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DOE OSTI2025

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data

High-dimensional mixed-effects models are an increasingly important form of regression in which the number of covariates rivals or exceeds the number of samples, which are collected in groups or clusters. The penalized likelihood approach to fitting these models relies on a coordinate descent algorithm that lacks guarantees of convergence to a global optimum. Here, we empirically study the behavior of this algorithm on simulated and real examples of three types of data that are common in modern biology: transcriptome, genome-wide association, and microbiome data. Our simulations provide new insights into the algorithm’s behavior in these settings, and, comparing the performance of two popular penalties, we demonstrate that the smoothly clipped absolute deviation (SCAD) penalty consistently outperforms the least absolute shrinkage and selection operator (LASSO) penalty in terms of both variable selection and estimation accuracy across omics data. To empower researchers in biology and other fields to fit models with the SCAD penalty, we implement the algorithm in a Julia package, HighDimMixedModels.jl .

Gorstein, Evan↗

DOE OSTI2024

Dark Energy Survey: Galaxy sample for the baryonic acoustic oscillation measurement from the final dataset

In this paper, we present and validate the galaxy sample used for the analysis of the baryon acoustic oscillation (BAO) signal in the Dark Energy Survey (DES) Y6 data. The definition is based on a color and redshift-dependent magnitude cut optimized to select galaxies at redshifts higher than 0.6, while ensuring a high-quality photo- z determination. The optimization is performed using a Fisher forecast algorithm, finding the optimal i -magnitude cut to be given by i < 19.64 + 2.894 z ph . For the optimal sample, we forecast an increase in precision in the BAO measurement of ∼ 25 % with respect to the Y3 analysis. Our BAO sample has a total of 15,937,556 galaxies in the redshift range 0.6 < z ph < 1.2 , and its angular mask covers 4 , 273.42 deg 2 to a depth of i = 22.5 . We validate its redshift distributions with three different methods: directional neighborhood fitting algorithm (DNF), which is our primary photo- z estimation; direct calibration with spectroscopic redshifts from VIPERS, which is a spectroscopic galaxy sample that overlaps with our BAO sample and is complete within our selection cuts; and clustering redshift using SDSS galaxies. The fiducial redshift distribution is a combination of these three techniques performed by modifying the mean and width of the DNF distributions to match those of VIPERS and clustering redshift. In this paper, we also describe the methodology used to mitigate the effect of observational systematics, which is analogous to the one used in the Y3 analysis. This paper is one of the two dedicated to the analysis of the BAO signal in DES Y6. In its companion paper, we present the angular diameter distance constraints obtained through the fitting to the BAO scale.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

FY21 Progress Report: SRNL Analysis of ICCWR LCM and WAMS data for Corrosion and Cracking

The development of algorithms for machine learning and data analysis for the 3013 Surveillance Program is a collaborative effort by the Savannah River National Laboratory (SRNL) and the University of South Carolina (USC). For corrosion detection, Laser Confocal Microscope (LCM) or Wide Area 3D Measurement System (WAMS) data is extracted from large binary files, with software written to convert the data to physical attributes (e.g., height, color and grayscale values; all as functions of a location in a plane projection). A user-friendly Matlab Graphical User Interface (GUI) that reads data from either LCM or WAMS files was developed to integrate input data with software developed for processing and evaluation. The GUI can selectively download binary data, interrogate data attributes, label data, flag significant features, execute Machine Learning (ML) algorithms, output parameters for trained ML algorithms, report ML model accuracy with respect to labeled data, and generate graphical representations for various analyses. Features can be called out by user-specified thresholds, manual labeling or machine learning algorithms when they have been completed. The ability to rapidly label data is important because of the volume of data required for training machine learning algorithms. The GUI has the flexibility to allow addition of improved ML algorithms, methods for data visualization, and statistical computations. Statistical analyses via the GUI include areas of pits within a defined range of pit depths, correlations between Red-Green-Blue (RGB) or grayscale intensity and relative surface height, covariances between values associated with features, and feature histograms. The development of supervised machine learning algorithms, however, has been hindered by a lack of training data. The machine learning algorithms for crack identification are being refined but require improvements to the true positive rate for crack detection. This shortcoming is an artifact of the limited training data currently available, perhaps more so than the structure of the neural networks. At present, the best results are had from a consensus over an ensemble of randomly generated Deep Neural Network (DNN) or Convolutional Neural Network (CNN) algorithms. Although the consensus accuracy method has yielded optimum true positive and true negative rates in excess of 80%, additional validation testing is necessary. In addition to the suite of LCM data that was initially used, and which represents the majority of the work presented in this report, WAMS image data was also reviewed at a preliminary level. The review included a comparison between image resolution and dynamic range for each method. WAMS (ZON file) image data was found to have a pixel pitch of 3.69μm compared to 1 μm for the LCM (vk4 file) data, which implies a lower resolution for the WAMS images. Conversely, the ratio of dynamic range of the WAMS data to the LCM data was approximately 41:20 for height data, suggesting that information from WAMS should more accurately determine the depth of pits. At present, the significance of the greater dynamic range of the WAMS data relative to the LCM data has not yet been evaluated.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

