methods of data exchange, protocols and interfaces) and to foster reuse of valuable questionnaire elements. The XML-file can be reused as a template, the PDF-file reproduces the original survey layout.
    Keywords: Open Access
    Language: English
    Type: other , doc-type:Other
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  • 243
    Publication Date: 2023-02-06
    Description: SCIP is a solver for a wide variety of mathematical optimization problems. It is written in C and extendable due to its plug-in based design. However, dealing with all C specifics when extending SCIP can be detrimental to development and testing of new ideas. This paper attempts to provide a remedy by introducing PySCIPOpt, a Python interface to SCIP that enables users to write new SCIP code entirely in Python. We demonstrate how to intuitively model mixed-integer linear and quadratic optimization problems and moreover provide examples on how new Python plug-ins can be added to SCIP.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 244
    Publication Date: 2023-02-06
    Description: The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. While often a strong relationship between different Steiner tree problem variants can be observed, solution approaches employed so far have been prevalently problem-specific. In contrast, this paper introduces a general-purpose solver that can be used to solve both the classical Steiner tree problem and many of its variants without modification. This versatility is achieved by transforming various problem variants into a general form and solving them by using a state-of-the-art MIP-framework. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 245
    Publication Date: 2023-02-06
    Description: The concept of reduction has frequently distinguished itself as a pivotal ingredient of exact solving approaches for the Steiner tree problem in graphs. In this paper we broaden the focus and consider reduction techniques for three Steiner problem variants that have been extensively discussed in the literature and entail various practical applications: The prize-collecting Steiner tree problem, the rooted prize-collecting Steiner tree problem and the maximum-weight connected subgraph problem. By introducing and subsequently deploying numerous new reduction methods, we are able to drastically decrease the size of a large number of benchmark instances, already solving more than 90 percent of them to optimality. Furthermore, we demonstrate the impact of these techniques on exact solving, using the example of the state-of-the-art Steiner problem solver SCIP-Jack.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 246
    Publication Date: 2023-02-06
    Description: This paper presents a novel application of operations research techniques to the analysis of HIV Env gene sequences, aiming to identify key features that are possible vaccine targets. These targets are identified as being critical to the transmission of HIV by being present in early transmitted (founder) sequences and absent in later chronic sequences. Identifying the key features of Env involves two steps: first, calculating the covariance of amino acid combinations and positions to form a network of related and compensatory mutations; and second, developing an integer program to identify the smallest connected subgraph of the constructed covariance network that exhibits a set covering property. The integer program developed for this analysis, labelled the unrooted set covering connected subgraph problem (USCCSP), integrates a set covering problem and connectivity evaluation, the latter formulated as a network flow problem. The resulting integer program is very large and complex, requiring the use of Benders' decomposition to develop an efficient solution approach. The results will demonstrate the necessity of applying acceleration techniques to the Benders' decomposition solution approach and the effectiveness of these techniques and heuristic approaches for solving the USCCSP.
    Language: English
    Type: article , doc-type:article
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  • 247
    Publication Date: 2023-02-06
    Description: SCIP is a solver for a wide variety of mathematical optimization problems. It is written in C and extendable due to its plug-in based design. However, dealing with all C specifics when extending SCIP can be detrimental to development and testing of new ideas. This paper attempts to provide a remedy by introducing PySCIPOpt, a Python interface to SCIP that enables users to write new SCIP code entirely in Python. We demonstrate how to intuitively model mixed-integer linear and quadratic optimization problems and moreover provide examples on how new Python plug-ins can be added to SCIP.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 248
    Publication Date: 2023-02-06
