Data-Parallel Halo Finding with Variable Linking Lengths|
W. Widanagamaachchi, P.-T. Bremer, C. Sewell, L.-T. Lo; J. Ahrens, V. Pascucci. In Proceedings of the 2014 IEEE 4th Symposium on Large Data Analysis and Visualization (LDAV), pp. 27--34. November, 2014.
State-of-the-art cosmological simulations regularly contain billions of particles, providing scientists the opportunity to study the evolution of the Universe in great detail. However, the rate at which these simulations generate data severely taxes existing analysis techniques. Therefore, developing new scalable alternatives is essential for continued scientific progress. Here, we present a dataparallel, friends-of-friends halo finding algorithm that provides unprecedented flexibility in the analysis by extracting multiple linking lengths. Even for a single linking length, it is as fast as the existing techniques, and is portable to multi-threaded many-core systems as well as co-processing resources. Our system is implemented using PISTON and is coupled to an interactive analysis environment used to study halos at different linking lengths and track their evolution over time.
Towards Paint and Click: Unified Interactions for Image Boundaries|
SCI Technical Report, B. Summa, A.A. Gooch, G. Scorzelli, V. Pascucci. No. UUSCI-2014-004, SCI Institute, University of Utah, December, 2014.
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 complimentary 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. Furthermore, we show how to increase performance and decrease memory consumption through novel strategies and/or optional approximations. Finally, we provide examples of common graphics applications impacted by our new approach.
In-situ feature extraction of large scale combustion simulations using segmented merge trees|
A.G. Landge, V. Pascucci, A. Gyulassy, J.C. Bennett, H. Kolla, J. Chen, P.-T. Bremer. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC 2014), New Orleans, Louisana, IEEE Press, Piscataway, NJ, USA pp. 1020--1031. 2014.
The ever increasing amount of data generated by scientific simulations coupled with system I/O constraints are fueling a need for in-situ analysis techniques. Of particular interest are approaches that produce reduced data representations while maintaining the ability to redefine, extract, and study features in a post-process to obtain scientific insights.
Efficient I/O and storage of adaptive-resolution data|
S. Kumar, J. Edwards, P.-T. Bremer, A. Knoll, C. Christensen, V. Vishwanath, P. Carns, J.A. Schmidt, V. Pascucci. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, IEEE Press, pp. 413--423. 2014.
We present an efficient, flexible, adaptive-resolution I/O framework that is suitable for both uniform and Adaptive Mesh Refinement (AMR) simulations. In an AMR setting, current solutions typically represent each resolution level as an independent grid which often results in inefficient storage and performance. Our technique coalesces domain data into a unified, multiresolution representation with fast, spatially aggregated I/O. Furthermore, our framework easily extends to importance-driven storage of uniform grids, for example, by storing regions of interest at full resolution and nonessential regions at lower resolution for visualization or analysis. Our framework, which is an extension of the PIDX framework, achieves state of the art disk usage and I/O performance regardless of resolution of the data, regions of interest, and the number of processes that generated the data. We demonstrate the scalability and efficiency of our framework using the Uintah and S3D large-scale combustion codes on the Mira and Edison supercomputers.
Robust Detection of Singularities in Vector Fields|
H. Bhatia, A. Gyulassy, H. Wang, P.-T. Bremer, V. Pascucci . In Topological Methods in Data Analysis and Visualization III, Mathematics and Visualization, Springer International Publishing, pp. 3--18. March, 2014.
Recent advances in computational science enable the creation of massive datasets of ever increasing resolution and complexity. Dealing effectively with such data requires new analysis techniques that are provably robust and that generate reproducible results on any machine. In this context, combinatorial methods become particularly attractive, as they are not sensitive to numerical instabilities or the details of a particular implementation. We introduce a robust method for detecting singularities in vector fields. We establish, in combinatorial terms, necessary and sufficient conditions for the existence of a critical point in a cell of a simplicial mesh for a large class of interpolation functions. These conditions are entirely local and lead to a provably consistent and practical algorithm to identify cells containing singularities.
|Scientific Visualization: Uncertainty, Multifield, Biomedical, and Scalable Visualization,
C.D. Hansen, M. Chen, C.R. Johnson, A.E. Kaufman, H. Hagen (Eds.). Mathematics and Visualization, Springer, 2014.
