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DOE OSTI2025

Statistical relationships across epigenomes using large-scale hierarchical clustering

Recent advances in genomics and sequencing platforms have revolutionized our ability to create immense data sets, particularly for studying epigenetic regulation of gene expression. However, the avalanche of epigenomic data is difficult to parse for biological interpretation given nonlinear complex patterns and relationships. This attractive challenge in epigenomic data lends itself to machine learning for discerning infectivity and susceptibility. In this study, we explore over 3000 epigenomes of uninfected individuals and provide a framework to characterize the relationships among epigenetic modifiers, their modifiers, genetic loci, and specific immune cell types across all chromosomes using hierarchical clustering. Hierarchical clustering of epigenomic data revealed consistent epigenetic patterns across chromosomes, demonstrating that variation due to epigenetic modifiers is greater than variation between cell types. Gene Ontology and KEGG pathway analyses indicated significant enrichment of genes involved in chromatin remodeling, mRNA splicing, immune responses, and the regulation of microRNAs and snoRNAs. Epigenetic modifiers frequently formed biologically relevant clusters, including the cohesin complex, RNA Polymerase II transcription factors, and PRC2 complex members. These clustering behaviors remained consistent across all chromosomes, supported by entropy analysis and high Adjusted Rand Index scores, indicating robust cross-chromosomal similarity. Co-occurrence analysis further revealed specific sets of modifiers that consistently appeared together within clusters, reflecting shared biological functions and interactions. Validation using another dataset confirmed the reproducibility of these clustering patterns and modifier co-occurrence relationships, underscoring the reliability and generalizability of the methodology.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Towards revealing intrinsic vortex-core states in Fe-based superconductors through statistical discovery

Abstract In type-II superconductors, electronic states within magnetic vortices hold crucial information about the paring mechanism and can reveal non-trivial topology. While scanning tunneling microscopy/spectroscopy (STM/S) is a powerful tool for imaging superconducting vortices, it is challenging to isolate the intrinsic electronic properties from extrinsic effects like subsurface defects and disorders. Here we combine STM/STS with basic machine learning to develop a method for screening out the vortices pinned by embedded disorder in iron-based superconductors. Through a principal component analysis of large STS data within vortices, we find that the vortex-core states in Ba(Fe 0.96 Ni 0.04 ) 2 As 2 start to split into two categories at certain magnetic field strengths, reflecting vortices with and without pinning by subsurface defects or disorders. Our machine-learning analysis provides an unbiased approach to reveal intrinsic vortex-core states in novel superconductors and shed light on ongoing puzzles in the possible emergence of a Majorana zero mode.

Guo, Yueming↗

DOE OSTI2025

Inference of the Mass Composition of Cosmic Rays with Energies from 10 18.5 to 10 20 eV Using the Pierre Auger Observatory and Deep Learning

We present measurements of the atmospheric depth of the shower maximum X max , inferred for the first time on an event-by-event level using the surface detector of the Pierre Auger Observatory. Using deep learning, we were able to extend measurements of the X max distributions up to energies of 100 EeV ( 10 20 eV ), not yet revealed by current measurements, providing new insights into the mass composition of cosmic rays at extreme energies. Gaining a 10-fold increase in statistics compared to the fluorescence detector data, we find evidence that the rate of change of the average X max with the logarithm of energy features three breaks at 6.5 ± 0.6 ( stat ) ± 1 ( syst ) EeV , 11 ± 2 ( stat ) ± 1 ( syst ) EeV , and 31 ± 5 ( stat ) ± 3 ( syst ) EeV , in the vicinity to the three prominent features (ankle, instep, suppression) of the cosmic-ray flux. The energy evolution of the mean and standard deviation of the measured X max distributions indicates that the mass composition becomes increasingly heavier and purer, thus being incompatible with a large fraction of light nuclei between 50 and 100 EeV. Published by the American Physical Society 2025

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Machine-learning-enabled on-the-fly analysis of RHEED patterns during thin film deposition by molecular beam epitaxy