    Description: Portfolio parallelization is an approach that runs several solver instances in parallel and terminates when one of them succeeds in solving the problem. Despite it's simplicity portfolio parallelization has been shown to perform well for modern mixed-integer programming (MIP) and boolean satisfiability problem (SAT) solvers. Domain propagation has also been shown to be a simple technique in modern MIP and SAT solvers that effectively finds additional domain reductions after a variables domain has been reduced. This paper investigates the impact of distributed domain propagation in modern MIP solvers that employ portfolio parallelization. Computational experiments were conducted for two implementations of this parallelization approach. While both share global variable bounds and solutions they communicate differently. In one implementation the communication is performed only at designated points in the solving process and in the other it is performed completely asynchronously. Computational experiments show a positive performance impact of communicating global variable bounds and provide valuable insights in communication strategies for parallel solvers.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 249
    Publication Date: 2023-02-06
    Description: In 2011, important priorities were set to realize green publications in the open access movement in Germany. With financial support from the German Research Foundation (DFG), libraries negotiated Alliance licenses with publishers that guarantee extensive open access rights. Authors of institutions, that have therewith access to licensed journals, can freely publish their articles immediately or after a short embargo period in a repository of their choice. However, authors hesitantly use these open access rights. Also libraries – as managers of institutional and subject based repositories and thus legitimated representatives for the authors – only rarely make use of these rights. The aim of DeepGreen is to make the majority of those publications available online. Together with publishers of the Alliance licenses, the project consortium wants to develop a nearly fully automated workflow that covers both the delivery of data, including the full texts, of the publishers, as well as the data transformation to the necessary import formats and the loading process into the repositories. An intermediate “publication router” will serve as a distribution platform. The DeepGreen metadata schema contains metadata properties describing a wide range of deliverable bibliographic metadata from the Alliance license publishers (most common standards are JATS and CrossRef XML) as well as its compliance with technical, quality and metadata standards of the repositories. The schema includes required metadata elements and optional properties providing additional information.The metadata schema is aligned to the OCLC repository best practices (“Best Practices for CONTENTdm and other OAI-PMH compliant repositories: creating sharable metadata”, URL: http://www.oclc.org/content/dam/support/wcdigitalcollectiongateway/MetadataBestPractices.pdf). The current version of the schema is subject to changes as the functional requirements and workflow practices are evolving during the project experiences and prototype production.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 250
    Publication Date: 2023-03-31
    Description: It is shown how piecewise differentiable functions \(F: R^n → R^m\) that are defined by evaluation programs can be approximated locally by a piecewise linear model based on a pair of sample points x̌ and x̂. We show that the discrepancy between function and model at any point x is of the bilinear order O(||x − x̌|| ||x − x̂||). This is a little surprising since x ∈ R^n may vary over the whole Euclidean space, and we utilize only two function samples F̌ = F(x̌) and F̂ = F(x̂), as well as the intermediates computed during their evaluation. As an application of the piecewise linearization procedure we devise a generalized Newton’s method based on successive piecewise linearization and prove for it sufficient conditions for convergence and convergence rates equaling those of semismooth Newton. We conclude with the derivation of formulas for the numerically stable implementation of the aforedeveloped piecewise linearization methods.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 251
    Publication Date: 2023-07-17
    Description: Circular RNAs (circRNAs) are a group of single-stranded RNAs in closed circular form. They are splicing-generated, widely expressed in various tissues and have functional implications in development and diseases. To facilitate genome-wide characterization of circRNAs using RNA-Seq data, we present a freely available software package named acfs. Acfs allows de novo, accurate and fast identification and abundance quantification of circRNAs from single- and paired-ended RNA-Seq data. On simulated datasets, acfs achieved the highest F1 accuracy and lowest false discovery rate among current state-of-the-art tools. On real-world datasets, acfs efficiently identified more bona fide circRNAs. Furthermore, we demonstrated the power of circRNA analysis on two leukemia datasets. We identified a set of circRNAs that are differentially expressed between AML and APL samples, which might shed light on the potential molecular classification of complex diseases using circRNA profiles. Moreover, chromosomal translocation, as manifested in numerous diseases, could produce not only fusion transcripts but also fusion circRNAs of clinical relevance. Featured with high accuracy, low FDR and the ability to identify fusion circRNAs, we believe that acfs is well suited for a wide spectrum of applications in characterizing the landscape of circRNAs from non-model organisms to cancer biology.