M.G. Genton, C.R. Johnson, K. Potter, G. Stenchikov, Y. Sun. In Stat Journal, Vol. 3, No. 1, pp. 1--11. 2014.
In this paper, we introduce a surface boxplot as a tool for visualization and exploratory analysis of samples of images. First, we use the notion of volume depth to order the images viewed as surfaces. In particular, we define the median image. We use an exact and fast algorithm for the ranking of the images. This allows us to detect potential outlying images that often contain interesting features not present in most of the images. Second, we build a graphical tool to visualize the surface boxplot and its various characteristics. A graph and histogram of the volume depth values allow us to identify images of interest. The code is available in the supporting information of this paper. We apply our surface boxplot to a sample of brain images and to a sample of climate model outputs.
Multivariate Volume Visualization through Dynamic Projections|
Shusen Liu, Bei Wang, J.J. Thiagarajan, P.-T. Bremer, V. Pascucci. In Proceedings of the IEEE Symposium on Large Data Analysis and Visualization (LDAV), 2014.
We propose a multivariate volume visualization framework that tightly couples dynamic projections with a high-dimensional transfer function design for interactive volume visualization. We assume that the complex, high-dimensional data in the attribute space can be well-represented through a collection of low-dimensional linear subspaces, and embed the data points in a variety of 2D views created as projections onto these subspaces. Through dynamic projections, we present animated transitions between different views to help the user navigate and explore the attribute space for effective transfer function design. Our framework not only provides a more intuitive understanding of the attribute space but also allows the design of the transfer function under multiple dynamic views, which is more flexible than being restricted to a single static view of the data. For large volumetric datasets, we maintain interactivity during the transfer function design via intelligent sampling and scalable clustering. Using examples in combustion and climate simulations, we demonstrate how our framework can be used to visualize interesting structures in the volumetric space.
Visual Exploration of High-Dimensional Data: Subspace Analysis through Dynamic Projections|
SCI Technical Report, Shusen Liu, Bei Wang, J.J. Thiagarajan, P.-T. Bremer, V. Pascucci. No. UUSCI-2014-003, SCI Institute, University of Utah, 2014.
Understanding high-dimensional data is rapidly becoming a central challenge in many areas of science and engineering. Most current techniques either rely on manifold learning based techniques which typically create a single embedding of the data or on subspace selection to find subsets of the original attributes that highlight the structure. However, the former creates a single, difficult-to-interpret view and assumes the data to be drawn from a single manifold, while the latter is limited to axis-aligned projections with restrictive viewing angles. Instead, we introduce ideas based on subspace clustering that can faithfully represent more complex data than the axis-aligned projections, yet do not assume the data to lie on a single manifold. In particular, subspace clustering assumes that the data can be represented by a union of low-dimensional subspaces, which can subsequently be used for analysis and visualization. In this paper, we introduce new techniques to reliably estimate both the intrinsic dimension and the linear basis of a mixture of subspaces extracted through subspace clustering. We show that the resulting bases represent the high-dimensional structures more reliably than traditional approaches. Subsequently, we use the bases to define different “viewpoints”, i.e., different projections onto pairs of basis vectors, from which to visualize the data. While more intuitive than non-linear projections, interpreting linear subspaces in terms of the original dimensions can still be challenging. To address this problem, we present new, animated transitions between different views to help the user navigate and explore the high-dimensional space. More specifically, we introduce the view transition graph which contains nodes for each subspace viewpoint and edges for potential transition between views. The transition graph enables users to explore both the structure within a subspace and the relations between different subspaces, for better understanding of the data. Using a number of case studies on well-know reference datasets, we demonstrate that the interactive exploration through such dynamic projections provides additional insights not readily available from existing tools.