Thin film deposition is a fundamental technology for the discovery, optimization, and manufacturing of functional materials. Deposition by molecular beam epitaxy (MBE) typically employs reflection high-energy electron diffraction (RHEED) as a real-time in situ probe of the growing film. However, the state-of-the-art for RHEED analysis during deposition requires human observation. Here, we present an approach using machine learning (ML) methods to monitor, analyze, and interpret RHEED images on-the-fly during thin film deposition. In the analysis workflow, RHEED pattern images are collected at one frame per second and featurized using a pretrained deep convolutional neural network. The feature vectors are then statistically analyzed to identify changepoints; these changepoints can be related to changes in the deposition mode from initial film nucleation to a transition regime, smooth film deposition, and in some cases, an additional transition to a rough, islanded deposition regime. The feature vectors are additionally analyzed via graph analysis and community classification. The graph is quantified as a stabilization plot, and we show that inflection points in the stabilization plot correspond to changes in the growth regime. The full RHEED analysis workflow is termed RHAAPsody and includes data transfer and output to a visual dashboard. We demonstrate the functionality of RHAAPsody by analyzing the precaptured RHEED images from epitaxial depositions of anatase TiO2 on SrTiO3(001) and show that the analysis workflow can be executed in less than 1 s. Our approach shows promise as one component of ML-enabled real-time feedback control of the MBE deposition process.

36 MATERIALS SCIENCE↗

DOE OSTI2026

V-HAMSTeR v1.0.0

V-HAMSTeR is a bioinformatics software tool designed to predict the hosts of viruses directly from genomic sequences. It can be used by researchers to predict animal, prokaryotic, plant, protist or fungal viral hosts including viruses that may be fragmented or discovered in environmental metagenomic datasets. Features & Uses: The software employs a novel dual-stream deep learning architecture that dynamically fuses implicit sequence embeddings from a genomic foundation model with 13 explicit, handcrafted biological features (e.g., coding density and strand switch rates). To ensure maximum reliability, V=HAMSTeR deploys a 5-fold deep ensemble calibrated via Joint Temperature Scaling, providing users with statistically rigorous confidence probabilities. It also features an automated sequence chunking and mean-pooling module to seamlessly process variable-length contigs. Advantages Over Similar Technologies: Existing tools (e.g., IPEV, RNAVirHost) typically rely on either basic k-mers or isolated neural networks. V-HAMSTeR's hybrid architecture captures both broad genomic context and specific biological motifs that standalone foundation models often miss. Furthermore, unlike competitor tools that struggle with incomplete data or exhibit extreme overconfidence, V-HAMSTeR is explicitly benchmarked and mathematically calibrated for fragmented assemblies (1kb–10kb). This makes it uniquely robust, accurate, and trustworthy for the messy reality of real-world environmental viromics.

Grigson, Susie [Lawrence Berkeley National Laborat↗

DOE OSTI2025

Multiscale ACI Satellite Database

The SATELLITE_EAGLES_PNNL NetCDF dataset contains a suite of satellite- and reanalysis-derived atmospheric and surface parameters on a regular latitude–longitude grid. The dataset includes core geophysical fields such as land fraction, aerosol optical depth at multiple wavelengths (465, 550, 667, and 865 nm), sea surface temperature, estimated inversion strength, and various thermodynamic and dynamic quantities (e.g., relative humidity, vertical velocity, boundary-layer height, and surface fluxes) from both MERRA and ERA reanalysis products, provided as daily-mean and instantaneous values. A major component of the dataset consists of MODIS-retrieved cloud microphysical properties, including cloud droplet number concentration, cloud effective radius, optical thickness, and liquid water path, provided for three compositing regimes (“All,” “Q06,” and “G18”). Corresponding cloud-top parameters—temperature, height, and pressure—along with total and domain-mean cloud fraction fields are also included. The file further integrates additional satellite data from AMSR-E (for cloud water, rain water, and surface precipitation retrievals) and CERES (for top-of-atmosphere radiative fluxes, cloud fractions, and albedo). This dataset is designed to evaluate aerosol–cloud interactions in warm clouds, emphasizing the use of MODIS for deriving cloud droplet number concentration and liquid water path statistics. The complementary satellite and reanalysis fields are co-located and time-matched to the same instantaneous MODIS observations, enabling consistent comparisons between cloud properties, aerosol loading, and large-scale meteorological conditions. The dataset is recently featured in Christensen et al. (2025), Machine Learning Reveals Strong Grid-Scale Dependence in the Satellite Nd–LWP Relationship, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2025-3850, 2025.

