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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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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

A comparison of methods for representing sparsely sampled random quantities.

This report discusses the treatment of uncertainties stemming from relatively few samples of random quantities. The importance of this topic extends beyond experimental data uncertainty to situations involving uncertainty in model calibration, validation, and prediction. With very sparse data samples it is not practical to have a goal of accurately estimating the underlying probability density function (PDF). Rather, a pragmatic goal is that the uncertainty representation should be conservative so as to bound a specified percentile range of the actual PDF, say the range between 0.025 and .975 percentiles, with reasonable reliability. A second, opposing objective is that the representation not be overly conservative; that it minimally over-estimate the desired percentile range of the actual PDF. The presence of the two opposing objectives makes the sparse-data uncertainty representation problem interesting and difficult. In this report, five uncertainty representation techniques are characterized for their performance on twenty-one test problems (over thousands of trials for each problem) according to these two opposing objectives and other performance measures. Two of the methods, statistical Tolerance Intervals and a kernel density approach specifically developed for handling sparse data, exhibit significantly better overall performance than the others.

Romero, Vicente Jose↗
DOE OSTI2018

Sparse coding of pathology slides compared to transfer learning with deep neural networks

Background Histopathology images of tumor biopsies present unique challenges for applying machine learning to the diagnosis and treatment of cancer. The pathology slides are high resolution, often exceeding 1GB, have non-uniform dimensions, and often contain multiple tissue slices of varying sizes surrounded by large empty regions. The locations of abnormal or cancerous cells, which may constitute a small portion of any given tissue sample, are not annotated. Cancer image datasets are also extremely imbalanced, with most slides being associated with relatively common cancers. Since deep representations trained on natural photographs are unlikely to be optimal for classifying pathology slide images, which have different spectral ranges and spatial structure, we here describe an approach for learning features and inferring representations of cancer pathology slides based on sparse coding. Results We show that conventional transfer learning using a state-of-the-art deep learning architecture pre-trained on ImageNet (RESNET) and fine tuned for a binary tumor/no-tumor classification task achieved between 85% and 86% accuracy. However, when all layers up to the last convolutional layer in RESNET are replaced with a single feature map inferred via a sparse coding using a dictionary optimized for sparse reconstruction of unlabeled pathology slides, classification performance improves to over 93%, corresponding to a 54% error reduction. Conclusions We conclude that a feature dictionary optimized for biomedical imagery may in general support better classification performance than does conventional transfer learning using a dictionary pre-trained on natural images.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

GPU-Accelerated Analytic Simulation of Sparse Ionization Signal Formation in Pixelated Projection Detector

This paper presents a GPU-accelerated simulation package, TRED, for next-generation neutrino detectors with pixelated charge readout, leveraging community-driven software ecosystems to ensure adaptability and extensibility. We introduce two generic contributions: (i) an effective-charge representation based on Gaussian quadrature rules, in which the linear- interpolation factors for the field response inside each voxel are absorbed into the effective charge, and (ii) a sparse, block- binned tensor representation that enables efficient FFT-based computation of induced signals on readout electrodes for sparsely activated detector volumes. The former captures structure inside a voxel without dense sampling, while the latter achieves low memory usage and scalable runtime, as demonstrated in bench- mark studies. The underlying data representation is applicable to large-scale detectors and to other computational problems involving sparse activity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Automating cell detection and classification in human brain fluorescent microscopy images using dictionary learning and sparse coding

Background Immunofluorescence (IF) plays a major role in quantifying protein expression in situ and understanding cell function. It is widely applied in assessing disease mechanisms and in drug discovery research. Automation of IF analysis can transform studies using experimental cell models. However, IF analysis of postmortem human tissue relies mostly on manual interaction, often subjected to low-throughput and prone to error, leading to low inter and intra-observer reproducibility. Human postmortem brain samples challenges neuroscientists because of the high level of autofluorescence caused by accumulation of lipofuscin pigment during aging, hindering systematic analyses. We propose a method for automating cell counting and classification in IF microscopy of human postmortem brains. Our algorithm speeds up the quantification task while improving reproducibility. New method Dictionary learning and sparse coding allow for constructing improved cell representations using IF images. These models are input for detection and segmentation methods. Classification occurs by means of color distances between cells and a learned set. Results Our method successfully detected and classified cells in 49 human brain images. We evaluated our results regarding true positive, false positive, false negative, precision, recall, false positive rate and F1 score metrics. We also measured user-experience and time saved compared to manual countings. Comparison with existing methods We compared our results to four open-access IF-based cell-counting tools available in the literature. Lastly, our method showed improved accuracy for all data samples. Conclusion The proposed method satisfactorily detects and classifies cells from human postmortem brain IF images, with potential to be generalized for applications in other counting tasks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Heterogeneous Point Set Transformers for Segmentation of Multiple View Particle Detectors

