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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Towards Automatically Matching Security Advisories to CPEs: String Similarity-based Vendor Matching

When a vulnerability is reported by the National Vulnerability Database (NVD), affected products are listed in the structured Common Platform Enumeration (CPE) format. Unfortunately, if the vulnerability is in a software library (e.g., Log4j), it will not include CPEs for each product containing that library. In these cases, security operators need to manually read the vendor's or third-party security advisories to see if their product is affected. However, these advisories do not report affected products in a structured format, which prevents automated processing, This paper makes the first effort towards automatically constructing structured CPEs for the vulnerable products in a non-NVD security advisory from the unstructured data in the advisory. Since this is a very challenging problem, this paper specifically focuses on the initial but key step of matching the un-structured vendor names in security advisories to the structured vendor representations in the standard CPE format. We explore the feasibility of using string similarity to solve the problem. The basic idea is to compare a vendor name from the non-NVD advisory with each vendor in the official CPE dictionary. The CPE vendor with the highest similarity score to the advisory's vendor will be considered as the match. We first conduct an experimental, comparative study of multiple mainstream string similarity metrics for this matching problem. To improve the performance, we then design a new string similarity metric that is adapted from an existing metric by weighing different tokens in the advisory's vendor name differently.

McClanahan, Kylie↗
DOE OSTI2021

Adaptive Spatially Aware I/O for Multiresolution Particle Data Layouts

Large-scale simulations on nonuniform particle distributions that evolve over time are widely used in cosmology, molecular dynamics, and engineering. Such data are often saved in an unstructured format that neither preserves spatial locality nor provides metadata for accelerating spatial or attribute subset queries, leading to poor performance of visualization tasks. Furthermore, the parallel I/O strategy used typically writes a file per process or a single shared file, neither of which is portable or scalable across different HPC systems. We present a portable technique for scalable, spatially aware adaptive aggregation that preserves spatial locality in the output. We evaluate our approach on two supercomputers, Stampede2 and Summit, and demonstrate that it outperforms prior approaches at scale, achieving up to 2.5× faster writes and reads for nonuniform distributions. Furthermore, the layout written by our method is directly suitable for visual analytics, supporting low-latency reads and attribute-based filtering with little overhead.

Usher, Will↗
DOE OSTI2025

A Perspective on Data and Privacy for AI in Healthcare [Industrial and Governmental Activities]

As large language models continue to push the bounds of AI model size, they are also being trained on unprecedented volumes of data. While individual hospitals are estimated to produce petabytes of data per year, only a small fraction is currently being used for developing AI models. Additionally, with such data resources available, healthcare is well-positioned to benefit from the current trends in AI. Moreover, the inherently multi-modal and longitudinal nature of clinical data – from omics to imaging to unstructured notes – provides a fertile ground for the development and application of cutting-edge architectures like foundation models.

Gounley, John [Oak Ridge National Laboratory (ORNL↗
DOE OSTI2023

VISILIENCE: An Interactive Visualization Framework for Resilience Analysis using Control-Flow Graph

Soft errors have become one of the major concerns for the error resilience of HPC applications, as those errors can cause HPC applications to generate serious outcomes such as Silent Data Corruptions (SDCs). A large body of approaches has been proposed to analyze the resilience of HPC applications. However, existing studies rarely address the challenges of the analysis result perception. Specifically, resilience analysis techniques often produce a massive volume of unstructured data, making it difficult for programmers to conduct the resilience analysis due to non-intuitive raw data. Furthermore, different analysis models produce diverse results with multiple levels of details, which may create hurdles to compare and explore the resilience of HPC program execution. To this end, we present VISILIENCE, an interactive VISual resILIENCE analysis framework to allow programmers to facilitate the resilience analysis of HPC applications. In particular, VISILIENCE leverages an effective visualization approach Control Flow Graph (CFG) to present a function execution. In addition, three widely-used models for resilience analysis (i.e., Y-Branch, IPAS, and TRIDENT) are seamlessly embedded into the framework for resilience analysis and result comparison. Multiple case studies have been conducted to demonstrate the effectiveness of our proposed framework VISILIENCE.

Jiang, Hailong↗
DOE OSTI2022

Hybrid Recurrent Neural Network Modeling for Traffic Delay Prediction at Signalized Intersections Along an Urban Arterial

This paper studies the traffic delay prediction modeling for multiple signalized intersections along the Ala Moana Boulevard and Nimitz Highway in Hawaii. Several machine learning (ML) based approaches have been studied in the literature, and most of them focused on prediction accuracy rather than the end use of real-time control and implementation. These ML models tend to be very complex and non-linear in nature, making it challenging to achieve fast inferences and are computationally heavy for real-time signal control implementation. As such, in this paper, a simple yet accurate hybrid modeling method is proposed to predict traffic delay one-step ahead with the model made suitable for real-time implementation to control traffic flow. Since real-time road-side measurements are recorded in unstructured form, the paper also discusses other issues related to data extraction and the pre-processing process. Finally, a simple signal control loop is developed to demonstrate the proposed modeling approach, which has shown advantages in model accuracy and computation efficiency compared against several existing modeling methods.