Christensen, Matthew [Pacific Northwest National L↗

DOE OSTI2025

Multiscale ACI Satellite Database

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Computing Nonlinear Power Spectra Across Dynamical Dark Energy Model Space with Neural ODEs

I show how to compute the nonlinear power spectrum across the entire $w(z)$ dynamical dark energy model space. Using synthetic ΛCDM data, I train a neural ordinary differential equation (ODE) to infer the evolution of the nonlinear matter power spectrum as a function of the background expansion and mean matter density across ∼9 Gyr of cosmic evolution. After training, the model generalises to any dynamical dark energy model parameterised by $w(z)$. With little optimisation, the neural ODE is accurate to within 4% up to $k = 5\, h\, {\mathrm Mpc}^{−1}$. Unlike simulation rescaling methods, neural ODEs naturally extend to summary statistics beyond the power spectrum that are sensitive to the growth history.

cosmology↗

DOE OSTI2026

Short-term electricity load forecasting: Application-driven evaluation of machine learning models across spatial and temporal scales

As we transition towards a decarbonized economy, the integration of variable renewable energy resources and new demands (e.g., electric vehicles, heat pumps) into the electricity grid places unprecedented pressure on grid operators to effectively anticipate and manage peak load. In this context, machine learning algorithms are proving to be indispensable for accurate short-term load forecasting, a crucial task to address these challenges. This study benchmarks 6 machine learning algorithms, including three neural networks and three tree-based algorithms, across various levels of spatial aggregation and time horizons (1, 4, 8, 24, and 48 h). The central contribution of this work is the comparison and analysis of load forecasting models not only based on statistical metrics, but also based on a novel error metric, which evaluates the cost implications of forecast errors for power system stakeholders. Results show that tree-based models outperform neural networks, based on statistical metrics, and yield less skewed error distributions for most spatial scales. However, through the lens of the novel error metric, neural networks are the more competitive choice, especially for forecast horizons that exceed 8 h. The study concludes with actionable recommendations to grid operators and highlights the need for the development of error metrics that link forecasting accuracy to operational costs. To promote transparency and open science, the datasets and Python code are open-sourced via a supplementary repository.

Houben, Nikolaus↗

DOE OSTI2026

RU-net for automatic characterization of TRISO fuel cross sections

During irradiation, phenomena such as kernel swelling and buffer densification may impact the performance of tristructural isotropic (TRISO) particle fuel. Post-irradiation microscopy is often used to identify these irradiation-induced morphologic changes. However, each fuel compact generally contains thousands of TRISO particles. Manually performing the work to get statistical information on these phenomena is cumbersome and subjective. Here, to reduce the subjectivity inherent in that process and to accelerate data analysis, we used convolutional neural networks (CNNs) to automatically segment cross-sectional images of microscopic TRISO layers. CNNs are a class of machine-learning algorithms specifically designed for processing structured grid data. They have gained popularity in recent years due to their remarkable performance in various computer vision tasks, including image classification, object detection, and image segmentation. In this research, we generated a large irradiated TRISO layer dataset with more than 2,000 microscopic images of cross-sectional TRISO particles and the corresponding annotated images. Based on these annotated images, we used different CNNs to automatically segment different TRISO layers. These CNNs include RU-Net (developed in this study), as well as three existing architectures: U-Net, Residual Network (ResNet), and Attention U-Net. The preliminary results show that the model based on RU-Net performs best in terms of Intersection over Union (IoU). Using CNN models, we can expedite the analysis of TRISO particle cross sections, significantly reducing the manual labor involved and improving the objectivity of the segmentation results.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

DiffESM: Conditional Emulation of Temperature and Precipitation in Earth System Models With 3D Diffusion Models

