DevLan/vispubs huggingface dataset:
Advection-Based Sparse Data Management for Visualizing Unsteady Flow
Authors: Hanqi Guo 0001, Jiang Zhang 0002, Richen Liu, Lu Liu 0017, Xiaoru Yuan, Jian Huang 0007, Xiangfei Meng, Jingshan Pan
Published at SciVis, 2014

When computing integral curves and integral surfaces for large-scale unsteady flow fields, a major bottleneck is the widening gap between data access demands and the available bandwidth (both I/O and in-memory). In this work, we explore a novel advection-based scheme to manage flow field data for both efficiency and scalability. The key is to first partition flow field into blocklets (e.g. cells or very fine-grained blocks of cells), and then (pre)fetch and manage blocklets on-demand using a parallel key-value store. The benefits are (1) greatly increasing the scale of local-range analysis (e.g. source-destination queries, streak surface generation) that can fit within any given limit of hardware resources; (2) improving memory and I/O bandwidth-efficiencies as well as the scalability of naive task-parallel particle advection. We demonstrate our method using a prototype system that works on workstation and also in supercomputing environments. Results show significantly reduced I/O overhead compared to accessing raw flow data, and also high scalability on a supercomputer for a variety of applications.
Attractive Flicker: Guiding Attention in Dynamic Narrative Visualizations
Authors: Manuela Waldner, Mathieu Le Muzic, Matthias Bernhard, Werner Purgathofer, Ivan Viola
Published at SciVis, 2014

Focus-context techniques provide visual guidance in visualizations by giving strong visual prominence to elements of interest while the context is suppressed. However, finding a visual feature to enhance for the focus to pop out from its context in a large dynamic scene, while leading to minimal visual deformation and subjective disturbance, is challenging. This paper proposes Attractive Flicker, a novel technique for visual guidance in dynamic narrative visualizations. We first show that flicker is a strong visual attractor in the entire visual field, without distorting, suppressing, or adding any scene elements. The novel aspect of our Attractive Flicker technique is that it consists of two signal stages: The first “orientation stage” is a short but intensive flicker stimulus to attract the attention to elements of interest. Subsequently, the intensive flicker is reduced to a minimally disturbing luminance oscillation (“engagement stage”) as visual support to keep track of the focus elements. To find a good trade-off between attraction effectiveness and subjective annoyance caused by flicker, we conducted two perceptual studies to find suitable signal parameters. We showcase Attractive Flicker with the parameters obtained from the perceptual statistics in a study of molecular interactions. With Attractive Flicker, users were able to easily follow the narrative of the visualization on a large display, while the flickering of focus elements was not disturbing when observing the context.
Boundary Aware Reconstruction of Scalar Fields
Authors: Stefan Lindholm, Daniel Jönsson, Charles D. Hansen, Anders Ynnerman
Published at SciVis, 2014

In visualization, the combined role of data reconstruction and its classification plays a crucial role. In this paper we propose a novel approach that improves classification of different materials and their boundaries by combining information from the classifiers at the reconstruction stage. Our approach estimates the targeted materials' local support before performing multiple material-specific reconstructions that prevent much of the misclassification traditionally associated with transitional regions and transfer function (TF) design. With respect to previously published methods our approach offers a number of improvements and advantages. For one, it does not rely on TFs acting on derivative expressions, therefore it is less sensitive to noisy data and the classification of a single material does not depend on specialized TF widgets or specifying regions in a multidimensional TF. Additionally, improved classification is attained without increasing TF dimensionality, which promotes scalability to multivariate data. These aspects are also key in maintaining low interaction complexity. The results are simple-to-achieve visualizations that better comply with the user's understanding of discrete features within the studied object.
Characterizing Molecular Interactions in Chemical Systems
Authors: David Günther, Roberto Álvarez Boto, Juila Contreras-Garcia, Jean-Philip Piquemal, Julien Tierny
Published at SciVis, 2014

