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Tensor Field Visualization,
Topological Data Analysis
Vials: Visualizing Alternative Splicing of Genes|
H. Strobelt, B. Alsallakh, J. Botros, B. Peterson, M. Borowsky, H. Pfister,, A. Lex. In IEEE Transactions on Visualization and Computer Graphics (InfoVis '15), Vol. 22, No. 1, pp. 399-408. 2015.
Alternative splicing is a process by which the same DNA sequence is used to assemble different proteins, called protein isoforms. Alternative splicing works by selectively omitting some of the coding regions (exons) typically associated with a gene. Detection of alternative splicing is difficult and uses a combination of advanced data acquisition methods and statistical inference. Knowledge about the abundance of isoforms is important for understanding both normal processes and diseases and to eventually improve treatment through targeted therapies. The data, however, is complex and current visualizations for isoforms are neither perceptually efficient nor scalable. To remedy this, we developed Vials, a novel visual analysis tool that enables analysts to explore the various datasets that scientists use to make judgments about isoforms: the abundance of reads associated with the coding regions of the gene, evidence for junctions, i.e., edges connecting the coding regions, and predictions of isoform frequencies. Vials is scalable as it allows for the simultaneous analysis of many samples in multiple groups. Our tool thus enables experts to (a) identify patterns of isoform abundance in groups of samples and (b) evaluate the quality of the data. We demonstrate the value of our tool in case studies using publicly available datasets.
OceanPaths: Visualizing Multivariate Oceanography Data|
C. Nobre, A. Lex. In Eurographics Conference on Visualization (EuroVis) - Short Papers, Edited by E. Bertini, J. Kennedy, E. Puppo, The Eurographics Association, 2015.
Geographical datasets are ubiquitous in oceanography. While map-based visualizations are useful for many different domains, they can suffer from cluttering and overplotting issues when used for multivariate data sets. As a result, spatial data exploration in oceanography has often been restricted to multiple maps showing various depths or time intervals. This lack of interactive exploration often hinders efforts to expose correlations between properties of oceanographic features, specifically currents. OceanPaths provides powerful interaction and exploration methods for spatial, multivariate oceanography datasets to remedy these situations. Fundamentally, our method allows users to define pathways, typically following currents, along which the variation of the high-dimensional data can be plotted efficiently. We present a case study conducted by domain experts to underscore the usefulness of OceanPaths in uncovering trends and correlations in oceanographic data sets.
Approximating the Generalized Voronoi Diagram of Closely Spaced Objects|
J. Edwards, E. Daniel, V. Pascucci, C. Bajaj. In Computer Graphics Forum, Vol. 34, No. 2, Wiley-Blackwell, pp. 299-309. May, 2015.
Generalized Voronoi Diagrams (GVDs) have far-reaching applications in robotics, visualization, graphics, and simulation. However, while the ordinary Voronoi Diagram has mature and efficient algorithms for its computation, the GVD is difficult to compute in general, and in fact, has only approximation algorithms for anything but the simplest of datasets. Our work is focused on developing algorithms to compute the GVD efficiently and with bounded error on the most difficult of datasets -- those with objects that are extremely close to each other.
Paint and Click: Unified Interactions for Image Boundaries|
B. Summa, A. A. Gooch, G. Scorzelli, V. Pascucci. In Computer Graphics Forum, Vol. 34, No. 2, Wiley-Blackwell, pp. 385--393. May, 2015.
Image boundaries are a fundamental component of many interactive digital photography techniques, enabling applications such as segmentation, panoramas, and seamless image composition. Interactions for image boundaries often rely on two complementary but separate approaches: editing via painting or clicking constraints. In this work, we provide a novel, unified approach for interactive editing of pairwise image boundaries that combines the ease of painting with the direct control of constraints. Rather than a sequential coupling, this new formulation allows full use of both interactions simultaneously, giving users unprecedented flexibility for fast boundary editing. To enable this new approach, we provide technical advancements. In particular, we detail a reformulation of image boundaries as a problem of finding cycles, expanding and correcting limitations of the previous work. Our new formulation provides boundary solutions for painted regions with performance on par with state-of-the-art specialized, paint-only techniques. In addition, we provide instantaneous exploration of the boundary solution space with user constraints. Finally, we provide examples of common graphics applications impacted by our new approach.
