Valerio Pascucci

Valerio Pascucci
University of Utah | UOU · Scientific Computing and Imaging Institute

Ph.D.

About

352
Publications
72,101
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10,641
Citations
Citations since 2016
22 Research Items
4097 Citations
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20162017201820192020202120220200400600
20162017201820192020202120220200400600

Publications

Publications (352)
Article
Single particle tracking (SPT) of fluorescent molecules provides significant insights into the diffusion and relative motion of tagged proteins and other structures of interest in biology. However, despite the latest advances in high‐resolution microscopy, individual particles are typically not distinguished from clusters of particles. This lack of...
Article
X-ray computed tomography (CT) is an established non-destructive tool for 3D imaging of multiphasic composites. Numerous applications of X-ray CT in medical diagnosis and materials characterization have been reported, many involving field-specific innovations in the imaging technology itself. Yet, quantitative summarization to link image features t...
Article
Full-text available
Parallel simulation codes often suffer from performance bottlenecks due to network congestion, leaving millions of dollars of investments underutilized. Given a network topology, it is critical to understand how different applications, job placements, routing schemes, etc., are affected by and contribute to network congestion, especially for large...
Article
We introduce Flexible Live‐Wire, a generalization of the Live‐Wire interactive segmentation technique with floating anchors. In our approach, the user input for Live‐Wire is no longer limited to the setting of pixel‐level anchor nodes, but can use more general anchor sets. These sets can be of any dimension, size, or connectedness. The generality o...
Conference Paper
Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’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 visualizat...
Conference Paper
Merge trees are topological structures that record changes in super-level set topology of a scalar function. They encapsulate a wide range of threshold based features which can be extracted for analysis and visualization. Several distributed and parallel algorithms for computing merge trees have been proposed in the past, but they are restricted to...
Article
This paper presents a novel approach to visualize the uncertainty in graph-based segmentations of scalar data. Segmentation of 2D scalar data has wide application in a variety of scientific and medical domains. Typically, a segmentation is presented as a single unambiguous boundary although the solution is often uncertain due to noise or blur in th...
Article
Li-ion battery performance is strongly influenced by the ionic conductivity, which depends on the mobility of the Li ions in solution, and is related to their solvation structure. In this work, we have performed first principles molecular dynamics (FPMD) of a LiPF6 salt solvated in different Li-ion battery organic electrolytes. We employ an analyti...
Article
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 d...
Conference Paper
Full-text available
As our ability to generate large and complex datasets grows, accessing and processing these massive data collections is increasingly the primary bottleneck in scientific analysis. Challenges include retrieving, converting, resampling, and combining remote and often disparately located data ensembles with only limited support from existing tools. In...
Article
Full-text available
The goal of the recently emerged field of connectomics is to generate a wiring diagram of the brain at different scales. To identify brain circuitry, neuroscientists use specialized microscopes to perform multichannel imaging of labeled neurons at a very high resolution. CLARITY tissue clearing allows imaging labeled circuits through entire tissue...
Article
Full-text available
Multifield data are common in visualization. However, reducing these data to comprehensible geometry is a challenging problem. Fiber surfaces, an analogy of isosurfaces to bivariate volume data, are a promising new mechanism for understanding multifield volumes. In this work, we explore direct ray casting of fiber surfaces from volume data without...
Article
Linear projections are one of the most common approaches to visualize high-dimensional data. Since the space of possible projections is large, existing systems usually select a small set of interesting projections by ranking a large set of candidate projections based on a chosen quality measure. However, while highly ranked projections can be infor...
Conference Paper
Exploration of atomic trajectories is fundamental to understanding and characterizing complex chemical systems important in many applications. For instance, any new insight into the mechanisms of ionic migration in catalytic materials could lead to a substantial increase in battery performance. A new statistical measure, called the relative-angle d...
Conference Paper
Full-text available