42 ENGINEERING↗
DOE OSTI2021

FTK: A Simplicial Spacetime Meshing Framework for Robust and Scalable Feature Tracking

In this work, we present the Feature Tracking Kit (FTK), a framework that simplifies, scales, and delivers various feature-tracking algorithms for scientific data. The key of FTK is our simplicial spacetime meshing scheme that generalizes both regular and unstructured spatial meshes to spacetime while tessellating spacetime mesh elements into simplices. The benefits of using simplicial spacetime meshes include (1) reducing ambiguity cases for feature extraction and tracking, (2) simplifying the handling of degeneracies using symbolic perturbations, and (3) enabling scalable and parallel processing. The use of simplicial spacetime meshing simplifies and improves the implementation of several feature-tracking algorithms for critical points, quantum vortices, and isosurfaces. As a software framework, FTK provides end users with VTK/ParaView filters, Python bindings, a command line interface, and programming interfaces for feature-tracking applications. We demonstrate use cases as well as scalability studies through both synthetic data and scientific applications including tokamak, fluid dynamics, and superconductivity simulations. We also conduct end-to-end performance studies on the Summit supercomputer. FTK is open sourced under the MIT license: https://github.com/hguo/ftk.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Reimagining Disassembly Interfaces With Visualization: Combining Instruction Tracing and Control Flow With DisViz

In applications where efficiency is critical, developers may examine their compiled binaries, seeking to understand how the compiler transformed their source code and what performance implications that transformation may have. This analysis is challenging due to the vast number of disassembled binary instructions and the many-to-many mappings between them and the source code. These problems are exacerbated as source code size increases, giving the compiler more freedom to map and disperse binary instructions across the disassembly space. Interfaces for disassembly typically display instructions as an unstructured listing or sacrifice the order of execution. Here, we design a new visual interface for disassembly code that combines execution order with control flow structure, enabling analysts to both trace through code and identify familiar aspects of the computation. Central to our approach is a novel layout of instructions grouped into basic blocks that displays a looping structure in an intuitive way. We add to this disassembly representation a unique block-based mini-map that leverages our layout and shows context across thousands of disassembly instructions. Finally, we embed our disassembly visualization in a web-based tool, DisViz, which adds dynamic linking with source code across the entire application. DizViz was developed in collaboration with program analysis experts following design study methodology and was validated through evaluation sessions with ten participants from four institutions. Participants successfully completed the evaluation tasks, hypothesized about compiler optimizations, and noted the utility of our new disassembly view. Our evaluation suggests that our new integrated view helps application developers in understanding and navigating disassembly code.

Computer science↗
DOE OSTI2026

Memory-Aware External Facelist Calculation: A Data-Parallel Atomic Hash Counting Approach

Unstructured volumetric meshes serve as fundamental data representations in various scientific simulations and analyses. They play a crucial role in representing complex computational domains and are essential for important numerical techniques, such as finite element analysis. Whenever such a mesh is read from a file, streamed in-situ, or generated by algorithms, scientific visualization libraries rely on calculating the external surface of a geometry, named “external facelist”, to produce a polygonal mesh for rendering. Consequently, external facelist calculation has become one of the most widely used algorithms in the scientific visualization domain, necessitating optimal performance. In this paper, we explore relevant work on external facelist calculation algorithms in two common visualization libraries, VTK and Viskores, assess their performance and memory constraints, and introduce a novel memory-aware external facelist calculation algorithm employing an atomic hash counting approach. This algorithm fully leverages Viskores' data-parallel primitive operations, facilitating its execution across diverse many-core architectures. Our algorithm features the lowest memory footprint on the GPU and the second-lowest on the CPU among all evaluated methods, and it also delivers the fastest performance on both CPU and GPU. It has been made available under an open-source license in the VTK and Viskores visualization systems.