Keywords: High-dimensional data, Subspace, Dynamic projection
Design Activity Framework for Visualization Design|
S. McKenna, D. Mazur, J. Agutter, M.D. Meyer. In IEEE Transactions on Visualization and Computer Graphics (TVCG), 2014.
An important aspect in visualization design is the connection between what a designer does and the decisions the designer makes. Existing design process models, however, do not explicitly link back to models for visualization design decisions. We bridge this gap by introducing the design activity framework, a process model that explicitly connects to the nested model, a well-known visualization design decision model. The framework includes four overlapping activities that characterize the design process, with each activity explicating outcomes related to the nested model. Additionally, we describe and characterize a list of exemplar methods and how they overlap among these activities. The design activity framework is the result of reflective discussions from a collaboration on a visualization redesign project, the details of which we describe to ground the framework in a real-world design process. Lastly, from this redesign project we provide several research outcomes in the domain of cybersecurity, including an extended data abstraction and rich opportunities for future visualization research.
Keywords: Design, frameworks, process, cybersecurity, nested model, decisions, models, evaluation, visualization
Information Visualization for Science and Policy: Engaging Users and Avoiding Bias|
G. McInerny, M. Chen, R. Freeman, D. Gavaghan, M.D. Meyer, F. Rowland, D. Spiegelhalter, M. Steganer, G. Tessarolo, J. Hortal. In Trends in Ecology & Evolution, Vol. 29, No. 3, pp. 148--157. 2014.
Visualisations and graphics are fundamental to studying complex subject matter. However, beyond acknowledging this value, scientists and science-policy programmes rarely consider how visualisations can enable discovery, create engaging and robust reporting, or support online resources. Producing accessible and unbiased visualisations from complicated, uncertain data requires expertise and knowledge from science, policy, computing, and design. However, visualisation is rarely found in our scientific training, organisations, or collaborations. As new policy programmes develop [e.g., the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES)], we need information visualisation to permeate increasingly both the work of scientists and science policy. The alternative is increased potential for missed discoveries, miscommunications, and, at worst, creating a bias towards the research that is easiest to display.
Reflections on How Designers Design With Data|
A. Bigelow, S. Drucker, D. Fisher, M.D. Meyer. In Proceedings of the ACM International Conference on Advanced Visual Interfaces (AVI), Note: Awarded Best Paper!, 2014.
In recent years many popular data visualizations have emerged that are created largely by designers whose main area of expertise is not computer science. Designers generate these visualizations using a handful of design tools and environments. To better inform the development of tools intended for designers working with data, we set out to understand designers' challenges and perspectives. We interviewed professional designers, conducted observations of designers working with data in the lab, and observed designers working with data in team settings in the wild. A set of patterns emerged from these observations from which we extract a number of themes that provide a new perspective on design considerations for visualization tool creators, as well as on known engineering problems.
Keywords: Visualization, infographics, design practice
The Nested Blocks and Guidelines Model|
M.D. Meyer, M. Sedlmair, P.S. Quinan, T. Munzner. In Journal of Information Visualization, Special Issue on Evaluation (BELIV), 2014.
We propose the nested blocks and guidelines model (NBGM) for the design and validation of visualization systems. The NBGM extends the previously proposed four-level nested model by adding finer grained structure within each level, providing explicit mechanisms to capture and discuss design decision rationale. Blocks are the outcomes of the design process at a specific level, and guidelines discuss relationships between these blocks. Blocks at the algorithm and technique levels describe design choices, as do data blocks at the abstraction level, whereas task abstraction blocks and domain situation blocks are identified as the outcome of the designer's understanding of the requirements. In the NBGM, there are two types of guidelines: within-level guidelines provide comparisons for blocks within the same level, while between-level guidelines provide mappings between adjacent levels of design. We analyze several recent papers using the NBGM to provide concrete examples of how a researcher can use blocks and guidelines to describe and evaluate visualization research. We also discuss the NBGM with respect to other design models to clarify its role in visualization design. Using the NBGM, we pinpoint two implications for visualization evaluation. First, comparison of blocks at the domain level must occur implicitly downstream at the abstraction level; and second, comparison between blocks must take into account both upstream assumptions and downstream requirements. Finally, we use the model to analyze two open problems: the need for mid-level task taxonomies to fill in the task blocks at the abstraction level, as well as the need for more guidelines mapping between the algorithm and technique levels.