In nuclear engineering, understanding the safety margins of the nuclear reactor via simulations is arguably of paramount importance in predicting and preventing nuclear accidents. It is therefore crucial to perform sensitivity analysis to understand how changes in the model inputs affect the outputs. Modern nuclear simulation tools rely on numerica...
Article
Vector field topology has been successfully applied to represent the structure of steady vector fields. Critical points, one of the essential components of vector field topology, play an important role in describing the complexity of the extracted structure. Simplifying vector fields via critical point cancellation has practical merit for interpret...
Article
We present a system for interactive in situ visualization of large particle simulations, suitable for general CPU-based HPC architectures. As simulations grow in scale, in situ methods are needed to alleviate IO bottlenecks and visualize data at full spatio-temporal resolution. We use a lightweight loosely-coupled layer serving distributed data fro...
Article
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 impossi...
Chapter
Full-text available
Approaches for computing geometrically accurate Morse-Smale complexes with discrete Morse theory utilize a probabilistic approach to mitigate the negative impact of restricting flow to the edges of a mesh. The most accurate technique (Gyulassy et al., IEEE Trans Vis Comput Graph 18:2014–2022, 2012) builds a discrete gradient field by computing the...
Conference Paper
Full-text available
Understanding the circuitry of the brain is necessary to understanding brain function. Recently there has been a renaissance in neuroanatomy, thanks to the discovery of cell-type specific tracers, and new methods for high-resolution imaging and 3D reconstruction of large data sets at much greater speed than previously possible. However, the large s...
Conference Paper
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 algorith...
Article
Full-text available
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...
Article
Dynamic probabilistic risk assessment (DPRA) methodologies couple system simulator codes (e.g., RELAP and MELCOR) with simulation controller codes (e.g., RAVEN and ADAPT). Whereas system simulator codes model system dynamics deterministically, simulation controller codes introduce both deterministic (e.g., system control logic and operating procedu...
Article
Full-text available
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...
Article
We present an algorithm to compute an approximation of the generalized Voronoi diagram (GVD) on arbitrary collections of 2D or 3D geometric objects. In particular, we focus on datasets with closely spaced objects; GVD approximation is expensive and sometimes intractable on these datasets using previous algorithms. With our approach, the GVD can be...
Article
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 no...
Article
Scientific simulations often generate massive amounts of data used for debugging, restarts, and scientific analysis and discovery. Challenges that practitioners face using these types of big data are unique. Of primary importance is speed of writing data during a simulation, but this need for fast I/O is at odds with other priorities, such as data...
Conference Paper
Full-text available
We present a simulation–visualization pipeline that uses the LAMMPS Molecular Dynamics Simulator and the Vi- sualization Toolkit to create a visualization and analysis environment for atomistic simulations of plasma–surface interactions. These simulations are used to understand the origin of fuzz-like, microscopic damage to tungsten and other metal...
Conference Paper
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 d...
Article
In the first week of January 2014 Schloss Dagstuhl hosted a Perspectives Workshop on “Connecting Performance Analysis and Visualization to Advance Extreme Scale Computing”. The workshop brought together two previously separate communities – from Visualization and Performance Analysis for High Performance Computing – to discuss a long term joint res...
Article
Full-text available
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 te...
Patent
An image mosaic is created from overlapping images. A first seam is shown between a first pair of overlapping images such that, on a first side, a first image of the first pair is shown, and on a second side, a second image of the first pair is shown. The first seam includes a plurality of pixels in the image mosaic. An indicator of an interaction...
Article
Full-text available
The Helmholtz-Hodge decomposition (HHD), which describes a flow as the sum of an incompressible, an irrotational, and a harmonic flow, is a fundamental tool for simulation and analysis. Unfortunately, for bounded domains, the HHD is not uniquely defined, traditionally, boundary conditions are imposed to obtain a unique solution. However, in general...
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
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 i...
Conference Paper
Full-text available
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 i...
Conference Paper
Full-text available
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 conti...
Patent
Full-text available