Tsalikis, Spiros [Kitware] (ORCID:0000000151137195↗
DOE OSTI2021

Impacts of Sea‐Level Rise on Hypoxia and Phytoplankton Production in Chesapeake Bay: Model Prediction and Assessment

In this study, the influence of sea-level rise (SLR) on seasonal hypoxia and phytoplankton production in Chesapeake Bay is investigated using a 3D unstructured grid model. Three SLR scenarios (0.17, 0.5, and 1.0 m) were conducted from 1991 to 1995. Results show that the summer hypoxic volume (HV) increases about 2%, 8%, and 16%, respectively, for these three scenarios, compared with Base Scenario. The contributions of physical and biological processes on the increase in the HV were analyzed. With the projected SLR, enhanced gravitational circulation transports more oxygen-rich water in the bottom layer from the mouth. However, the pycnocline moves upwards along with increasing water depth, which largely prolongs the time for dissolved oxygen (DO) to be transported to the bottom. The altered physical processes contribute greatly to a larger HV bay-wide. Besides, SLR increases the whole Bay phytoplankton production, with a larger increase in shallow areas (e.g., 53% in areas with depth <1 m under SLR of 0.5 m). Enhanced light availability is suggested to be the major driver of blooming phytoplankton under SLR in shallow areas. While increased DO production over the euphotic zone is mostly released to the atmosphere and transported downstream, the increase in settled organic matter greatly promotes DO consumption in the water column. The increased respiration is another major cause of the HV increase besides the physical contributions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Wassersplines for Neural Vector Field-Controlled Animation

Much of computer-generated animation is created by manipulating meshes with rigs. While this approach works well for animating articulated objects like animals, it has limited flexibility for animating less structured free-form objects. Here we introduce Wassersplines, a novel trajectory inference method for animating unstructured densities based on recent advances in continuous normalizing flows and optimal transport. The key idea is to train a neurally-parameterized velocity field that represents the motion between keyframes. Trajectories are then computed by advecting keyframes through the velocity field. We solve an additional Wasserstein barycenter interpolation problem to guarantee strict adherence to keyframes. Our tool can stylize trajectories through a variety of PDE-based regularizers to create different visual effects. We demonstrate our tool on various keyframe interpolation problems to produce temporally-coherent animations without meshing or rigging.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free-electron laser sources to reveal the formation and ready identification of angstrom-scale features in structured and unstructured RNAs. Previously unrecognized structural signatures of RNA secondary and tertiary structures are identified through wide-angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base-paired intermediate to assume a triple-helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. This method may help to rapidly characterize and identify structural elements in nucleic acids in both equilibrium and time-resolved experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A New Semistructured Algebraic Multigrid Method

Multigrid methods are well suited to large massively parallel computer architectures because they are mathematically optimal and display good parallelization properties. Since current architecture trends are favoring regular compute patterns to achieve high performance, the ability to express structure has become much more important. The hypre software library provides high-performance multigrid preconditioners and solvers through conceptual interfaces, including a semistructured interface that describes matrices primarily in terms of stencils and logically structured grids. This paper presents a new semistructured algebraic multigrid (SSAMG) method built on this interface. The numerical convergence and performance of a CPU implementation of this method are evaluated for a set of semistructured problems. In conclusion, SSAMG achieves significantly better setup times than hypre’s unstructured AMG solvers and comparable convergence. In addition, the new method is capable of solving more complex problems than hypre’s structured solvers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Parallel Randomized Tucker Decomposition Algorithms

The Tucker tensor decomposition is a natural extension of the singular value decomposition (SVD) to multiway data. Here, we propose to accelerate Tucker tensor decomposition algorithms by using randomization and parallelization. We present two algorithms that scale to large data and many processors, significantly reduce both computation and communication cost compared to previous deterministic and randomized approaches, and obtain nearly the same approximation errors. The key idea in our algorithms is to perform randomized sketches with Kronecker-structured random matrices, which reduces computation compared to unstructured matrices and can be implemented using a fundamental tensor computational kernel. We provide probabilistic error analysis of our algorithms and implement a new parallel algorithm for the structured randomized sketch. Our experimental results demonstrate that our combination of randomization and parallelization achieves accurate Tucker decompositions much faster than alternative approaches. We observe up to a 16X speedup over the fastest deterministic parallel implementation on 3D simulation data.

Tucker decompositions↗
DOE OSTI2024

Scalable Multiphysics Block Preconditioning for Low Mach Number Compressible Resistive MHD with Application to Magnetic Confinement Fusion