Interactions between atoms have a major influence on the chemical properties of molecular systems. While covalent interactions impose the structural integrity of molecules, noncovalent interactions govern more subtle phenomena such as protein folding, bonding or self assembly. The understanding of these types of interactions is necessary for the interpretation of many biological processes and chemical design tasks. While traditionally the electron density is analyzed to interpret the quantum chemistry of a molecular system, noncovalent interactions are characterized by low electron densities and only slight variations of them - challenging their extraction and characterization. Recently, the signed electron density and the reduced gradient, two scalar fields derived from the electron density, have drawn much attention in quantum chemistry since they enable a qualitative visualization of these interactions even in complex molecular systems and experimental measurements. In this work, we present the first combinatorial algorithm for the automated extraction and characterization of covalent and noncovalent interactions in molecular systems. The proposed algorithm is based on a joint topological analysis of the signed electron density and the reduced gradient. Combining the connectivity information of the critical points of these two scalar fields enables to visualize, enumerate, classify and investigate molecular interactions in a robust manner. Experiments on a variety of molecular systems, from simple dimers to proteins or DNA, demonstrate the ability of our technique to robustly extract these interactions and to reveal their structural relations to the atoms and bonds forming the molecules. For simple systems, our analysis corroborates the observations made by the chemists while it provides new visual and quantitative insights on chemical interactions for larger molecular systems.
City Forensics: Using Visual Elements to Predict Non-Visual City Attributes
Authors: Sean M. Arietta, Alexei A. Efros, Ravi Ramamoorthi, Maneesh Agrawala
Published at SciVis, 2014

We present a method for automatically identifying and validating predictive relationships between the visual appearance of a city and its non-visual attributes (e.g. crime statistics, housing prices, population density etc.). Given a set of street-level images and (location, city-attribute-value) pairs of measurements, we first identify visual elements in the images that are discriminative of the attribute. We then train a predictor by learning a set of weights over these elements using non-linear Support Vector Regression. To perform these operations efficiently, we implement a scalable distributed processing framework that speeds up the main computational bottleneck (extracting visual elements) by an order of magnitude. This speedup allows us to investigate a variety of city attributes across 6 different American cities. We find that indeed there is a predictive relationship between visual elements and a number of city attributes including violent crime rates, theft rates, housing prices, population density, tree presence, graffiti presence, and the perception of danger. We also test human performance for predicting theft based on street-level images and show that our predictor outperforms this baseline with 33% higher accuracy on average. Finally, we present three prototype applications that use our system to (1) define the visual boundary of city neighborhoods, (2) generate walking directions that avoid or seek out exposure to city attributes, and (3) validate user-specified visual elements for prediction.
Combined Visualization of Wall Thickness and Wall Shear Stress for the Evaluation of Aneurysms
Authors: Sylvia Saalfeld, Kai Lawonn, Thomas Hoffmann 0002, Martin Skalej, Bernhard Preim
Published at SciVis, 2014

For an individual rupture risk assessment of aneurysms, the aneurysm's wall morphology and hemodynamics provide valuable information. Hemodynamic information is usually extracted via computational fluid dynamic (CFD) simulation on a previously extracted 3D aneurysm surface mesh or directly measured with 4D phase-contrast magnetic resonance imaging. In contrast, a noninvasive imaging technique that depicts the aneurysm wall in vivo is still not available. Our approach comprises an experiment, where intravascular ultrasound (IVUS) is employed to probe a dissected saccular aneurysm phantom, which we modeled from a porcine kidney artery. Then, we extracted a 3D surface mesh to gain the vessel wall thickness and hemodynamic information from a CFD simulation. Building on this, we developed a framework that depicts the inner and outer aneurysm wall with dedicated information about local thickness via distance ribbons. For both walls, a shading is adapted such that the inner wall as well as its distance to the outer wall is always perceivable. The exploration of the wall is further improved by combining it with hemodynamic information from the CFD simulation. Hence, the visual analysis comprises a brushing and linking concept for individual highlighting of pathologic areas. Also, a surface clustering is integrated to provide an automatic division of different aneurysm parts combined with a risk score depending on wall thickness and hemodynamic information. In general, our approach can be employed for vessel visualization purposes where an inner and outer wall has to be adequately represented.
Conforming Morse-Smale Complexes
Authors: Attila Gyulassy, David Günther, Joshua A. Levine, Julien Tierny, Valerio Pascucci
Published at SciVis, 2014

Morse-Smale (MS) complexes have been gaining popularity as a tool for feature-driven data analysis and visualization. However, the quality of their geometric embedding and the sole dependence on the input scalar field data can limit their applicability when expressing application-dependent features. In this paper we introduce a new combinatorial technique to compute an MS complex that conforms to both an input scalar field and an additional, prior segmentation of the domain. The segmentation constrains the MS complex computation guaranteeing that boundaries in the segmentation are captured as separatrices of the MS complex. We demonstrate the utility and versatility of our approach with two applications. First, we use streamline integration to determine numerically computed basins/mountains and use the resulting segmentation as an input to our algorithm. This strategy enables the incorporation of prior flow path knowledge, effectively resulting in an MS complex that is as geometrically accurate as the employed numerical integration. Our second use case is motivated by the observation that often the data itself does not explicitly contain features known to be present by a domain expert. We introduce edit operations for MS complexes so that a user can directly modify their features while maintaining all the advantages of a robust topology-based representation.
Curve Boxplot: Generalization of Boxplot for Ensembles of Curves
Authors: Mahsa Mirzargar, Ross T. Whitaker, Robert M. Kirby
Published at SciVis, 2014