    Language: English
    Type: article , doc-type:article
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  • 252
    Publication Date: 2023-07-17
    Description: Regulatory authorities often receive poorly structured safety reports requiring considerable effort to investigate potential adverse events post hoc. Automated question-and-answer systems may help to improve the overall quality of safety information transmitted to pharmacovigilance agencies. This paper explores the use of the VACC-Tool (ViVI Automated Case Classification Tool) 2.0, a mobile application enabling physicians to classify clinical cases according to 14 pre-defined case definitions for neuroinflammatory adverse events (NIAE) and in full compliance with data standards issued by the Clinical Data Interchange Standards Consortium. METHODS: The validation of the VACC-Tool 2.0 (beta-version) was conducted in the context of a unique quality management program for children with suspected NIAE in collaboration with the Robert Koch Institute in Berlin, Germany. The VACC-Tool was used for instant case classification and for longitudinal follow-up throughout the course of hospitalization. Results were compared to International Classification of Diseases , Tenth Revision (ICD-10) codes assigned in the emergency department (ED). RESULTS: From 07/2013 to 10/2014, a total of 34,368 patients were seen in the ED, and 5243 patients were hospitalized; 243 of these were admitted for suspected NIAE (mean age: 8.5 years), thus participating in the quality management program. Using the VACC-Tool in the ED, 209 cases were classified successfully, 69 \% of which had been missed or miscoded in the ED reports. Longitudinal follow-up with the VACC-Tool identified additional NIAE. CONCLUSION: Mobile applications are taking data standards to the point of care, enabling clinicians to ascertain potential adverse events in the ED setting and during inpatient follow-up. Compliance with Clinical Data Interchange Standards Consortium (CDISC) data standards facilitates data interoperability according to regulatory requirements.
    Language: English
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  • 253
    Publication Date: 2023-07-17
    Description: BACKGROUND: Influenza-like illness (ILI) is a common reason for paediatric consultations. Viral causes predominate, but antibiotics are used frequently. With regard to influenza, pneumococcal coinfections are considered major contributors to morbidity/mortality. METHODS: In the context of a perennial quality management (QM) programme at the Charit{\'e} Departments of Paediatrics and Microbiology in collaboration with the Robert Koch Institute, children aged 0-18 years presenting with signs and symptoms of ILI were followed from the time of initial presentation until hospital discharge (Charit{\'e} Influenza-Like Disease = ChILD Cohort). An independent QM team performed highly standardized clinical assessments using a disease severity score based on World Health Organization criteria for uncomplicated and complicated/progressive disease. Nasopharyngeal and pharyngeal samples were collected for viral reverse transcription polymerase chain reaction and bacterial culture/sensitivity and MaldiTOF analyses. The term 'detection' was used to denote any evidence of viral or bacterial pathogens in the (naso)pharyngeal cavity. With the ChILD Cohort data collected, a standard operating procedure (SOP) was created as a model system to reduce the inappropriate use of antibiotics in children with ILI. Monte Carlo simulations were performed to assess cost-effectiveness. RESULTS: Among 2,569 ChILD Cohort patients enrolled from 12/2010 to 04/2013 (55\% male, mean age 3.2 years, range 0-18, 19\% {\ensuremath{〉}}5 years), 411 patients showed laboratory-confirmed influenza, with bacterial co-detection in 35\%. Influenza and pneumococcus were detected simultaneously in 12/2,569 patients, with disease severity clearly below average. Pneumococcal vaccination rates were close to 90\%. Nonetheless, every fifth patient was already on antibiotics upon presentation; new antibiotic prescriptions were issued in an additional 20\%. Simulation of the model SOP in the same dataset revealed that the proposed decision model could have reduced the inappropriate use of antibiotics significantly (P{\ensuremath{〈}}0.01) with an incremental cost-effectiveness ratio of -99.55?. CONCLUSIONS: Physicians should be made aware that in times of pneumococcal vaccination the prevalence and severity of influenza infections complicated by pneumococci may decline. Microbiological testing in combination with standardized disease severity assessments and review of vaccination records could be cost-effective, as well as promoting stringent use of antibiotics and a personalized approach to managing children with ILI.
    Language: English
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  • 254
    Publication Date: 2023-07-17
    Description: Feature selection technique is often applied in identifying cancer prognosis biomarkers. However, many feature selection methods are prone to over-fitting or poor biological interpretation when applied on biological high-dimensional data. Network-based feature selection and data integration approaches are proposed to identify more robust biomarkers. We conducted experiments to investigate the advantages of the two approaches using epithelial mesenchymal transition regulatory network, which is demonstrated as highly relevant to cancer prognosis. We obtained data from The Cancer Genome Atlas. Prognosis prediction was made using Support Vector Machine. Under our experimental settings, the results showed that network-based features gave significantly more accurate predictions than individual molecular features, and features selected from integrated data (RNA-Seq and micro-RNA data) gave significantly more accurate predictions than features selected from single source data (RNA-Seq data). Our study indicated that biological network-based feature transformation and data integration are two useful approaches to identify robust cancer biomarkers.