NOvA is a long-baseline neutrino oscillation experiment that detects neutrino particles from the NuMI beam at Fermilab. Before data from this experiment can be used in analyses, raw hits in the detector must be matched to their source particles, and the type of each particle must be identified. This task has commonly been done using a mix of traditional clustering approaches and convolutional neural networks (CNNs). Due to the construction of the detector, the data is presented as two sparse 2D images: an XZ and a YZ view of the detector, rather than a 3D representation. We propose a point set neural network that operates on the sparse matrices with an operation that mixes information from both views. Our model uses less than 10% of the memory required using previous methods while achieving a 96.8% AUC score, a higher score than obtained when both views are processed independently (85.4%).

Robles, Edgar E. [UC, Irvine (main)]↗
DOE OSTI2023

Sparse Symmetric Format for Tucker Decomposition

Tensor-based methods are receiving renewed attention in recent years due to their prevalence in diverse real-world applications. There is considerable literature on tensor representations and algorithms for tensor decompositions, both for dense and sparse tensors. Many applications in hypergraph analytics, machine learning, psychometry, and signal processing result in tensors that are both sparse and symmetric, making them an important class for further study. Similar to the critical Tensor Times Matrix chain operation (TTM c ) in general sparse tensors, the $\underline{S}$ parse $\underline{S}$ ymmetric $\underline{T}$ ensor $\underline{T}$ imes $\underline{S}$ ame $\underline{M}$ atrix $\underline{c}$ hain (S 3 TTM c ) operation is compute and memory intensive due to high tensor order and the associated factorial explosion in the number of non-zeros. We present the novel Compressed Sparse Symmetric (CSS) format for sparse symmetric tensors, along with an efficient parallel algorithm for the S 3 TTM c operation. We theoretically establish that S 3 TTM c on CSS achieves a better memory versus run-time trade-off compared to state-of-the-art implementations, and visualize the variation of the performance gap over the parameter space. We demonstrate experimental findings that confirm these results and achieve up to 2.72× speedup on synthetic and real datasets. The scaling of the algorithm on different test architectures is also showcased to highlight the effect of machine characteristics on algorithm performance.

42 ENGINEERING↗
DOE OSTI2019

Nonnegative tensor decomposition with custom clustering for microphase separation of block copolymers

High–dimensional datasets are becoming ubiquitous in many applications and therefore unsupervised tensor methods to interrogate them are needed. Here, we report a new unsupervised machine learning (ML) approach (NTFk) based on nonnegative tensor factorization integrated with a custom k–means clustering. We demonstrate the ability of NTFk to extracting temporal and spatial features of phase separation of copolymers as they are modeled by self–consistent field theory. Microphase separation of block copolymers has been extensively studied both experimentally and theoretically. However, the interpretation of computer simulations and/or experimental data, representing temporal and spatial changes of molecular species concentration is still a challenging task. Thus, extracting the phase diagram from simulations or experimental data as well as the interpretation of data requires discernment of the model/experimental parameters (such as, temperature, concentrations, the number of molecular species and the interaction between species) impact on the microphase separation process. An attractive and unique aspect of the introduced ML method is that it ensures the nonnegativity of the extracted latent features. Nonnegativity is an essential constraint needed to obtain interpretable and sparse latent features that are parts–based representation of the data. The custom clustering in NTFk serves to estimate the number of latent features in the data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Predictions of first passage times in sparse discrete fracture networks using graph-based reductions