Using pile-up collisions as an abundant source of low-energy hadronic physics processes in ATLAS and an extraction of the jet energy resolution

During the 2015–2018 data-taking period, the Large Hadron Collider delivered proton-proton bunch crossings at a centre-of-mass energy of 13 TeV to the ATLAS experiment at a rate of roughly 30 MHz, where each bunch crossing contained an average of 34 independent inelastic proton-proton collisions. The ATLAS trigger system selected roughly 1 kHz of these bunch crossings to be recorded to disk. Offline algorithms then identify one of the recorded collisions as the collision of interest for subsequent data analysis, and the remaining collisions are referred to as pile-up. Pile-up collisions represent a trigger-unbiased dataset, which is evaluated to have an integrated luminosity of 1.33 pb -1 in 2015–2018. This is small compared with the normal trigger-based ATLAS dataset, but when combined with vertex-by-vertex jet reconstruction it provides up to 50 times more dijet events than the conventional single-jet-trigger-based approach, and does so without adding any additional cost or requirements on the trigger system, readout, or storage. The pile-up dataset is validated through comparisons with a special trigger-unbiased dataset recorded by ATLAS, and its utility is demonstrated by means of a measurement of the jet energy resolution in dijet events, where the statistical uncertainty is significantly reduced for jet transverse momenta below 65 GeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Analysis of the ratio of ℓ 1 and ℓ 2 norms in compressed sensing

We study the ratio of ℓ 1 and ℓ 2 norms ( ℓ 1 / ℓ 2 ) as a sparsity-promoting objective in compressed sensing. We first propose a novel criterion that guarantees that an s-sparse signal is the local minimizer of the ℓ 1 / ℓ 2 objective; our criterion is interpretable and useful in practice. We also give the first uniform recovery condition using a geometric characterization of the null space of the measurement matrix, and show that this condition is satisfied for a class of random matrices. We also present analysis on the robustness of the procedure when noise pollutes data. Numerical experiments are provided that compare ℓ 1 / ℓ 2 with some other popular non-convex methods in compressed sensing. Finally, we propose a novel initialization approach to accelerate the numerical optimization procedure. We call this initialization approach support selection, and we demonstrate that it empirically improves the performance of existing ℓ 1 / ℓ 2 algorithms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Local modeling for FRF estimation with noisy input measurements

The frequency response function (FRF) is an essential means by which dynamic systems are qualified. In recent years, local modeling approaches have been extensively researched and shown to significantly outperform traditional FRF estimators. However, the standard local modeling approach assumes a perfectly-known system input, which results in biased FRF estimates in the presence of input noise. This paper derives a simple adjustment that can be used to improve FRF estimation for systems subjected to random excitation with noisy input data. This improvement can be implemented with little modification to standard local modeling algorithms and with little additional computational burden. The adjustment is coupled with a model selection procedure to avoid underfitting and overfitting. In conclusion, the methods presented in this paper are validated on a simulation, and they are shown to reduce bias due to input noise.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Systematic Generation of Moment Invariant Bases for 2D and 3D Tensor Fields

Moment invariants have been successfully applied to pattern detection tasks in 2D and 3D scalar, vector, and matrix valued data. However so far no flexible basis of invariants exists, i.e., no set that is optimal in the sense that it is complete and independent for every input pattern. Here, we prove that a basis of moment invariants can be generated that consists of tensor contractions of not more than two different moment tensors each under the conjecture of the set of all possible tensor contractions to be complete. This result allows us to derive the first generator algorithm that produces flexible bases of moment invariants with respect to orthogonal transformations by selecting a single non-zero moment to pair with all others in these two-factor products. Since at least one non-zero moment can be found in every non-zero pattern, this approach always generates a complete set of descriptors.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

RE-INTEGRATE EMT Simulation Software: Graph Convolutional Network for Sparse Matrix Pattern Detection