Distortion-Guided Structure-Driven Interactive Exploration of High-Dimensional Data|
S. Liu, Bei Wang, P.-T. Bremer, V. Pascucci. In Computer Graphics Forum, Vol. 33, No. 3, Wiley-Blackwell, pp. 101--110. June, 2014.
Dimension reduction techniques are essential for feature selection and feature extraction of complex high-dimensional data. These techniques, which construct low-dimensional representations of data, are typically geometrically motivated, computationally efficient and approximately preserve certain structural properties of the data. However, they are often used as black box solutions in data exploration and their results can be difficult to interpret. To assess the quality of these results, quality measures, such as co-ranking [ LV09 ], have been proposed to quantify structural distortions that occur between high-dimensional and low-dimensional data representations. Such measures could be evaluated and visualized point-wise to further highlight erroneous regions [ MLGH13 ]. In this work, we provide an interactive visualization framework for exploring high-dimensional data via its two-dimensional embeddings obtained from dimension reduction, using a rich set of user interactions. We ask the following question: what new insights do we obtain regarding the structure of the data, with interactive manipulations of its embeddings in the visual space? We augment the two-dimensional embeddings with structural abstrac- tions obtained from hierarchical clusterings, to help users navigate and manipulate subsets of the data. We use point-wise distortion measures to highlight interesting regions in the domain, and further to guide our selection of the appropriate level of clusterings that are aligned with the regions of interest. Under the static setting, point-wise distortions indicate the level of structural uncertainty within the embeddings. Under the dynamic setting, on-the-fly updates of point-wise distortions due to data movement and data deletion reflect structural relations among different parts of the data, which may lead to new and valuable insights.
Overview of New Tools to Perform Safety Analysis: BWR Station Black Out Test Case|
D. Mandelli, C. Smith, T. Riley, J. Nielsen, J. Schroeder, C. Rabiti, A. Alfonsi, J. Cogliati, R. Kinoshita, V. Pascucci, Bei Wang, D. Maljovec. In Proceedings of the Probabilistic Safety Assessment & Management conference (PSAM), 2014.
The existing fleet of nuclear power plants is in the process of extending its lifetime and increasing the power generated from these plants via power uprates. In order to evaluate the impacts of these two factors on the safety of the plant, the Risk Informed Safety Margin Characterization project aims to provide insights to decision makers through a series of simulations of the plant dynamics for different initial conditions (e.g., probabilistic analysis and uncertainty quantification). This paper focuses on the impacts of power uprate on the safety margin of a boiling water reactor for a station black-out event. Analysis is performed by using a combination of thermal-hydraulic codes and a stochastic analysis tool currently under development at the Idaho National Laboratory, i.e. RAVEN. We employed both classical statistical tools, i.e. Monte-Carlo, and more advanced machine learning based algorithms to perform uncertainty quantification in order to quantify changes in system performance and limitations as a consequence of power uprate. We also employed advanced data analysis and visualization tools that helped us to correlate simulation outcomes such as maximum core temperature with a set of input uncertain parameters. Results obtained give a detailed investigation of the issues associated with a plant power uprate including the effects of station black-out accident scenarios. We were able to quantify how the timing of specific events was impacted by a higher nominal reactor core power. Such safety insights can provide useful information to the decision makers to perform risk-informed margins management.
Analyzing Simulation-Based PRA Data Through Clustering: a BWR Station Blackout Case Study|
D. Maljovec, S. Liu, Bei Wang, V. Pascucci, P.-T. Bremer, D. Mandelli, C. Smith. In Proceedings of the Probabilistic Safety Assessment & Management conference (PSAM), 2014.