Here, we present a graph-based methodology to reduce the computational cost of obtaining first passage times through sparse fracture networks. We also derive graph representations of generic three-dimensional discrete fracture networks (DFNs) using the DFN topology and flow boundary conditions. Subgraphs corresponding to the union of the k shortest paths between the inflow and outflow boundaries are identified and transport on their equivalent subnetworks is compared to transport through the full network. The number of paths included in the subgraphs is based on the scaling behavior of the number of edges in the graph with the number of shortest paths. First passage times through the subnetworks are in good agreement with those obtained in the full network, both for individual realizations and in distribution. We obtain accurate estimates of first passage times with an order of magnitude reduction of CPU time and mesh size using the proposed method.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Initial CEED API (CEED-MS10)

Key components of CEED software development involve fast finite element operator storage and evaluation, architecture optimizations, performant algorithms for all orders, global kernels for finite element operators, efficient use of the memory sub-system, optimal data locality and motion, enhanced scalability and parallelism, and fast tensor contractions. As ultimate goals of the project, CEED is exploring and identifying the best algorithms for the full range of discretizations and applying algorithmic and software development to support ECP applications’ needs. In this milestone, we initiated the development and implementation of a common CEED API consisting of two main components: low-level and high-level APIs. We accomplished the goal of having the low-level component ready for the release of CEED v1.0 in the next quarter, see CEED-MS13. In this report we also provide a highlight from CEED’s integration with the MARBL app and the corresponding Laghos miniapp. A main theme in this work has been the systematic transition of advanced algorithms, developed and tested in Laghos, to the large-scale multi-physics settings of the MARBL code. The low-level CEED API provides a set of FE kernels and components for writing new low-level kernels. Examples include: vector and sparse linear algebra, element matrix assembly over a batch of elements, partial assembly and action for efficient high-order operators like mass, diffusion, advection, etc. The main goal of the low-level API is to establish the basis for the high-level API. Also, identifying such low-level kernels and providing a reference implementation for them serves as the basis for collaboration with vendors and STs. Another goal for the low-level API is to make it easy for applications with their own discretization infrastructure, who do not want to switch directly to using the high-level CEED API, to still evaluate and use the core operations provided by the low-level API. One of the challenges with high-order methods is that a global sparse matrix is no longer a good representation of a high-order linear operator, both with respect to the FLOPs needed for its evaluation, as well as the memory transfer needed for a matvec. Thus, another important question we tried to address while developing the low-level API is: is it possible to abstract out in a natural and efficient way the different implementations and data structures that arise when dealing with various computational device types: CPUs, GPUs, etc. Fully answering this question is beyond the scope of this particular milestone, since that requires longer time as we develop and expand the devices we support. The future high-level API will be the frontend provided by CEED consisting of high-level abstractions such as meshes, finite element spaces and solutions, bilinear forms, solvers, etc. At this high-level, an important aspect of the API will be to provide a uniform abstraction layer for writing code in a portable manner. To achieve that, we plan to utilize the MPI programming model combined with a device abstraction layer (DAL) for finite element computations that we will develop. The DAL will serve as the bridge between the low- and the high-level APIs, allowing a variety of programming models to be used for the low-level kernel implementations. The software artifacts delivered as part of this milestone include an initial CEED API software implementation (libCEED) provided through the CEED website, http://ceed.exascaleproject.org and the CEED GitHub organization, http://github.com/ceed. In addition to details and results from the above R&D efforts, in this document we are also reporting on other project-wide activities performed in Q1 of FY18, including: the Nek5000 v17.0 MFEM v3.3.2 and PETSc v3.8 releases, collaborations with ECP/ST and SciDAC projects, the inaugural Nek5000 hackathon and various outreach activities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

BCSR on GPU: A Way Forward Extreme-scale Graph Processing on Accelerator-enabled Frontier Supercomputer

Handling large graphs in a distributed environment requires effective partitioning across processors and efficient management of local partitions. In 2D partitioning, local graphs often become too sparse, making memory-efficient data structures crucial. Using the Compressed Sparse Row (CSR) format wastes space, especially for > 83% of vertices with empty edges for the sparse graphs. This study explores bit-CSR (BCSR), a modified CSR representation, on GPUs to reduce memory usage in graph computations. We achieved 16.67% memory savings on a sparse rmat dataset with 268 million vertices and 357 million edges, without performance degradation, supported by both theoretical and experimental storage savings of 33%. However, we observed a 1.7× slowdown in degree lookup times due to bitwise operations on AMD CPUs. This analysis highlights the potential of BCSR on GPUs for improving Graph500 benchmark performance on GPU-accelerated systems, such as the Frontier supercomputer.