The increasing complexity of power networks, driven by proliferation of inverters, presents analytical challenges that simplified models often fail to capture, necessitating Electromagnetic Transient (EMT) simulations. EMT models are represented as discretized differential-algebraic equations (DAEs), forming a linear system Ax = b that is computationally intensive to solve. Due to inherent sparsity of adjacency matrix A, distinct patterns emerge that, when accurately identified, enable efficient solver selection to minimize computation time. However, identifying ideal pattern is complicated by numerous reordering algorithms and limited structural insights. To address this, we introduce a Graph Convolutional Network (GCN) model for classifying sparse matrix patterns common in power system analysis. The model, achieving 96% test accuracy, is validated using PV plant models of 125 MW capacities connected to New England 39-bus transmission system (TS), and further scaled to a 4,992-bus network with 384 PV plants, yielding 191, 616 × 191, 616 sized A matrix. For all cases, the GCN model accurately identifies the matrix’s intrinsic sparse pattern, demonstrating its potential to enhance solver performance in EMT analysis.

Hossain, Md Rifat [Florida International Universit↗

DOE OSTI2024

Event Detection and Classification Using Machine Learning Applied to PMU Data for the Western US Power System

Smart grid technology enhances our comprehension and reliability of the power grid, leveraging Phasor Measurement Unit (PMU) data—time-synchronized, high-frequency measurements gathered across the US power grid. This paper employs machine learning techniques to effectively analyze the vast PMU data in Wide Area Monitoring Systems (WAMS) for power grid event detection and classification. Analyzing several months of real-world PMU data, the paper focuses on machine learning for fast, precise event detection and classification, corroborated by utility event logs. Practical challenges like feature extraction, dimensionality reduction, and model selection are addressed. A novel feature yielding improved results is discovered, and a supplementary algorithm for detecting small power grid faults is developed. The final algorithm is validated using a month-long real PMU data set, demonstrating its capability in accurately identifying power grid events in near real-time.

machine learning, event detection, PMU↗

DOE OSTI2022

Verification of MOOSE/Bison's Heat Conduction Solver Using Combined Spatiotemporal Convergence Analysis

Bison is a computational physics code that uses the finite element method to model the thermo-mechanical response of nuclear fuel. Since Bison is used to inform high-consequence decisions, it is important that its computational results are reliable and predictive. One important step in assessing the reliability and predictive capabilities of a simulation tool is the verification process, which quantifies numerical errors in a discrete solution relative to the exact solution of the mathematical model. One step in the verification process—called code verification—ensures that the implemented numerical algorithm is a faithful representation of the underlying mathematical model, including partial differential or integral equations, initial and boundary conditions, and auxiliary relationships. In this paper, the code verification process is applied to spatiotemporal heat conduction problems in Bison. Simultaneous refinement of the discretization in space and time is employed to reveal any potential mistakes in the numerical algorithms for the interactions between the spatial and temporal components of the solution. For each verification problem, the correct spatial and temporal order of accuracy is demonstrated for both first- and second-order accurate finite elements and a variety of time-integration schemes. Furthermore, these results provide strong evidence that the Bison numerical algorithm for solving spatiotemporal problems reliably represents the underlying mathematical model in MOOSE. The selected test problems can also be used in other simulation tools that numerically solve for conduction or diffusion.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Tusqh

SAND2025-00675O Tusqh is a software tool that generates cubical meshes in 2D and 3D and computes the homology of these meshes using persistent homology. It includes a grid cell in the output if its volume-fraction is above a selectable threshold, estimated by sampling points within the cell. Tusqh incorporates anti-aliasing algorithms to mitigate grid orientation and scale effects. It is designed for creating finite element meshes for simulations and can be used in various applications such as heat diffusion, mechanical simulations, and computer graphics rendering. The software outputs meshes in an open format compatible with downstream software. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