This study investigates multiphysics block preconditioners that are critical in devising scalable Newton–Krylov iterative solvers for longer time-scale fully implicit fluid plasma models. The specific model of interest is the visco-resistive, low Mach number, compressible magnetohydrodynamics (MHD) model. This model describes the dynamics of conducting fluids in the presence of electromagnetic fields and can be used to study aspects of astrophysical phenomena, important science and technology applications, and basic plasma physics. The specific application of interest that motivates this study is the macroscopic simulation of longer time-scale stability and disruptions of magnetic confinement fusion devices, specifically the ITER Tokamak. The computational solution of the governing balance equations for mass, momentum, heat transfer, and magnetic induction for resistive MHD systems can be extremely challenging. These difficulties arise from both the strong nonlinear, nonsymmetric coupling of fluid and electromagnetic phenomena as well as the significant range of time and length scales that the interactions of these physical mechanisms produce. To handle the range of time and spatial scales of interest, a fully implicit unstructured variational multiscale finite element formulation is employed. For the scalable solution of the Newton linearized systems, fully coupled block preconditioners are designed to leverage algebraic multigrid subsolves. In conclusion, results are presented for the strong and weak scaling of the method as well as the robustness of these techniques for a large range of Lundquist numbers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Session Introduction: Graph Representations and Algorithms in Biomedicine

Connectivity is a fundamental property of biological systems: on the cellular level, proteins interact with each other to form protein-protein interaction networks (PPIs); on the organism level, neurons are arranged in a network; and on a community-level, species can have complex relationships with one another that drive the development and balance of an ecosystem. Graphs, representations of systems consisting of entities as vertices and their connections as edges, are a useful structure to characterize many such systems. Such models can be used to understand biological systems that naturally have a network structure, including PPIs, biological neurons, and ecosystems. In today’s information age, graph representations and algorithms (often in combination with machine learning techniques) are used to organize massive amounts of related data, much of which may be heterogeneous or unstructured, and identify patterns that represent novel biological insights. PSB’s 2023 session “Graph Representations and algorithms in Biomedicine,” encompasses modern developments in graph theory and its applications to various fields of biomedicine. This session includes a wide range of research - knowledge graphs built from text-mined health data, heterogeneous networks using multi-omic databases, and graphs refined to represent uncertainty or improve memory usage.

Chrisman, Brianna S.↗
DOE OSTI2023

KiT-RT: An Extendable Framework for Radiative Transfer and Therapy

Here, in this article, we present Kinetic Transport Solver for Radiation Therapy (KiT-RT), an open-source C++-based framework for solving kinetic equations in therapy applications available at https://github.com/CSMMLab/KiT-RT . This software framework aims to provide a collection of classical deterministic solvers for unstructured meshes that allow for easy extendability. Therefore, KiT-RT is a convenient base to test new numerical methods in various applications and compare them against conventional solvers. The implementation includes spherical harmonics, minimal entropy, neural minimal entropy, and discrete ordinates methods. Solution characteristics and efficiency are presented through several test cases ranging from radiation transport to electron radiation therapy. Due to the variety of included numerical methods and easy extendability, the presented open-source code is attractive for both developers, who want a basis to build their numerical solvers, and users or application engineers, who want to gain experimental insights without directly interfering with the codebase.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Robust Containment Queries over Collections of Rational Parametric Curves via Generalized Winding Numbers

Point containment queries for regions bound by watertight geometric surfaces, i.e., closed and without self-intersections, can be evaluated straightforwardly with a number of well-studied algorithms. When this assumption on domain geometry is not met, such methods are either unusable, or prone to misclassifications that can lead to cascading errors in downstream applications. More robust point classification schemes based on generalized winding numbers have been proposed, as they are indifferent to these imperfections. However, existing algorithms are limited to point clouds and collections of linear elements. We extend this methodology to encompass more general curved shapes with an algorithm that evaluates the winding number scalar field over unstructured collections of rational parametric curves. In particular, we evaluate the winding number for each curve independently, making the derived containment query robust to how the curves are arranged. We ensure geometric fidelity in our queries by treating each curve as equivalent to an adaptively constructed polyline that provably has the same generalized winding number at the point of interest. Our algorithm is numerically stable for points that are arbitrarily close to the model, and explicitly treats points that are coincident with curves. We demonstrate the improvements in computational performance granted by this method over conventional techniques as well as the robustness induced by its application.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Data Readiness for AI: A 360-Degree Survey

Artificial Intelligence (AI) applications critically depend on data. Poor-quality data produces inaccurate and ineffective AI models that may lead to incorrect or unsafe use. Evaluation of data readiness is a crucial step in improving the quality and appropriateness of data usage for AI. R&D efforts have been spent on improving data quality. However, standardized metrics for evaluating data readiness for use in AI training are still evolving. In this study, we perform a comprehensive survey of metrics used to verify data readiness for AI training. This survey examines more than 140 papers published by ACM Digital Library, IEEE Xplore, journals such as Nature, Springer, and Science Direct, and online articles published by prominent AI experts. This survey aims to propose a taxonomy of data readiness for AI (DRAI) metrics for structured and unstructured datasets. We anticipate that this taxonomy will lead to new standards for DRAI metrics that would be used for enhancing the quality, accuracy, and fairness of AI training and inference.

97 MATHEMATICS AND COMPUTING↗