Sattar, Naw Safrin↗
DOE OSTI2021

Efficient Parallel Sparse Symmetric Tucker Decomposition for High-Order Tensors

Tensor based methods are receiving renewed attention in recent years due to their prevalence in diverse real-world applications. There is considerable literature on tensor representations and algorithms for tensor decompositions, both for dense and sparse tensors. Many applications in hypergraph analytics, machine learning, psychometry, and signal processing result in tensors that are both sparse and symmetric, making it an important class for further study. Similar to the critical Tensor Times Matrix chain operation (TTMc) in general sparse tensors, the Sparse Symmetric Tensor Times Same Matrix chain (S3TTMc) operation is compute and memory intensive due to high tensor order and the associated factorial explosion in the number of non-zeros. In this work, we present a novel compressed storage format CSS for sparse symmetric tensors, along with an efficient parallel algorithm for the S3TTMc operation. We theoretically establish that S3TTMc on CSS achieves a better memory versus run-time trade-off compared to state-of-the-art implementations. We demonstrate experimental findings that confirm these results and achieve up to 2.9× speedup on synthetic and real datasets.

Shivakumar, Shruti↗
DOE OSTI2015

A Hyperspherical Adaptive Sparse-Grid Method for High-Dimensional Discontinuity Detection

This study proposes and analyzes a hyperspherical adaptive hierarchical sparse-grid method for detecting jump discontinuities of functions in high-dimensional spaces. The method is motivated by the theoretical and computational inefficiencies of well-known adaptive sparse-grid methods for discontinuity detection. Our novel approach constructs a function representation of the discontinuity hypersurface of an N-dimensional discontinuous quantity of interest, by virtue of a hyperspherical transformation. Then, a sparse-grid approximation of the transformed function is built in the hyperspherical coordinate system, whose value at each point is estimated by solving a one-dimensional discontinuity detection problem. Due to the smoothness of the hypersurface, the new technique can identify jump discontinuities with significantly reduced computational cost, compared to existing methods. In addition, hierarchical acceleration techniques are also incorporated to further reduce the overall complexity. Rigorous complexity analyses of the new method are provided as are several numerical examples that illustrate the effectiveness of the approach.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

A hyper-spherical adaptive sparse-grid method for high-dimensional discontinuity detection

This work proposes and analyzes a hyper-spherical adaptive hierarchical sparse-grid method for detecting jump discontinuities of functions in high-dimensional spaces is proposed. The method is motivated by the theoretical and computational inefficiencies of well-known adaptive sparse-grid methods for discontinuity detection. Our novel approach constructs a function representation of the discontinuity hyper-surface of an N-dimensional dis- continuous quantity of interest, by virtue of a hyper-spherical transformation. Then, a sparse-grid approximation of the transformed function is built in the hyper-spherical coordinate system, whose value at each point is estimated by solving a one-dimensional discontinuity detection problem. Due to the smoothness of the hyper-surface, the new technique can identify jump discontinuities with significantly reduced computational cost, compared to existing methods. Moreover, hierarchical acceleration techniques are also incorporated to further reduce the overall complexity. Rigorous error estimates and complexity analyses of the new method are provided as are several numerical examples that illustrate the effectiveness of the approach.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

DECOVALEX-2019 (Task G Final Report)

The DECOVALEX Project is an on-going international research collaboration, established in 1992, to advance the understanding and modeling of coupled Thermal (T), Hydrological (H), Mechanical (M) and Chemical (C) processes in geological in geological systems. This document is the final report of Task G which was proposed by the Swedish Radiation Safety Authority (SSM) and coordinated by geomecon GmbH, presenting the technical definitions of the problems studied, approaches applied, achievements made and outstanding issues for future research. Task G in DECOVALEX-2019 is primarily concerned with the evolution of transmissivity throughout the lifetime of a repository for radioactive waste, and in particular of spent nuclear fuel, in sparsely fractured and competent crystalline rock masses, and the representation of these processes via numerical simulation. The numerical simulations were to be evaluated for their suitability, and to be validated. Over the course of the work presented here, not only were transmissivity changes and the best approaches to simulate those change examined, but also strategies were to be developed on how to monitor transmissivity change. Guidelines on what a control program and a monitoring system for a repository should include and be able to measure, and how this can be done in practice, was a key objective of the research project.