    Language: English
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  • 255
    Publication Date: 2023-07-17
    Description: In the framework of time series analysis with recurrence networks, we introduce a self-adaptive method that determines the elusive recurrence threshold and identifies metastable states in complex real-world time series. As initial step, we introduce a way to set the embedding parameters used to reconstruct the state space from the time series. We set them as the ones giving the maximum Shannon entropy of the diagonal line length distribution for the first simultaneous minima of recurrence rate and Shannon entropy. To identify metastable states, as well as the transitions between them, we use a soft partitioning algorithm for module finding which is specifically developed for the case in which a system shows metastability. We illustrate our method with a complex time series example. Finally, we show the robustness of our method for identifying metastable states. Our results suggest that our method is robust for identifying metastable states in complex time series, even when introducing considerable levels of noise and missing data points.
    Language: English
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  • 256
    Publication Date: 2023-07-17
    Description: One of the widely recognized features of biological systems is their modularity. The modules that comprise biological systems are said to be redeployed and combined across several conditions. In this work, we analyze to what extent are these modules indeed reusable as compared to randomized versions of a system. We develop a notion of modular decompositions of systems that allows for modules to overlap while maximizing the number of times a module is reused across several conditions. Different biological systems present modules whose reusability ranges from the condition specific to the constitutive, although their average reusability is not always higher than random equivalents of the system. These decompositions reveal a distinct distribution of module sizes in real biological systems. This distribution stems, in part, from the peculiar usage pattern of the elements of biological systems, and constitutes a new angle to study the evolution of modularity.
    Language: English
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  • 257
    Publication Date: 2023-07-17
    Description: Infectious and inflammatory diseases of the central nervous system are difficult to identify early. Case definitions for aseptic meningitis, encephalitis, myelitis, and acute disseminated encephalomyelitis (ADEM) are available, but rarely put to use. The VACC-Tool (Vienna Vaccine Safety Initiative Automated Case Classification-Tool) is a mobile application enabling immediate case ascertainment based on consensus criteria at the point-of-care. The VACC-Tool was validated in a quality management program in collaboration with the Robert-Koch-Institute. Results were compared to ICD-10 coding and retrospective analysis of electronic health records using the same case criteria. Of 68,921 patients attending the emergency room in 10/2010-06/2013, 11,575 were hospitalized, with 521 eligible patients (mean age: 7.6 years) entering the quality management program. Using the VACC-Tool at the point-of-care, 180/521 cases were classified successfully and 194/521 ruled out with certainty. Of the 180 confirmed cases, 116 had been missed by ICD-10 coding, 38 misclassified. By retrospective application of the same case criteria, 33 cases were missed. Encephalitis and ADEM cases were most likely missed or misclassified. The VACC-Tool enables physicians to ask the right questions at the right time, thereby classifying cases consistently and accurately, facilitating translational research. Future applications will alert physicians when additional diagnostic procedures are required.
    Language: English
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  • 258
    Publication Date: 2023-11-03
    Description: In multiscale modeling of heterogeneous catalytic processes, one crucial point is the solution of a Markovian master equation describing the stochastic reaction kinetics. Usually, this is too high-dimensional to be solved with standard numerical techniques and one has to rely on sampling approaches based on the kinetic Monte Carlo method. In this study we break the curse of dimensionality for the direct solution of the Markovian master equation by exploiting the Tensor Train Format for this purpose. The performance of the approach is demonstrated on a first principles based, reduced model for the CO oxidation on the RuO2(110) surface. We investigate the complexity for increasing system size and for various reaction conditions. The advantage over the stochastic simulation approach is illustrated by a problem with increased
    Language: English
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  • 259
    Publication Date: 2023-11-03
    Language: English
    Type: masterthesis , doc-type:masterThesis
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  • 260
    Publication Date: 2023-11-03
    Description: In several applications of network flows, additional constraints have to be considered. In this paper, we study flows, where the flow particles have an orientation. For example, cargo containers with doors only on one side and train coaches with 1st and 2nd class compartments have such an orientation. If the end position has a mandatory orientation, not every path from source to sink is feasible for routing or additional transposition maneuvers have to be made. As a result, a source-sink path may visit a certain vertex several times. We describe structural properties of optimal solutions, determine the computational complexity, and present an approach for approximating such flows.