SciDAC↗

DOE OSTI2026

Multi‐Scale Model‐Informed Deep Learning for Plasma‐Nanoparticle Interaction

The Overarching Goal of this proposed research is to understand and quantitively determine the interactions between non-thermal plasma (hot electrons, reactive radicals, vibrationally excited species) and surface reactions on influencing the activity and selectivity of the desired reactions via developing multi-scale model informed deep learning algorithm. Investigating non-thermal plasma-surface interaction is feasible due to the low bulk temperature in the discharge region. To investigate the role of plasma-nanoparticle interaction on enhancing the reaction kinetics, we will focus on ammonia cracking to generate clean hydrogen over earth-abundant, non-critical metallic nanoparticles, which is of great significance for decarbonization. We hypothesize that (1) reactive radicals interacting with surface reaction species via Eley–Rideal mechanism will significantly lower the energetics of the potential rate-limiting step of nitrogen formation; (2) the surface will be charged heterogeneously under non-thermal plasma conditions and the charged site will lower the energetics of ammonia cracking through Langmuir– Hinshelwood mechanism; (3) vibrationally excited ammonia will further promote the initial N-H bond cleavage. To access the hypothesis, we will (1) reveal the surface charge effects on tunning the reaction energetics via interpretable, physics-informed deep learning accelerated density functional theory (DFT) calculations; (2) determine the reactive radicals interacting with surface reaction species on tuning the reaction energetics via DFT; (3) reveal the surface charge effects on tunning the reaction energetics via DFT and deep learning models, (4) quantify how vibrationally excited species, reactive radicals, and surface charging effects on enhancing the catalysis via developing DFT-based microkinetic modeling (MKM) and active learning. Deep and active learning of plasma-nanoparticle interactions effects on enhancing ammonia cracking to generate hydrogen represents a new paradigm for designing high performance plasma materials. The fundamental science of how plasma-nanoparticle interactions will change the plasma kinetics and will improve the energy efficiency for decarbonization and sustainability. The interpretable and physics-informed machine learning model will accelerate low temperature plasma chemistry and material discovery with physics rules and model interpretation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2026

Neutrino Physics with Deep Learning on NOvA

The NOvA experiment has made both νμ \nu_\mu disappearance and νe \nu_e appearance measurements in Fermilab's NuMI beam, and is working on cross section measurements using near detector data. At the core of NOvA's measurements is the use of deep learning algorithms for identification and reconstruction of the neutrino flavor and energy. These algorithms, used for the first time on NOvA in 2016, yielded large improvements in selection efficiency, and will be applied to our first anti-neutrino results to be released this year. Presented here is the extension of our deep learning efforts for identification of neutrino signal events, final state identification, single particle tagging, and reconstruction using instance segmentation techniques. We will describe the new implementations of modified Convolutional Neural Networks for anti-neutrino events, single particles and their performance for analysis final states selection, standard candle measurements, and reconstruction.

Psihas, Fernanda [Indiana U.]↗

DOE OSTI2021

Unsupervised Resource Allocation with Graph Neural Networks

We present an approach for maximizing a global utility function by learning how to allocate resources in an unsupervised way. We expect interactions between allocation targets to be important and therefore propose to learn the reward structure for near-optimal allocation policies with a GNN. By relaxing the resource constraint, we can employ gradient-based optimization in contrast to more standard evolutionary algorithms. Our algorithm is motivated by a problem in modern astronomy, where one needs to select-based on limited initial information-among $10^9$ galaxies those whose detailed measurement will lead to optimal inference of the composition of the universe. Our technique presents a way of flexibly learning an allocation strategy by only requiring forward simulators for the physics of interest and the measurement process. We anticipate that our technique will also find applications in a range of resource allocation problems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Training reinforcement learning models via an adversarial evolutionary algorithm

When training for control problems, more episodes used in training usually leads to better generalizability, but more episodes also requires significantly more training time. There are a variety of approaches for selecting the way that training episodes are chosen, including fixed episodes, uniform sampling, and stochastic sampling, but they can all leave gaps in the training landscape. In this work, we describe an approach that leverages an adversarial evolutionary algorithm to identify the worst performing states for a given model. We then use information about these states in the next cycle of training; this process can be repeated until the desired level of model performance is met. We demonstrate this approach with the OpenAI Gym cart-pole problem. With this problem, we show that the adversarial evolutionary algorithm did not reduce the number of episodes required in training needed to attain model generalizability when compared with stochastic sampling, and actually performed slightly worse.