In simulation science, computational scientists often study the behavior of their simulations by repeated solutions with variations in parameters and/or boundary values or initial conditions. Through such simulation ensembles, one can try to understand or quantify the variability or uncertainty in a solution as a function of the various inputs or model assumptions. In response to a growing interest in simulation ensembles, the visualization community has developed a suite of methods for allowing users to observe and understand the properties of these ensembles in an efficient and effective manner. An important aspect of visualizing simulations is the analysis of derived features, often represented as points, surfaces, or curves. In this paper, we present a novel, nonparametric method for summarizing ensembles of 2D and 3D curves. We propose an extension of a method from descriptive statistics, data depth, to curves. We also demonstrate a set of rendering and visualization strategies for showing rank statistics of an ensemble of curves, which is a generalization of traditional whisker plots or boxplots to multidimensional curves. Results are presented for applications in neuroimaging, hurricane forecasting and fluid dynamics.
Decomposition and Simplification of Multivariate Data using Pareto Sets
Authors: Lars Huettenberger, Christian Heine 0002, Christoph Garth
Published at SciVis, 2014

Topological and structural analysis of multivariate data is aimed at improving the understanding and usage of such data through identification of intrinsic features and structural relationships among multiple variables. We present two novel methods for simplifying so-called Pareto sets that describe such structural relationships. Such simplification is a precondition for meaningful visualization of structurally rich or noisy data. As a framework for simplification operations, we introduce a decomposition of the data domain into regions of equivalent structural behavior and the reachability graph that describes global connectivity of Pareto extrema. Simplification is then performed as a sequence of edge collapses in this graph; to determine a suitable sequence of such operations, we describe and utilize a comparison measure that reflects the changes to the data that each operation represents. We demonstrate and evaluate our methods on synthetic and real-world examples.
Design and Evaluation of Interactive Proofreading Tools for Connectomics
Authors: Daniel Haehn, Seymour Knowles-Barley, Mike Roberts 0001, Johanna Beyer, Narayanan Kasthuri, Jeff Lichtman, Hanspeter Pfister
Published at SciVis, 2014

Proofreading refers to the manual correction of automatic segmentations of image data. In connectomics, electron microscopy data is acquired at nanometer-scale resolution and results in very large image volumes of brain tissue that require fully automatic segmentation algorithms to identify cell boundaries. However, these algorithms require hundreds of corrections per cubic micron of tissue. Even though this task is time consuming, it is fairly easy for humans to perform corrections through splitting, merging, and adjusting segments during proofreading. In this paper we present the design and implementation of Mojo, a fully-featured single-user desktop application for proofreading, and Dojo, a multi-user web-based application for collaborative proofreading. We evaluate the accuracy and speed of Mojo, Dojo, and Raveler, a proofreading tool from Janelia Farm, through a quantitative user study. We designed a between-subjects experiment and asked non-experts to proofread neurons in a publicly available connectomics dataset. Our results show a significant improvement of corrections using web-based Dojo, when given the same amount of time. In addition, all participants using Dojo reported better usability. We discuss our findings and provide an analysis of requirements for designing visual proofreading software.
Escape Maps
Authors: Gustavo Mello Machado, Filip Sadlo, Thomas Müller 0005, Thomas Ertl
Published at SciVis, 2014

We present a technique to visualize the streamline-based mapping between the boundary of a simply-connected subregion of arbitrary 3D vector fields. While the streamlines are seeded on one part of the boundary, the remaining part serves as escape border. Hence, the seeding part of the boundary represents a map of streamline behavior, indicating if streamlines reach the escape border or not. Since the resulting maps typically exhibit a very fine and complex structure and are thus not amenable to direct sampling, our approach instead aims at topologically consistent extraction of their boundary. We show that isocline surfaces of the projected vector field provide a robust basis for stream-surface-based extraction of these boundaries. The utility of our technique is demonstrated in the context of transport processes using vector field data from different domains.
Fast and Memory-Efficienty Topological Denoising of 2D and 3D Scalar Fields
Authors: David Günther, Alec Jacobson, Jan Reininghaus, Hans-Peter Seidel, Olga Sorkine-Hornung, Tino Weinkauf
Published at SciVis, 2014