A method, a system, and a computer-readable medium are provided which provide interactive editing of image data. Image data is sampled, by a computing device, at a first resolution. The first resolution is lower than a full resolution of the image data. Gradients for the sampled image data are calculated by the computing device. The computing devic...
Article
Molecular dynamics (MD) simulation is a crucial tool for understanding principles behind important biochemical processes such as protein folding and molecular interaction. With the rapidly increasing power of modern computers, large-scale MD simulation experiments can be performed regularly, generating huge amounts of MD data. An important question...
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
Today’s massively parallel simulation codes can produce output ranging up to many terabytes of data. Utilizing this data to support scientific inquiry requires analysis and visualization, yet the sheer size of the data makes it cumbersome or impossible to read without computational resources similar to the original simulation. We identify two broad...
Article
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 t...
Article
Recently, dissipation elements have been gaining popularity as a mechanism for measurement of fundamental properties of turbulent flow, such as turbulence length scales and zonal partitioning. Dissipation elements segment a domain according to the source and destination of streamlines in the gradient flow field of a scalar function f : ℝ. They have...
Article
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 ar...
Chapter
Full-text available
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 t...
Chapter
Full-text available
We present a new combinatorial algorithm for the optimal general topological simplification of scalar fields on surfaces. Given a piecewise linear (PL) scalar field f, our algorithm generates a simplified PL field g that provably admits critical points only from a constrained subset of the singularities of f while minimizing the distance | | f − g...
Article
Gigapixel panoramas are an increasingly popular digital image application. They are often created as a mosaic of many smaller images. The mosaic acquisition can take many hours causing the individual images to differ in exposure and lighting conditions. A blending operation is often necessary to give the appearance of a seamless image. The blending...
Conference Paper
Full-text available
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 proce...
Article
Efficient and effective performance analysis techniques are critical for the development of future generation systems. They are the drivers behind the required co-design process that helps establish the principles needed for their design. In this paper, we will highlight two such approaches: PAVE, a project that investigates mapping of performance...
Article
Full-text available
As the visualization field matures, an increasing number of general toolkits are developed to cover a broad range of applications. However, no general tool can incorporate the latest capabilities for all possible applications, nor can the user interfaces and workflows be easily adjusted to accommodate all user communities. As a result, users will o...
Conference Paper
Full-text available
Parallel I/O library performance can vary greatly in response to user-tunable parameter values such as aggregator count, file count, and aggregation strategy. Unfortunately, manual selection of these values is time consuming and dependent on characteristics of the target machine, the underlying file system, and the dataset itself. Some characterist...
Conference Paper
Full-text available
As scientific applications target exascale, challenges related to data and energy are becoming dominating concerns. For example, coupled simulation workflows are increasingly adopting in-situ data processing and analysis techniques to address costs and overheads due to data movement and I/O. However it is also critical to understand these overheads...
Conference Paper
Full-text available
State of the art PRA methods, i.e. Dynamic PRA (DPRA) methodologies [1], largely employ system simulator codes to accurately model system dynamics. Typically, these system simulator codes (e.g., RELAP5 [2]) are coupled with other codes (e.g., ADAPT [3], RAVEN [4] that monitor and control the simulation. The latter codes, in particular, introduce bo...
Technical Report
Full-text available
There currently exist a number of excellent techniques to capture, register, and blend digital panoramas. However, the problem is treated as an automated batch process, which can take several minutes to produce a panorama. Unfortunately, many of the algorithms involved are prone to errors and/or artifacts and may require meticulous tuning to achiev...
Conference Paper
Analysis of 4D medical images presenting pathology (i.e., lesions) is significantly challenging due to the presence of complex changes over time. Image analysis methods for 4D images with lesions need to account for changes in brain structures due to deformation, as well as the formation and deletion of new structures (e.g., edema, bleeding) due to...