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  • 261
    Publication Date: 2023-11-06
    Description: In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature. In this article, we contribute to this discussion: We first show that if we start with an ergodic diffusion processes whose invariant measure is unique then these properties are inherited by the effective dynamics. Then, we give equations for the effective dynamics, discuss whether the dominant timescales and reaction rates inferred from the effective dynamics are accurate approximations of such quantities for the full dynamics, and compare our findings to results from approaches like Zwanzig-Mori, averaging, or homogenization. Finally, by discussing the algorithmic realization of the effective dynamics, we demonstrate that recent algorithmic techniques like the ”equation-free” approach and the ”heterogeneous multiscale method” can be seen as special cases of our approach.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 262
    Publication Date: 2023-11-06
    Description: We propose numerical algorithms for solving optimal control and importance sampling problems based on simplified models. The algorithms combine model reduction techniques for multiscale diffusions and stochastic optimization tools, with the aim of reducing the original, possibly high-dimensional problem to a lower dimensional representation of the dynamics, in which only a few relevant degrees of freedom are controlled or biased. Specifically, we study situations in which either a reaction coordinate onto which the dynamics can be projected is known, or situations in which the dynamics shows strongly localized behavior in the small noise regime. No explicit assumptions about small parameters or scale separation have to be made. We illustrate the approach with simple, but paradigmatic numerical examples.
    Language: English
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  • 263
    Publication Date: 2023-11-06
    Language: English
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  • 264
    Publication Date: 2023-11-06
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
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  • 265
    Publication Date: 2023-12-11
    Description: This paper presents a numerical simulation of the tidal flow in Danang Bay (Vietnam) based on the non-hydrostatic shallow water equations. First, to test the simulation capability of the non-hydrostatic model, we have made a test simulation comparing it with the experiment by Beji and Battjes 1993. Simulation results for this case are compared with both the experimental data and calculations obtained from the traditional hydrostatic model. It is shown that the non-hydrostatic model is better than the hydrostatic model when the seabed topography variation is complex. The usefulness of the non-hydrostatic model is father shown by successfully simulating the tidal flow of Danang Bay.
    Language: English
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  • 266
    Publication Date: 2024-01-12
    Language: German
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  • 267
    Publication Date: 2024-01-12
    Description: In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations representing non-reversible biological processes, in particular molecular simulations. Here, the discrete time steps of the simulation are often very small compared to the time scale of interest, i.e., of the whole process. In this setting, the detection of a global cyclic behavior of the process becomes difficult because transitions between individual states may appear almost reversible on the small time scale of the simulation. We address this difficulty using a mixed-integer programming model that allows us to compute a cycle of clusters with maximum net flow, i.e., large forward and small backward probability. For a synthetic genetic regulatory network consisting of a ring-oscillator with three genes, we show that this approach can detect the most productive overall cycle, outperforming classical spectral analysis methods. Our method applies to general non-equilibrium steady state systems such as catalytic reactions, for which the objective value computes the effectiveness of the catalyst.
    Language: English
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  • 268
    Publication Date: 2024-01-12
    Description: We present a novel framework for fully automated and highly accurate determination of facial landmarks and dense correspondence, e.g. a topologically identical mesh of arbitrary resolution, across the entire surface of 3D face models. For robustness and reliability of the proposed approach, we are combining 2D landmark detectors and 3D statistical shape priors with a variational matching method. Instead of matching faces in the spatial domain only, we employ image registration to align the 2D parametrization of the facial surface to a planar template we call the Unified Facial Parameter Domain (ufpd). This allows us to simultaneously match salient photometric and geometric facial features using robust image similarity measures while reasonably constraining geometric distortion in regions with less significant features. We demonstrate the accuracy of the dense correspondence established by our framework on the BU3DFE database with 2500 facial surfaces and show, that our framework outperforms current state-of-the-art methods with respect to the fully automated location of facial landmarks.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
    Format: application/pdf
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  • 269
    Publication Date: 2024-01-12
    Description: The SCIP Optimization Suite is a software toolbox for generating and solving various classes of mathematical optimization problems. Its major components are the modeling language ZIMPL, the linear programming solver SoPlex, the constraint integer programming framework and mixed-integer linear and nonlinear programming solver SCIP, the UG framework for parallelization of branch-and-bound-based solvers, and the generic branch-cut-and-price solver GCG. It has been used in many applications from both academia and industry and is one of the leading non-commercial solvers. This paper highlights the new features of version 3.2 of the SCIP Optimization Suite. Version 3.2 was released in July 2015. This release comes with new presolving steps, primal heuristics, and branching rules within SCIP. In addition, version 3.2 includes a reoptimization feature and improved handling of quadratic constraints and special ordered sets. SoPlex can now solve LPs exactly over the rational number and performance improvements have been achieved by exploiting sparsity in more situations. UG has been tested successfully on 80,000 cores. A major new feature of UG is the functionality to parallelize a customized SCIP solver. GCG has been enhanced with a new separator, new primal heuristics, and improved column management. Finally, new and improved extensions of SCIP are presented, namely solvers for multi-criteria optimization, Steiner tree problems, and mixed-integer semidefinite programs.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 270
    Publication Date: 2024-01-12
    Description: The analysis of infeasible subproblems plays an import role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. There are two fundamentally different concepts to generate valid global constraints from infeasible subproblems. The first is to analyze the sequence of implications obtained by domain propagation that led to infeasibility. The result of the analysis is one or more sets of contradicting variable bounds from which so-called conflict constraints can be generated. This concept has its origin in solving satisfiability problems and is similarly used in constraint programming. The second concept is to analyze infeasible linear programming (LP) relaxations. The dual LP solution provides a set of multipliers that can be used to generate a single new globally valid linear constraint. The main contribution of this short paper is an empirical evaluation of two ways to combine both approaches. Experiments are carried out on general MIP instances from standard public test sets such as Miplib2010; the presented algorithms have been implemented within the non-commercial MIP solver SCIP. Moreover, we present a pool-based approach to manage conflicts which addresses the way a MIP solver traverses the search tree better than aging strategies known from SAT solving.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
    Format: application/pdf
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  • 271
    Publication Date: 2024-02-12
    Description: Periodic timetabling is an important strategic planning problem in public transport. The task is to determine periodic arrival and departure times of the lines in a given network, minimizing the travel time of the passengers. We extend the modulo network simplex method, a well-established heuristic for the periodic timetabling problem, by integrating a passenger (re)routing step into the pivot operations. Computations on real-world networks show that we can indeed find timetables with much shorter total travel time, when we take the passengers' travel paths into consideration.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 272
    Publication Date: 2024-02-12
    Description: The optimal design of wireless networks has been widely studied in the literature and many optimization models have been proposed over the years. However, most models directly include the signal-to-interference ratios representing service coverage conditions. This leads to mixed-integer linear programs with constraint matrices containing tiny coefficients that vary widely in their order of magnitude. These formulations are known to be challenging even for state-of-the-art solvers: the standard numerical precision supported by these solvers is usually not sufficient to reliably guarantee feasible solutions. Service coverage errors are thus commonly present. Though these numerical issues are known and become evident even for small-sized instances, just a very limited number of papers has tried to tackle them, by mainly investigating alternative non-compact formulations in which the sources of numerical instabilities are eliminated. In this work, we explore a new approach by investigating how recent advances in exact solution algorithms for linear and mixed-integer programs over the rational numbers can be applied to analyze and tackle the numerical difficulties arising in wireless network design models.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 273
    Title: OPR3 - Operations Research Peripatetic Postgraduate Program Conference at the Johannes Kepler University in Linz, Austria /; 236/2
    Year of publication: 2016
    Pages: [208 S.]
    Type of Medium: Book
    Language: German
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  • 274
    Book
    Book
    Title: Regular Volume; 238
    Year of publication: 2016
    Pages: 657 S.
    Type of Medium: Book
    Language: English
    Library Location Call Number Volume/Issue/Year Availability
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  • 275
    Book
    Book
    Basel :Springer International Publishinbg,
    Title: Spinal Imaging and Image Analysis /; 18
    Author: Shuo Li
    Edition: Softcover reprint of the original 1st ed. 2015
    Publisher: Basel :Springer International Publishinbg,
    Year of publication: 2016
    Pages: 508 S.