Data acquisition, numerical inaccuracies, and sampling often introduce noise in measurements and simulations. Removing this noise is often necessary for efficient analysis and visualization of this data, yet many denoising techniques change the minima and maxima of a scalar field. For example, the extrema can appear or disappear, spatially move, and change their value. This can lead to wrong interpretations of the data, e.g., when the maximum temperature over an area is falsely reported being a few degrees cooler because the denoising method is unaware of these features. Recently, a topological denoising technique based on a global energy optimization was proposed, which allows the topology-controlled denoising of 2D scalar fields. While this method preserves the minima and maxima, it is constrained by the size of the data. We extend this work to large 2D data and medium-sized 3D data by introducing a novel domain decomposition approach. It allows processing small patches of the domain independently while still avoiding the introduction of new critical points. Furthermore, we propose an iterative refinement of the solution, which decreases the optimization energy compared to the previous approach and therefore gives smoother results that are closer to the input. We illustrate our technique on synthetic and real-world 2D and 3D data sets that highlight potential applications.
Fixed-Rate Compressed Floating-Point Arrays
Authors: Peter Lindstrom 0001
Published at SciVis, 2014

Current compression schemes for floating-point data commonly take fixed-precision values and compress them to a variable-length bit stream, complicating memory management and random access. We present a fixed-rate, near-lossless compression scheme that maps small blocks of 4&lt;sup&gt;d&lt;/sup&gt; values in d dimensions to a fixed, user-specified number of bits per block, thereby allowing read and write random access to compressed floating-point data at block granularity. Our approach is inspired by fixed-rate texture compression methods widely adopted in graphics hardware, but has been tailored to the high dynamic range and precision demands of scientific applications. Our compressor is based on a new, lifted, orthogonal block transform and embedded coding, allowing each per-block bit stream to be truncated at any point if desired, thus facilitating bit rate selection using a single compression scheme. To avoid compression or decompression upon every data access, we employ a software write-back cache of uncompressed blocks. Our compressor has been designed with computational simplicity and speed in mind to allow for the possibility of a hardware implementation, and uses only a small number of fixed-point arithmetic operations per compressed value. We demonstrate the viability and benefits of lossy compression in several applications, including visualization, quantitative data analysis, and numerical simulation.
FLDA: Latent Dirichlet Allocation Based Unsteady Flow Analysis
Authors: Fan Hong, Chufan Lai, Hanqi Guo 0001, Enya Shen, Xiaoru Yuan, Sikun Li
Published at SciVis, 2014

In this paper, we present a novel feature extraction approach called FLDA for unsteady flow fields based on Latent Dirichlet allocation (LDA) model. Analogous to topic modeling in text analysis, in our approach, pathlines and features in a given flow field are defined as documents and words respectively. Flow topics are then extracted based on Latent Dirichlet allocation. Different from other feature extraction methods, our approach clusters pathlines with probabilistic assignment, and aggregates features to meaningful topics at the same time. We build a prototype system to support exploration of unsteady flow field with our proposed LDA-based method. Interactive techniques are also developed to explore the extracted topics and to gain insight from the data. We conduct case studies to demonstrate the effectiveness of our proposed approach.
Interactive Progressive Visualization with Space-Time Error Control
Authors: Steffen Frey, Filip Sadlo, Kwan-Liu Ma, Thomas Ertl
Published at SciVis, 2014

We present a novel scheme for progressive rendering in interactive visualization. Static settings with respect to a certain image quality or frame rate are inherently incapable of delivering both high frame rates for rapid changes and high image quality for detailed investigation. Our novel technique flexibly adapts by steering the visualization process in three major degrees of freedom: when to terminate the refinement of a frame in the background and start a new one, when to display a frame currently computed, and how much resources to consume. We base these decisions on the correlation of the errors due to insufficient sampling and response delay, which we estimate separately using fast yet expressive heuristics. To automate the configuration of the steering behavior, we employ offline video quality analysis. We provide an efficient implementation of our scheme for the application of volume raycasting, featuring integrated GPU-accelerated image reconstruction and error estimation. Our implementation performs an integral handling of the changes due to camera transforms, transfer function adaptations, as well as the progression of the data to in time. Finally, the overall technique is evaluated with an expert study.
Ligand Excluded Surface: A New Type of Molecular Surface
Authors: Norbert Lindow, Daniel Baum, Hans-Christian Hege
Published at SciVis, 2014

The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes - including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules.