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All sourcesNASA NTRSDOE OSTI
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 OSTI2025

Intelligent Sampling of Extreme-Scale Turbulence Datasets for Accurate and Efficient Spatiotemporal Model Training

With the end of Moore’s law and Dennard scaling, efficient training increasingly requires rethinking data volume. Can we train better models with significantly less data via intelligent subsampling? To explore this, we develop SICKLE, a sparse intelligent curation framework for efficient learning, featuring a novel maximum entropy (MaxEnt) sampling approach, scalable training, and energy benchmarking. We compare MaxEnt with random and phase-space sampling on large direct numerical simulation (DNS) datasets of turbulence. Evaluating SICKLE at scale on Frontier, we show that subsampling as a preprocessing step can, in many cases, improve model accuracy and substantially lower energy consumption, with observed reductions of up to 38×.

Brewer, Wes [ORNL] (ORCID:0000000236393956)↗
DOE OSTI2017

Compressive Classification for TEM-EELS

Acquiring atomic-resolution images of beam sensitive materials or under dynamic conditions (e.g. operando STEM) is very difficult and requires precise dose fractioning to minimize the dose delivered to the sample and acquire the data more rapidly than dynamics present. Typical methods of low-dose STEM imaging include adjusting the beam current, dwell-time, and probe Scanning transmission electron microscopy (STEM) is used routinely to obtain atomic-resolution images of a small selection of radiation tolerant materials under stable conditions.size. All three of these determine the dose over a spatial area in STEM. Recently, compressive sensing [1] has been applied to electron microscopy. The computational imaging method of inpainting [2] has been proposed as a method to reduce dose and increase acquisition speed for STEM. Inpainting is a technique to recover missing pixels in an image. By skipping pixels (randomly) during acquisition, a fourth dose-control mechanism is realized [3]. A few implementations of randomly-subsampled STEM exist (e.g., [4]). To make the concepts of compressive sensing accessible to the microscopy community we begin with an example using atomic resolution images of a GaAs crystal (see Figure 1). Because the crystal is periodic it has a sparse representation in reciprocal space. In fact, a sparse representation is a key component of compressive sensing. If an image is sub-sampled randomly we find that the Fourier transform remains sparse, but becomes increasing noisy as less and less data is acquired. Yet, by finding the peaks in the reciprocal image and removing the noise it is possible to recover atomic resolution images with only 1% of the pixels. Figure 1 shows the reconstruction process for GaAs sub-sampled at 50%, 10%, 5%, and 1%. Periodic images form a special class for which the optimal sampling approach (according to CS theory) is a random selection of pixels. For non-periodic images, such as those arising in in-situ STEM, methods such as dictionary learning are necessary [2,5]. The data can be compressed in time for TEM [5] or pixels can be skipped randomly for STEM. There are several issues that arise in developing a random scan for STEM [4] and a coded aperture for TEM. The remainder of the talk will address these issues. References: [1] E Candes and M Wakin. Signal Processing Magazine, IEEE. 2(25) (2008), pp. 21. [2] A Stevens, Pu Y, Sun Y, et al. Artificial Intelligence & Statistics (AISTATS), 2017. [3] A Stevens, H Yang, L Carin et al. Microscopy 63(1), (2014), pp. 41. [4] L Kovarik, A Stevens, A Liyu et al. Appl. Phys. Lett. 109, 164102 (2016). [5] A Stevens, L Kovarik, P Abellan et al. Adv. Structural and Chemical Imaging 1(10), (2015), pp. 1. [6] Supported by the Chemical Imaging, Signature Discovery, and Analytics in Motion Initiatives at PNNL. PNNL is operated by Battelle Memorial Inst. for the US DOE; contract DE-AC05-76RL01830.

Hao, Weituo↗
DOE OSTI2022

Automated Crystal Orientation Mapping in py4DSTEM using Sparse Correlation Matching

Crystalline materials used in technological applications are often complex assemblies composed of multiple phases and differently oriented grains. Robust identification of the phases and orientation relationships from these samples is crucial, but the information extracted from the diffraction condition probed by an electron beam is often incomplete. We have developed an automated crystal orientation mapping (ACOM) procedure which uses a converged electron probe to collect diffraction patterns from multiple locations across a complex sample. We provide an algorithm to determine the orientation of each diffraction pattern based on a fast sparse correlation method. We demonstrate the speed and accuracy of our method by indexing diffraction patterns generated using both kinematical and dynamical simulations. We have also measured orientation maps from an experimental dataset consisting of a complex polycrystalline twisted helical AuAgPd nanowire. From these maps we identify twin planes between adjacent grains, which may be responsible for the twisted helical structure. All of our methods are made freely available as open source code, including tutorials which can be easily adapted to perform ACOM measurements on diffraction pattern datasets.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Pseudo spectral Chebyshev representation of few-group cross sections on sparse grids

This paper presents a pseudo spectral method for representing few-group homogenised cross sections, based on hierarchical polynomial interpolation. The interpolation is performed on a multi-dimensional sparse grid built from Chebyshev nodes. The representation is assembled directly from the samples using basis functions that are constructed as tensor products of the classical one-dimensional Lagrangian interpolation functions. The advantage of this representation is that it combines the accuracy of Chebyshev interpolation with the efficiency of sparse grid methods. As an initial test, this interpolation method was used to construct a representation for the two-group macroscopic cross sections of a VVER pin cell. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2016

SU-G-IeP3-07: High-Resolution, High-Sensitivity Imaging and Quantification of Intratumoral Distributions of Gold Nanoparticles Using a Benchtop L-Shell XRF Imaging System

Purpose: To demonstrate the ability to perform high-resolution imaging and quantification of sparse distributions of gold nanoparticles (GNPs) within ex vivo tumor samples using a highly-sensitive benchtop L-shell x-ray fluorescence (XRF) imaging system. Methods: An optimized L-shell XRF imaging system was assembled using a tungsten-target x-ray source (operated at 62 kVp and 45 mA). The x-rays were filtered (copper: 0.08 mm & aluminum: 0.04 mm) and collimated (lead: 5 cm thickness, 3 cm aperture diameter) into a cone-beam in order to irradiate small samples or objects. A collimated (stainless steel: 4 cm thickness, 2 mm aperture diameter) silicon drift detector, capable of 2D translation, was placed at 90° with respect to the beam to acquire XRF/scatter spectra from regions of interest. Spectral processing involved extracting XRF signal from background, followed by attenuation correction using a Compton scatter-based normalization algorithm. Calibration phantoms with water/GNPs (0 and 0.00001–10 mg/cm{sup 3}) were used to determine the detection limit of the system at a 10-second acquisition time. The system was then used to map the distribution of GNPs within a 12×11×2 mm{sup 3} slice excised from the center of a GNP-loaded ex vivo murine tumor sample; a total of 110 voxels (2.65×10{sup −3} cm{sup 3}) were imaged with 1.3-mm spatial resolution. Results: The detection limit of the current cone-beam benchtop L-shell XRF system was 0.003 mg/cm{sup 3} (3 ppm). Intratumoral GNP concentrations ranging from 0.003 mg/cm{sup 3} (3 ppm) to a maximum of 0.055 mg/cm{sup 3} (55 ppm) and average of 0.0093 mg/cm{sup 3} (9.3 ppm) were imaged successfully within the ex vivo tumor slice. Conclusion: The developed cone-beam benchtop L-shell XRF imaging system can immediately be used for imaging of ex vivo tumor samples containing low concentrations of GNPs. With minor finetuning/optimization, the system can be directly adapted for performing routine preclinical in vivo imaging tasks. Supported by NIH/NCI grant R01CA155446 This investigation was supported by NIH/NCI grant R01CA155446.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Vadose Zone Flow and Transport Parameters Data Package for the Hanford Site Composite Analysis and Cumulative Impact Evaluation

This report provides a description of the basis for the development and implementation of a conceptual model for vadose zone flow and transport for the composite analysis (CA) groundwater pathway analysis and the cumulative impact evaluation (CIE). The parameterization for a numerical model is intimately linked to the conceptual model framework. The report describes the basis for the selection of hydraulic and transport parameters for the hydrostratigraphic units (HSUs) identified in the 200 East and 200 West Areas. Whenever data are sparse or unavailable, surrogate hydraulic properties are chosen based on samples collected within the 200 Areas and nearby locations that are representative of sediments characteristic of the HSUs identified elsewhere.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

MAPPING THE GAS TURBULENCE IN THE COMA CLUSTER: PREDICTIONS FOR ASTRO-H

Astro-H will be able for the first time to map gas velocities and detect turbulence in galaxy clusters. One of the best targets for turbulence studies is the Coma cluster, due to its proximity, absence of a cool core, and lack of a central active galactic nucleus. To determine what constraints Astro-H will be able to place on the Coma velocity field, we construct simulated maps of the projected gas velocity and compute the second-order structure function, an analog of the velocity power spectrum. We vary the injection scale, dissipation scale, slope, and normalization of the turbulent power spectrum, and apply measurement errors and finite sampling to the velocity field. We find that even with sparse coverage of the cluster, Astro-H will be able to measure the Mach number and the injection scale of the turbulent power spectrum—the quantities determining the energy flux down the turbulent cascade and the diffusion rate for everything that is advected by the gas (metals, cosmic rays, etc.). Astro-H will not be sensitive to the dissipation scale or the slope of the power spectrum in its inertial range, unless they are outside physically motivated intervals. We give the expected confidence intervals for the injection scale and the normalization of the power spectrum for a number of possible pointing configurations, combining the structure function and velocity dispersion data. Importantly, we also determine that measurement errors on the line shift will bias the velocity structure function upward, and show how to correct this bias.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Optimized sub-sampling in an electron microscope

Disclosed are methods for optimized sub-sampling in an electron microscope. With regard at least to utilization of electron dose budgets, of time for acquisition of measurements, and of computing/processing capabilities, very high efficiencies can be achieved by informing and/or adapting subsequent sub-sampling measurements according to one or more earlier-acquired sparse datasets and/or according to analyzes thereof.

Stevens, Andrew J.↗
DOE OSTI2017

Sparse Representations to Replace TOFD Images in Non-destructive Testing of Materials

This paper describes a proposed method for the selection of relevant samples of ultrasonic signals during automatic material inspection. Instead of the well-known time of flight diffraction (TOFD) images, data are stored as a sparse matrix in which the elements only indicate whether a defect has been detected. This technique avoids storage of useless signals received during probe displacement in cases of low and high signal-to-noise ratios that correspond to coarse-grained and fine-grained materials, respectively. The approach is based on comparing the positions of maximum amplitudes, which are randomly located when signals only consist of noise but are in the same signal range when a defect is detected. The matrix elements are then applied as inputs to a self organizing map by neural networks to produce a normalized sparse matrix as the output, with a constant number of elements. This approach will be beneficial to enable the use of selected data in intelligent systems requiring a fixed number of inputs to characterize defects.

42 ENGINEERING↗
DOE OSTI2014

Reconstruction Techniques for Sparse Multistatic Linear Array Microwave Imaging

Sequentially-switched linear arrays are an enabling technology for a number of near-field microwave imaging applications. Electronically sequencing along the array axis followed by mechanical scanning along an orthogonal axis allows dense sampling of a two-dimensional aperture in near real-time. In this paper, a sparse multi-static array technique will be described along with associated Fourier-Transform-based and back-projection-based image reconstruction algorithms. Simulated and measured imaging results are presented that show the effectiveness of the sparse array technique along with the merits and weaknesses of each image reconstruction approach.

concealed-weapon detection↗
DOE OSTI2019

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

ABSTRACT The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics. Here, we propose a compositional beta diversity metric rooted in a centered log-ratio transformation and matrix completion called robust Aitchison PCA. We demonstrate the benefits of compositional transformations upstream of beta diversity calculations through simulations. Additionally, we demonstrate improved effect size, classification accuracy, and robustness to sequencing depth over the current methods on several decreased sample subsets of real microbiome data sets. Finally, we highlight the ability of this new beta diversity metric to retain the feature loadings linked to sample ordinations revealing salient intercommunity niche feature importance. IMPORTANCE By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE ; additionally, a QIIME 2 plugin is provided to perform this analysis at https://library.qiime2.org/plugins/q2-deicode .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Dynamic sparse x-ray nanotomography reveals ionomer hydration mechanism in polymer electrolyte fuel-cell catalyst

Tomographic imaging of time-evolving samples is a challenging yet important task for various research fields. At the nanoscale, current approaches face limitations of measurement speed or resolution due to lengthy acquisitions. We developed a dynamic nanotomography technique based on sparse dynamic imaging and 4D tomography modeling. We demonstrated the technique, using ptychographic x-ray computed tomography as its imaging modality, on resolving the in situ hydration process of polymer electrolyte fuel cell (PEFC) catalyst. The technique provides a 40-time increase in temporal resolution compared to conventional approaches, yielding 28 nm half-period spatial and 12 min temporal resolution. The results allow a quantitative characterization of the water intake process inside PEFC catalysts with nanoscale resolution, which is crucial for understanding their electrochemical mechanisms and optimizing their performance. Our technique enables high-speed operando nanotomography studies and paves the way for wider application of dynamic tomography at the nanoscale.

Science & Technology - Other Topics↗
DOE OSTI2017

Implicit sampling combined with reduced order modeling for the inversion of vadose zone hydrological data

Bayesian inverse modeling techniques are computationally expensive because many forward simulations are needed when sampling the posterior distribution of the parameters. Here, in this paper, we combine the implicit sampling method and generalized polynomial chaos expansion (gPCE) to significantly reduce the computational cost of performing Bayesian inverse modeling. There are three steps in this approach: (1) find the maximizer of the likelihood function using deterministic approaches; (2) construct a gPCE-based surrogate model using the results from a limited number of forward simulations; and (3) efficiently sample the posterior distribution of the parameters using implicit sampling method. The cost of constructing the gPCE-based surrogate model is further decreased by using sparse Bayesian learning to reduce the number of gPCE coefficients that have to be determined. We demonstrate the approach for a synthetic ponded infiltration experiment simulated with TOUGH2. The surrogate model is highly accurate with mean relative error that is < 0.035% in predicting saturation and < 0.25% in predicting the likelihood function. The posterior distribution of the parameters obtained using our proposed technique is nearly indistinguishable from the results obtained from either an implicit sampling method or a Markov chain Monte Carlo method utilizing the full mode.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Development and Demonstration of a Prototype Molten Salt Sampling System

Molten salt reactors (MSRs) offer potential operability and safety advantages when compared to commercial light water reactors (LWRs). However, operating experience with MSRs is sparse in comparison to what exists for LWRs. Further, the chemical and isotopic composition of the fuel and/or coolant salt is dynamic and difficult to characterize continuously, posing potential safety, operability, and safeguards unknowns that need to be addressed. A molten salt sampling system (MSSS) is regarded as a necessary subsystem within first generation MSRs used to obtain samples of salt for chemical and isotopic analysis in support of the need to monitor and control salt composition during operation. The MSSS is being developed using the Safety-in-Design (SiD) methodology, which incorporates incremental integration of safety analysis into the design process. The MSSS conceptual design emerging from the application of the early stages of the SiD methodology consists of a sample collection system and its housing, a freeze port, and inert gas control and delivery systems. This article describes the prototypes developed to test the functions of these MSSS subsystems, presents the results of testing in both dry and molten salt environments (including reliability data collection performed in accordance with the principles of SiD and the development of a semiquantitative fault tree model), and summarizes the opportunities for future design and testing enhancements based on the results of prototype testing.

molten salt reactor↗
DOE OSTI2016

Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers have high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30–60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than what is required by the Shannon-Nyquist sampling theorem for output-only modal analysis. In particular, the spatio-temporal uncoupling property of the modal expansion of structural vibration responses enables a direct modal decoupling of the temporally-aliased vibration measurements by existing output-only modal analysis methods, yielding (full-field) mode shapes estimation directly. Then the signal aliasing properties in modal analysis is exploited to estimate the modal frequencies and damping ratios. Furthermore, the proposed method is validated by laboratory experiments where output-only modal identification is conducted on temporally-aliased acceleration responses and particularly the temporally-aliased video measurements of bench-scale structures, including a three-story building structure and a cantilever beam.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗
DOE OSTI2018

Compressed sensing with sparse corruptions: Fault-tolerant sparse collocation approximations

The recovery of approximately sparse or compressible coefficients in a polynomial chaos expansion is a common goal in many modern parametric uncertainty quantification (UQ) problems. However, relatively little effort in UQ has been directed toward theoretical and computational strategies for addressing the sparse corruptions problem, where a small number of measurements are highly corrupted. Such a situation has become pertinent today since modern computational frameworks are sufficiently complex with many interdependent components that may introduce hardware and software failures, some of which can be difficult to detect and result in a highly polluted simulation result. In this paper we present a novel compressive sampling-based theoretical analysis for a regularized t1 minimization algorithm that aims to recover sparse expansion coefficients in the presence of measurement corruptions. Our recovery results are uniform (the theoretical guarantees hold for all compressible signals and compressible corruptions vectors), and prescribe algorithmic regularization parameters in terms of a user-defined a priori estimate on the ratio of measurements that are believed to be corrupted. We also propose an iteratively reweighted optimization algorithm that automatically refines the value of the regularization parameter, and empirically produces superior results. Our numerical results test our framework on several medium-to-high dimensional examples of solutions to parameterized differential equations, and demonstrate the effectiveness of our approach.

97 MATHEMATICS AND COMPUTING↗