    Series Statement: Lecture notes in computational vision and biomechanics 18
    Type of Medium: Book
    Language: German
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  • 276
    Title: ¬Das¬ Paper-Protokoll : eine systematische Schreibanleitung für biomedizinische Originalartikel
    Author: Lang, Dr. Stefan
    Publisher: Hamburg :tredition,
    Year of publication: 2016
    Pages: X, 137 Seiten
    ISBN: 978-3-7345-4168-1
    Type of Medium: Book
    Language: German
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  • 277
    Book
    Book
    Birmingham :Packt Publishing,
    Title: OpenStack administration with Ansible 2 /
    Author: Bentley, Walter
    Edition: Second edition
    Publisher: Birmingham :Packt Publishing,
    Year of publication: 2016
    ISBN: 978-1-78712-013-6
    Type of Medium: Book
    Language: English
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  • 278
    Title: Optimization in the real world : toward solving real-world optimization problems; 13
    Contributer: Fujisawa, Katsuki , Shinano, Yuji , Waki, Hayato
    Publisher: Tokyo [u. a.] :Springer,
    Year of publication: 2016
    Pages: XII, 194 S.
    Series Statement: Mathematics for industry 13
    ISBN: 978-4-431-55419-6
    Type of Medium: Book
    Language: English
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  • 279
    Book
    Book
    Title: Policy analytics /; 236/1
    Year of publication: 2016
    Pages: 289 S.
    Type of Medium: Book
    Language: English
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  • 280
    Title: AngularJS, JavaScript, and jQuery all in one in 24 hours /
    Author: Dayley, Brad
    Contributer: Dayley, Brendan
    Publisher: Sams Publishing (Verlag),
    Year of publication: 2016
    Pages: 816 S. : , illustrations
    Series Statement: Sams teach yourself
    Type of Medium: Book
    Language: English
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  • 281
    Book
    Book
    Oxford :Oxford University Press,
    Title: Knowledge through imagination /
    Contributer: Kind, Amy
    Publisher: Oxford :Oxford University Press,
    Year of publication: 2016
    Pages: 272 S.
    ISBN: 978-0-19-871680-8
    Type of Medium: Book
    Language: English
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  • 282
    Book
    Book
    De Gruyter,
    Title: Inside Finite Elements /
    Author: Weiser, Martin
    Publisher: De Gruyter,
    Year of publication: 2016
    Pages: XI, 146 Seiten
    Series Statement: Graduate
    ISBN: 978-3-11-037317-2
    Type of Medium: Book
    Language: English
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  • 283
    Title: Web Fatale : wie Sie Webseiten gestalten, denen niemand widerstehen kann
    Author: Ippen, Johannes
    Edition: 1. Auflage, neue Ausgabe
    Year of publication: 2016
    Pages: 330 Seiten ; , 24 cm x 19 cm
    ISBN: 978-3-8362-3898-4 , 3-8362-3898-5
    Type of Medium: Book
    Language: German
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  • 284
    Title: ¬Das¬ Website Kompendium : Programmierung und Design
    Author: Wenz, Christian
    Contributer: Maurice, Florence , Hauser, Tobias
    Edition: [5. Auflage]
    Year of publication: 2016
    Pages: 815 Seiten : , Illustrationen, Diagramme
    ISBN: 978-3-95982-029-5 , 3-95982-029-1
    Type of Medium: Book
    Language: German
    Former Title: :Wenz, Christian: Das Website-Handbuch
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  • 285
    Title: Policy Analytics /; 236/1
    Author: Daniell, Katherine A.
    Contributer: Morton, Alec , Insua, David Ríos
    Year of publication: 2016
    Pages: 289 S.
    Series Statement: Annals of operations research 236/1
    Type of Medium: Book
    Language: English
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  • 286
    Title: Risk management and operations research /; 237
    Author: Wu, Desheng
    Contributer: Olson, David L. , Birge, John
    Year of publication: 2016
    Pages: 300 S.
    Series Statement: Annals of operations research 237
    Type of Medium: Book
    Language: German
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  • 287
    Title: ¬The¬ practice and theory of automated timetabling (PATAT 2012) /; 239/1
    Author: Özcan, Ender
    Contributer: Burke, Edmund K. , McCollum, Barry , Kjenstad, Dag , Riise, Atle
    Year of publication: 2016
    Pages: 354 S.
    Series Statement: Annals of operations research 239/1
    Type of Medium: Book
    Language: German
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  • 288
    Book
    Book
    Title: Regular volume; 238
    Year of publication: 2016
    Pages: 657 S.
    Series Statement: Annals of operations research 238
    Type of Medium: Book
    Language: German
    Library Location Call Number Volume/Issue/Year Availability
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  • 289
    Title: Analytical and stochastic modelling techniques /; 239/2
    Author: Al-Begain, Khalid
    Contributer: Fiems, Dieter , Vincent, Jean-Marc
    Year of publication: 2016
    Pages: 368 S.