An Introduction to Verification of Visualization Techniques|
T. Etiene, R.M. Kirby, C. Silva. Morgan & Claypool Publishers, 2015.
C.R. Johnson. In Encyclopedia of Applied and Computational Mathematics, Edited by Björn Engquist, Springer, pp. 1537-1546. 2015.
Evaluating Alignment of Shapes by Ensemble Visualization|
M. Raj, M. Mirzargar, R. Kirby, R. Whitaker, J. Preston. In IEEE Computer Graphics and Applications, IEEE, 2015.
The visualization of variability in 3D shapes or surfaces, which is a type of ensemble uncertainty visualization for volume data, provides a means of understanding the underlying distribution for a collection or ensemble of surfaces. While ensemble visualization for surfaces is already described in the literature, we conduct an expert-based evaluation in a particular medical imaging application: the construction of atlases or templates from a population of images. In this work, we extend contour boxplots to 3D, allowing us to evaluate it against an enumeration-style visualization of the ensemble members and also other conventional visualizations used by atlas builders, namely examining the atlas image and the corresponding images/data provided as part of the construction process. We present feedback from domain experts on the efficacy of contour boxplots compared to other modalities when used as part of the atlas construction and analysis stages of their work.
Interstitial and Interlayer Ion Diffusion Geometry Extraction in Graphitic Nanosphere Battery Materials|
A. Gyulassy, A. Knoll, K. C. Lau, Bei Wang, PT. Bremer, M.l E. Papka, L. A. Curtiss, V. Pascucci. In Proceedings IEEE Visualization Conference, 2015.
Large-scale molecular dynamics (MD) simulations are commonly used for simulating the synthesis and ion diffusion of battery materials. A good battery anode material is determined by its capacity to store ion or other diffusers. However, modeling of ion diffusion dynamics and transport properties at large length and long time scales would be impossible with current MD codes. To analyze the fundamental properties of these materials, therefore, we turn to geometric and topological analysis of their structure. In this paper, we apply a novel technique inspired by discrete Morse theory to the Delaunay triangulation of the simulated geometry of a thermally annealed carbon nanosphere. We utilize our computed structures to drive further geometric analysis to extract the interstitial diffusion structure as a single mesh. Our results provide a new approach to analyze the geometry of the simulated carbon nanosphere, and new insights into the role of carbon defect size and distribution in determining the charge capacity and charge dynamics of these carbon based battery materials.
Workshop on Quantification, Communication, and Interpretation of Uncertainty in Simulation and Data Science|
R. Whitaker, W. Thompson, J. Berger, B. Fischhof, M. Goodchild, M. Hegarty, C. Jermaine, K. S. McKinley, A. Pang, J. Wendelberger. Note: Computing Community Consortium, 2015.
Modern science, technology, and politics are all permeated by data that comes from people, measurements, or computational processes. While this data is often incomplete, corrupt, or lacking in sufficient accuracy and precision, explicit consideration of uncertainty is rarely part of the computational and decision making pipeline. The CCC Workshop on Quantification, Communication, and Interpretation of Uncertainty in Simulation and Data Science explored this problem, identifying significant shortcomings in the ways we currently process, present, and interpret uncertain data. Specific recommendations on a research agenda for the future were made in four areas: uncertainty quantification in large-scale computational simulations, uncertainty quantification in data science, software support for uncertainty computation, and better integration of uncertainty quantification and communication to stakeholders.
Fiber Surfaces: Generalizing Isosurfaces to Bivariate Data|
H. Carr, Z. Geng, J. Tierny, A. Chattophadhyay,, A. Knoll. In Computer Graphics Forum, Vol. 34, No. 3, pp. 241-250. 2015.