58 GEOSCIENCES↗
DOE OSTI2026

Prong Segmentation using Point Set Transformers in Multiple View Neutrino Detectors

NOvA is a long-baseline neutrino experiment studying neutrino oscillations by detecting neutrinos from the NuMI beam at Fermilab. Its physics analysis relies on accurate prong segmentation, which involves matching each hit to its source particle and identifying the particle type. This task has commonly been addressed using a combination of traditional clustering algorithms and convolutional neural networks (CNNs). However, NOvA’s detector design presents data as two sparse and decoupled 2D images (XZ and YZ views) rather than a native 3D representation, posing a significant challenge for traditional CNN-based models. In this talk, we propose a novel neural network based on the Point Set Transformer. By treating detector hits as sparse point clouds and implementing a cross-view attention mechanism, our model enables efficient information mixing between both views. Evaluated on NOvA simulated data, our model achieves superior accuracy while requiring significantly fewer computational resources compared to other models. Furthermore, the model demonstrates great performance when applied to Liquid Argon Time Projection Chamber (LArTPC) data, which shows its potential as a universal prong segmentation algorithm for multiple view neutrino detectors.

Liu, Jiaxi [UC, Irvine]↗
DOE OSTI2013

A dynamically bi-orthogonal method for time-dependent stochastic partial differential equations I: Derivation and algorithms

We propose a dynamically bi-orthogonal method (DyBO) to solve time dependent stochastic partial differential equations (SPDEs). The objective of our method is to exploit some intrinsic sparse structure in the stochastic solution by constructing the sparsest representation of the stochastic solution via a bi-orthogonal basis. It is well-known that the Karhunen–Loeve expansion (KLE) minimizes the total mean squared error and gives the sparsest representation of stochastic solutions. However, the computation of the KL expansion could be quite expensive since we need to form a covariance matrix and solve a large-scale eigenvalue problem. The main contribution of this paper is that we derive an equivalent system that governs the evolution of the spatial and stochastic basis in the KL expansion. Unlike other reduced model methods, our method constructs the reduced basis on-the-fly without the need to form the covariance matrix or to compute its eigendecomposition. In the first part of our paper, we introduce the derivation of the dynamically bi-orthogonal formulation for SPDEs, discuss several theoretical issues, such as the dynamic bi-orthogonality preservation and some preliminary error analysis of the DyBO method. We also give some numerical implementation details of the DyBO methods, including the representation of stochastic basis and techniques to deal with eigenvalue crossing. In the second part of our paper [11], we will present an adaptive strategy to dynamically remove or add modes, perform a detailed complexity analysis, and discuss various generalizations of this approach. An extensive range of numerical experiments will be provided in both parts to demonstrate the effectiveness of the DyBO method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Bayesian State-Space Modeling Framework for Understanding and Predicting Golden Eagle Movements Using Telemetry Data

Predicting raptor movements through a wind power plant under given atmospheric and topographical conditions is a crucial first step in the overall goal of quantifying the risk of turbine-related collisions and mortalities. Extracting behavioral traits of golden eagles (Aquila chrysaetos) from telemetry data requires the fusion of noisy and sparse movement data (location, heading, velocity) with a stochastic mathematical representation of the eagles' decision-making processes. In this study, we framed this problem in a Bayesian state-space framework where both observations and decision-making are assumed to be stochastic processes connected through hidden states (mode of flight, intent), and the unknown model parameters are assumed to be random variables that are calibrated using the available telemetry data. This framework allowed for rigorous consideration of underlying uncertainties while allowing for both data and prior biological knowledge to contribute to a probabilistic and predictive agent-based movement model. We implemented and applied the Bayesian framework to understand movement behavior of 23 GPS-tagged golden eagles travelling in the western US for years 2019 and 2020. Our preliminary findings show that the Bayesian state-space framework provides a robust inverse modeling apparatus to decode eagle behavioral characteristics from telemetry data. This study was primarily aimed at verifying and validating the framework with selected golden eagle tracks (both long- and short-ranged), with future research aimed at extending the framework to include multi-mode flight, consideration of atmospheric data and uplift mechanisms, eagle-to-eagle interaction, and eagle-to-turbine interaction.

Bayesian modeling↗