Coletti, Mark↗

DOE OSTI2022

Searching for Clues for a Matter Dominated Universe in Liquid Argon Time Projection Chambers

Liquid Argon Time Projection Chambers (LArTPCs) represent one of the most widely utilized neutrino detection techniques in neutrino experiments, for instance, in the Short Baseline Neutrino (SBN) program and the future large-scale LArTPC: Deep Underground Neutrino Experiment (DUNE). The high-end technique, facilitating excellent spatial and calorimetric reconstruction resolution, also enables testing exotic Beyond Standard Model (BSM) theories, such as baryon number violation (BNV) processes (e.g., proton-decay, neutron-antineutron oscillation). At the same time, Machine Learning (ML) techniques have demonstrated their ubiquitous use in recent decades; ML techniques have also become some of the most powerful tools in high-energy physics (HEP) analyses. Furthermore, the development of algorithms to cater to the needs of problems in HEP (i.e., triggering, reconstruction, improving sensitivity, etc.) has also become an active area of research. By developing a combined approach using Convolutional Neural Network (CNN) and Boosted Decision Tree (BDT) techniques, the sensitivity of neutron-antineutron oscillation in DUNE is evaluated for a projected exposure of 400kton·years. Additionally, to meet the triggering requirement to select such rare events in DUNE, such a search is only supported with highly efficient self-triggering algorithms. An ML-based self-triggering scheme for large-scale LArTPCs, such as DUNE, is also developed with the intention of implementation on field-programmable gate arrays (FPGAs). The ML-based approach for searching for neutron-antineutron oscillation can be demonstrated and validated on the current LArTPC MicroBooNE. The analysis in MicroBooNE represents the first-ever search for neutron-antineutron oscillation in a LArTPC. DUNE's projected 90% C.L. sensitivity to the neutron antineutron oscillation lifetime is 6.45×10³² years, assuming 1.327×10³⁵ neutron·years, equivalent to 10 years of DUNE far detector exposure (400kton·years). For MicroBooNE, assuming 372 seconds of exposure (equivalent to 3.13×10³⁶ neutron·years), the 90% C.L. lifetime sensitivity is found at 3.07×10²⁵ yrs, after accounting for Monte-Carlo statistical uncertainty and systematic uncertainty from detector effects.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Recovered supernova Ia rate from simulated LSST images

Aims.TheVera C. RubinObservatory’s Legacy Survey of Space and Time (LSST) will revolutionize time-domain astronomy by detecting millions of different transients. In particular, it is expected to increase the number of known type Ia supernovae (SN Ia) by a factor of 100 compared to existing samples up to redshift ∼1.2. Such a high number of events will dramatically reduce statistical uncertainties in the analysis of the properties and rates of these objects. However, the impact of all other sources of uncertainty on the measurement of the SN Ia rate must still be evaluated. The comprehension and reduction of such uncertainties will be fundamental both for cosmology and stellar evolution studies, as measuring the SN Ia rate can put constraints on the evolutionary scenarios of different SN Ia progenitors. Methods.We used simulated data from the Dark Energy Science Collaboration (DESC) Data Challenge 2 (DC2) and LSST Data Preview 0 to measure the SN Ia rate on a 15 deg 2 region of the “wide-fast-deep” area. We selected a sample of SN candidates detected in difference images, associated them to the host galaxy with a specially developed algorithm, and retrieved their photometric redshifts. We then tested different light-curve classification methods, with and without redshift priors (albeit ignoring contamination from other transients, as DC2 contains only SN Ia). We discuss how the distribution in redshift measured for the SN candidates changes according to the selected host galaxy and redshift estimate. Results.We measured the SN Ia rate, analyzing the impact of uncertainties due to photometric redshift, host-galaxy association and classification on the distribution in redshift of the starting sample. We find that we are missing 17% of the SN Ia, on average, with respect to the simulated sample. As 10% of the mismatch is due to the uncertainty on the photometric redshift alone (which also affects classification when used as a prior), we conclude that this parameter is the major source of uncertainty. We discuss possible reduction of the errors in the measurement of the SN Ia rate, including synergies with other surveys, which may help us to use the rate to discriminate different progenitor models.

Astronomy & Astrophysics↗

DOE OSTI2022

Learning Planar Ising Models Software

Learning Planar Ising Models is a software package written in Matlab for learning relationships among variable in a dataset using graphical models. The software package implements a generally-applicable algorithm for learning planar Ising models from any multivariate dataset. The code provides an algorithm for learning the best planar Ising model to approximate an arbitrary collection of binary random variables (possibly from sample data). Given the set of all pairwise correlations among variables, we select a planar graph and optimal planar Ising model defined on this graph to best approximate that set of correlations. The software includes demonstrations of the algorithm in simulations and for applications on publicly available datasets. Details of the algorithm, demonstration simulations, and applications are given in Johnson, et al; 2016. Reference: Johnson, J. K., Oyen, D., Chertkov, M., and Netrapalli, P. (2016). Learning planar Ising models. Journal of Machine Learning Research.

Oyen, Diane↗