Scientific visualization has many effective methods for examining and exploring scalar and vector fields, but rather fewer for multi-variate fields. We report the first general purpose approach for the interactive extraction of geometric separating surfaces in bivariate fields. This method is based on fiber surfaces: surfaces constructed from sets of fibers, the multivariate analogues of isolines. We show simple methods for fiber surface definition and extraction. In particular, we show a simple and efficient fiber surface extraction algorithm based on Marching Cubes. We also show how to construct fiber surfaces interactively with geometric primitives in the range of the function. We then extend this to build user interfaces that generate parameterized families of fiber surfaces with respect to arbitrary polylines and polygons. In the special case of isovalue-gradient plots, fiber surfaces capture features geometrically for quantitative analysis that have previously only been analysed visually and qualitatively using multi-dimensional transfer functions in volume rendering. We also demonstrate fiber surface extraction on a variety of bivariate data
CPU Ray Tracing Large Particle Data with Balanced P-k-d Trees|
I. Wald, A. Knoll, G. P. Johnson, W. Usher, V. Pascucci, M. E. Papka. In 2015 IEEE Scientific Visualization Conference, IEEE, Oct, 2015.
We present a novel approach to rendering large particle data sets from molecular dynamics, astrophysics and other sources. We employ a new data structure adapted from the original balanced k-d tree, which allows for representation of data with trivial or no overhead. In the OSPRay visualization framework, we have developed an efficient CPU algorithm for traversing, classifying and ray tracing these data. Our approach is able to render up to billions of particles on a typical workstation, purely on the CPU, without any approximations or level-of-detail techniques, and optionally with attribute-based color mapping, dynamic range query, and advanced lighting models such as ambient occlusion and path tracing.
|Data Science: What Is It and How Is It Taught?,
H. De Sterck, C.R. Johnson. In SIAM News, SIAM, July, 2015.
C.R. Johnson, K. Potter. In The Princeton Companion to Applied Mathematics, Edited by Nicholas J. Higham, Princeton University Press, pp. 843-846. September, 2015.
|Morse-Smale Analysis of Ion Diffusion for DFT Battery Materials Simulations,
A. Gyulassy, A. Knoll, K. C. Lau, Bei Wang, P. T. Bremer, M. E. Papka, L. A. Curtiss, V. Pascucci. In Topology-Based Methods in Visualization (TopoInVis), 2015.
Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrodinger's equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ion diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.
ND2AV: N-Dimensional Data Analysis and Visualization -- Analysis for the National Ignition Campaign|
P. T. Bremer, D. Maljovec, A. Saha, Bei Wang, J. Gaffney, B. K. Spears, V. Pascucci. In Computing and Visualization in Science, 2015.
One of the biggest challenges in high-energy physics is to analyze a complex mix of experimental and simulation data to gain new insights into the underlying physics. Currently, this analysis relies primarily on the intuition of trained experts often using nothing more sophisticated than default scatter plots. Many advanced analysis techniques are not easily accessible to scientists and not flexible enough to explore the potentially interesting hypotheses in an intuitive manner. Furthermore, results from individual techniques are often difficult to integrate, leading to a confusing patchwork of analysis snippets too cumbersome for data exploration. This paper presents a case study on how a combination of techniques from statistics, machine learning, topology, and visualization can have a significant impact in the field of inertial confinement fusion. We present the ND2AV: N-Dimensional Data Analysis and Visualization framework, a user-friendly tool aimed at exploiting the intuition and current work flow of the target users. The system integrates traditional analysis approaches such as dimension reduction and clustering with state-of-the-art techniques such as neighborhood graphs and topological analysis, and custom capabilities such as defining combined metrics on the fly. All components are linked into an interactive environment that enables an intuitive exploration of a wide variety of hypotheses while relating the results to concepts familiar to the users, such as scatter plots. ND2AV uses a modular design providing easy extensibility and customization for different applications. ND2AV is being actively used in the National Ignition Campaign and has already led to a number of unexpected discoveries.
Local, Smooth, and Consistent Jacobi Set Simplification|
H. Bhatia, Bei Wang, G. Norgard, V. Pascucci, P. T. Bremer. In Computational Geometry, Vol. 48, No. 4, Elsevier, pp. 311-332. May, 2015.