Dynamic probabilistic risk assessment (DPRA) methodologies couple system simulator codes (e.g., RELAP, MELCOR) with simulation controller codes (e.g., RAVEN, ADAPT). Whereas system simulator codes accurately model system dynamics deterministically, simulation controller codes introduce both deterministic (e.g., system control logic, operating procedures) and stochastic (e.g., component failures, parameter uncertainties) elements into the simulation. Typically, a DPRA is performed by 1) sampling values of a set of parameters from the uncertainty space of interest (using the simulation controller codes), and 2) simulating the system behavior for that specific set of parameter values (using the system simulator codes). For complex systems, one of the major challenges in using DPRA methodologies is to analyze the large amount of information (i.e., large number of scenarios ) generated, where clustering techniques are typically employed to allow users to better organize and interpret the data. In this paper, we focus on the analysis of a nuclear simulation dataset that is part of the risk-informed safety margin characterization (RISMC) boiling water reactor (BWR) station blackout (SBO) case study. We apply a software tool that provides the domain experts with an interactive analysis and visualization environment for understanding the structures of such high-dimensional nuclear simulation datasets. Our tool encodes traditional and topology-based clustering techniques, where the latter partitions the data points into clusters based on their uniform gradient flow behavior. We demonstrate through our case study that both types of clustering techniques complement each other in bringing enhanced structural understanding of the data.
Keywords: PRA, computational topology, clustering, high-dimensional analysis
Topological Methods in Data Analysis and Visualization III|
Edited by Peer-Timo Bremer and Ingrid Hotz and Valerio Pascucci and Ronald Peikert, Springer International Publishing, 2014.
The Natural Helmholtz-Hodge Decomposition For Open-Boundary Flow Analysis|
H. Bhatia, V. Pascucci, P.-T. Bremer. In IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 99, pp. 1566--1578. 2014.
The Helmholtz-Hodge decomposition (HHD) describes a flow as the sum of an incompressible, an irrotational, and a harmonic flow, and is a fundamental tool for simulation and analysis. Unfortunately, for bounded domains, the HHD is not uniquely defined, and traditionally, boundary conditions are imposed to obtain a unique solution. However, in general, the boundary conditions used during the simulation may not be known and many simulations use open boundary conditions. In these cases, the flow imposed by traditional boundary conditions may not be compatible with the given data, which leads to sometimes drastic artifacts and distortions in all three components, hence producing unphysical results. Instead, this paper proposes the natural HHD, which is defined by separating the flow into internal and external components. Using a completely data-driven approach, the proposed technique obtains uniqueness without assuming boundary conditions a priori. As a result, it enables a reliable and artifact-free analysis for flows with open boundaries or unknown boundary conditions. Furthermore, our approach computes the HHD on a point-wise basis in contrast to the existing global techniques, and thus supports computing inexpensive local approximations for any subset of the domain. Finally, the technique is easy to implement for a variety of spatial discretizations and interpolated fields in both two and three dimensions.
Extracting Features from Time-Dependent Vector Fields Using Internal Reference Frames|
H. Bhatia, V. Pascucci, R.M. Kirby, P.-T. Bremer. In Computer Graphics Forum, Vol. 33, No. 3, pp. 21--30. June, 2014.
Extracting features from complex, time-dependent flow fields remains a significant challenge despite substantial research efforts, especially because most flow features of interest are defined with respect to a given reference frame. Pathline-based techniques, such as the FTLE field, are complex to implement and resource intensive, whereas scalar transforms, such as λ2, often produce artifacts and require somewhat arbitrary thresholds. Both approaches aim to analyze the flow in a more suitable frame, yet neither technique explicitly constructs one.
Topology-Based Active Learning|
SCI Technical Report, D. Maljovec, Bei Wang, J. Moeller, V. Pascucci. No. UUSCI-2014-001, SCI Institute, University of Utah, 2014.
A common problem in simulation and experimental research involves obtaining time-consuming, expensive, or potentially hazardous samples from an arbitrary dimension parameter space. For example, many simulations modeled on supercomputers can take days or weeks to complete, so it is imperative to select samples in the most informative and interesting areas of the parameter space. In such environments, maximizing the potential gain of information is achieved through active learning (adaptive sampling). Though the topic of active learning is well-studied, this paper provides a new perspective on the problem. We consider topologybased batch selection strategies for active learning which are ideal for environments where parallel or concurrent experiments are able to be run, yet each has a heavy cost. These strategies utilize concepts derived from computational topology to choose a collection of locally distinct, optimal samples before updating the surrogate model. We demonstrate through experiments using a several different batch sizes that topology-based strategies have comparable and sometimes superior performance, compared to conventional approaches.