    Series Statement: Annals of operations research 239/2
    Type of Medium: Book
    Language: German
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  • 290
    Title: Digitale Rechnungen und E-Invoicing : Unter Berücksichtigung der aktuellen GoBD und des ZUGFeRD-Verfahrens
    Author: Lamprecht, Dirk J.
    Contributer: Glück, Oliver
    Edition: neue Ausgabe
    Publisher: Hamburg :Dashöfer,
    Year of publication: 2016
    Pages: 48 Seiten
    ISBN: 978-3-89236-110-7
    Type of Medium: Book
    Language: German
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  • 291
    Book
    Book
    Chichester, West Sussex, United Kingdom :Wiley,
    Title: Electronic structure calculations on graphics processing units /
    Contributer: Walker, Ross C.
    Publisher: Chichester, West Sussex, United Kingdom :Wiley,
    Year of publication: 2016
    Pages: xxiii, 334 Seiten : , Illustrationen, Diagramme
    ISBN: 978-1-118-66178-9 , 978-1-118-67069-9
    Type of Medium: Book
    Language: English
    URL: 93
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  • 292
    Title: Modern statistical methods for HCI /
    Contributer: Robertson, Judy , Kaptein, Maurits
    Year of publication: 2016
    Pages: xx, 348 Seiten : , Illustrationen, Diagramme
    Series Statement: Human-computer interaction series
    ISBN: 978-3-319-26631-2
    Type of Medium: Book
    Language: English
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  • 293
    Title: Emerging production optimization issues in supply chain systems /; 240/2
    Author: Choi, Tsan-Ming
    Contributer: Wang, Mingzheng , Yue, Xiaohang
    Year of publication: 2016
    Pages: [378 S.]
    Series Statement: Annals of operations research 240/2
    Type of Medium: Book
    Language: German
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  • 294
    Title: Optimization under uncertainty: costs, risks and revenues Cyrus Derman memorial volume I /; 241/1-2
    Author: Katehakis, Michael N.
    Contributer: Ross, Sheldon M. , Yang, Jian
    Year of publication: 2016
    Pages: 573 S.
    Series Statement: Annals of operations research 241/1-2
    Type of Medium: Book
    Language: German
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  • 295
    Title: Multivariate Analysemethoden : eine anwendungsorientierte Einführung
    Contributer: Backhaus, Klaus , Erichson, Bernd , Plinke, Wulff , Weiber, Rolf
    Edition: 14., überarbeitete und aktualisierte Auflage
    Publisher: Berlin :Springer Gabler,
    Year of publication: 2016
    Pages: XII, 647 Seiten : , Illustrationen, Diagramme
    ISBN: 978-3-662-46075-7 , 978-3-662-46076-4
    Type of Medium: Book
    Language: German
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  • 296
    Title: Operations Research Proceedings 2014 /
    Contributer: Lübbecke, Marco , Gesellschaft für Operations-Research
    Publisher: Springer,
    Year of publication: 2016
    Pages: XIV, 659 S. : , Illustrationen, Diagramme
    ISBN: 978-3-319-28697-6 , 978-3-319-28695-2
    Type of Medium: Book
    Language: English
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  • 297
    Title: Location Analysis /; 246/1-2
    Contributer: Santos-Penate, Dolores R.
    Year of publication: 2016
    Pages: 369 S.
    Series Statement: Annals of operations research 246/1-2
    Type of Medium: Book
    Language: English
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  • 298
    Title: Weapons of math destruction : how big data increases inequality and threatens democracy
    Author: O'Neil, Cathy
    Edition: Allen Lane, Penguin Random House
    Publisher: London,
    Year of publication: 2016
    Pages: X, 259 Seiten
    ISBN: 978-0-241-29681-3
    Type of Medium: Book
    Language: English
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  • 299
    Title: Retrial Queues and Related Models /; 247/1
    Contributer: Gómez-Corral, Antonio
    Year of publication: 2016
    Pages: 389 S.
    Series Statement: Annals of operations research 247/1
    Type of Medium: Book
    Language: English
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  • 300
    Title: Mathematical Berlin : science, sights and stories
    Author: Grötschel, Iris
    Contributer: Grötschel, Martin
    Edition: First edition
    Year of publication: 2016
    Pages: 159 Seiten : , Illustrationen, Karten
    ISBN: 978-3-95723-080-5
    Type of Medium: Book
    Language: English
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