The relation between two Morse functions defined on a smooth, compact, and orientable 2-manifold can be studied in terms of their Jacobi set. The Jacobi set contains points in the domain where the gradients of the two functions are aligned. Both the Jacobi set itself as well as the segmentation of the domain it induces, have shown to be useful in various applications. In practice, unfortunately, functions often contain noise and discretization artifacts, causing their Jacobi set to become unmanageably large and complex. Although there exist techniques to simplify Jacobi sets, they are unsuitable for most applications as they lack fine-grained control over the process, and heavily restrict the type of simplifications possible.
Visual Exploration of High-Dimensional Data through Subspace Analysis and Dynamic Projections|
S. Liu, Bei Wang, J. J. Thiagarajan, P. T. Bremer, V. Pascucci. In Computer Graphics Forum, Vol. 34, No. 3, Wiley-Blackwell, pp. 271--280. June, 2015.
We introduce a novel interactive framework for visualizing and exploring high-dimensional datasets based on subspace analysis and dynamic projections. We assume the high-dimensional dataset can be represented by a mixture of low-dimensional linear subspaces with mixed dimensions, and provide a method to reliably estimate the intrinsic dimension and linear basis of each subspace extracted from the subspace clustering. Subsequently, we use these bases to define unique 2D linear projections as viewpoints from which to visualize the data. To understand the relationships among the different projections and to discover hidden patterns, we connect these projections through dynamic projections that create smooth animated transitions between pairs of projections. We introduce the view transition graph, which provides flexible navigation among these projections to facilitate an intuitive exploration. Finally, we provide detailed comparisons with related systems, and use real-world examples to demonstrate the novelty and usability of our proposed framework.
Visualizing High-Dimensional Data: Advances in the Past Decade|
S. Liu, D. Maljovec, Bei Wang, P. T. Bremer, V. Pascucci. In State of The Art Report, Eurographics Conference on Visualization (EuroVis), 2015.
Massive simulations and arrays of sensing devices, in combination with increasing computing resources, have generated large, complex, high-dimensional datasets used to study phenomena across numerous fields of study. Visualization plays an important role in exploring such datasets. We provide a comprehensive survey of advances in high-dimensional data visualization over the past 15 years. We aim at providing actionable guidance for data practitioners to navigate through a modular view of the recent advances, allowing the creation of new visualizations along the enriched information visualization pipeline and identifying future opportunities for visualization research.
Geometric Inference on Kernel Density Estimates|
J. M. Phillips, Bei Wang, Y. Zheng. In CoRR, Vol. abs/1307.7760, 2015.
We show that geometric inference of a point cloud can be calculated by examining its kernel density estimate with a Gaussian kernel. This allows one to consider kernel density estimates, which are robust to spatial noise, subsampling, and approximate computation in comparison to raw point sets. This is achieved by examining the sublevel sets of the kernel distance, which isomorphically map to superlevel sets of the kernel density estimate. We prove new properties about the kernel distance, demonstrating stability results and allowing it to inherit reconstruction results from recent advances in distance-based topological reconstruction. Moreover, we provide an algorithm to estimate its topology using weighted Vietoris-Rips complexes.
Robustness-Based Simplification of 2D Steady and Unsteady Vector Fields|
P. Skraba, Bei Wang, G. Chen, P. Rosen. In IEEE Transactions on Visualization and Computer Graphics (to appear), 2015.
Vector field simplification aims to reduce the complexity of the flow by removing features in order of their relevance and importance, to reveal prominent behavior and obtain a compact representation for interpretation. Most existing simplification techniques based on the topological skeleton successively remove pairs of critical points connected by separatrices, using distance or area-based relevance measures. These methods rely on the stable extraction of the topological skeleton, which can be difficult due to instability in numerical integration, especially when processing highly rotational flows. In this paper, we propose a novel simplification scheme derived from the recently introduced topological notion of robustness which enables the pruning of sets of critical points according to a quantitative measure of their stability, that is, the minimum amount of vector field perturbation required to remove them. This leads to a hierarchical simplification scheme that encodes flow magnitude in its perturbation metric. Our novel simplification algorithm is based on degree theory and has minimal boundary restrictions. Finally, we provide an implementation under the piecewise-linear setting and apply it to both synthetic and real-world datasets. We show local and complete hierarchical simplifications for steady as well as unsteady vector fields.