Earth system models (ESMs) are essential for understanding the interaction between human activities and the Earth's climate. However, the computational demands of ESMs often limit the number of simulations that can be run, hindering the robust analysis of risks associated with extreme weather events. While low-cost climate emulators have emerged as an alternative to emulate ESMs and enable rapid analysis of future climate, many of these emulators only provide output on at most a monthly frequency. This temporal resolution is insufficient for analyzing events that require daily characterization, such as heat waves or heavy precipitation. We propose using diffusion models, a class of generative deep learning models, to effectively downscale ESM output from a monthly to a daily frequency. Trained on a handful of ESM realizations, reflecting a wide range of radiative forcings, our DiffESM model takes monthly mean precipitation or temperature as input, and is capable of producing daily values with statistical characteristics close to ESM output. Combined with a low-cost emulator providing monthly means, this approach requires only a small fraction of the computational resources needed to run a large ensemble. We evaluate model behavior using a number of extreme metrics, showing that DiffESM closely matches the spatio-temporal behavior of the ESM output it emulates in terms of the frequency and spatial characteristics of phenomena such as heat waves, dry spells, or rainfall intensity.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Generic and ML Workloads in an HPC Datacenter: Node Energy, Job Failures, and Node-Job Analysis

HPC datacenters offer a backbone to the modern digital society. Increasingly, they run Machine Learning (ML) jobs next to generic, compute-intensive workloads, supporting science, business, and other decision-making processes. However, understanding how ML jobs impact the operation of HPC datacenters, relative to generic jobs, remains desirable but understudied. In this work, we leverage long-term operational data, collected from a national-scale production HPC datacenter, and statistically compare how ML and generic jobs can impact the performance, failures, resource utilization, and energy consumption of HPC datacenters. Our study provides key insights, e.g., ML-related power usage causes GPU nodes to run into temperature limitations, median/mean runtime and failure rates are higher for ML jobs than for generic jobs, both ML and generic jobs exhibit highly variable arrival processes and resource demands, significant amounts of energy are spent on unsuccessfully terminating jobs, and concurrent jobs tend to terminate in the same state. We open-source our cleaned-up data traces on Zenodo (https://doi. org/10.5281/zenodo.13685426), and provide our analysis toolkit as software hosted on GitHub (https://github.com/atlarge-research/2024-icpads-hpc-workload-characterization). This study offers multiple benefits for data center administrators, who can improve operational efficiency, and for researchers, who can further improve system designs, scheduling techniques, etc.

crossanalysis↗

DOE OSTI2024

Learning new physics from data: A symmetrized approach

Thousands of person years have been invested in searches for new physics (NP), the majority of them motivated by theoretical considerations. Yet, no evidence of beyond the Standard Model physics has been found. This suggests that model-agnostic searches might be an important key to explore NP, and help discover unexpected phenomena which can inspire future theoretical developments. A possible strategy for such searches is identifying asymmetries between data samples that are expected to be symmetric within the Standard Model. We propose exploiting neural networks (NNs) to quickly fit and statistically test the differences between two samples. Our method is based on an earlier work, originally designed for inferring the deviations of an observed dataset from that of a much larger reference dataset. We present a symmetric formalism, generalizing the original one, avoiding fine-tuning of the NN parameters and any constraints on the relative sizes of the samples. Our formalism could be used to detect small symmetry violations, extending the discovery potential of current and future particle physics experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Deep learning-based predictive models for laser direct drive at the Omega Laser Facility

The rich and complex physics of inertial confinement fusion provides a unique and challenging space for high-fidelity first-principles modeling. Consequently, simulation codes that are used to design experiments are computationally expensive and lack the predictive capability required for extensive parameter exploration in search of a high-performing design for laser direct drive. In this article, we present two deep-learning-based predictive models intended to address these difficulties. The first model (TL DNN) acts as a fast emulator of simulations as well as experiments at the Omega Laser Facility. This model is trained on a simulation database and subsequently calibrated on experimental data using transfer learning. To facilitate the development of this model, an autoencoder is developed to reduce the dimensionality of the input space by compressing the laser pulse input. The model predicts key experimental scalar observables of Omega experiments with high accuracy and minimal computational cost. This deep neural net enables rapid exploration of a high-dimensional input parameter space for an optimal implosion design. The second model (DNN SM+) aims to extend the statistical modeling work of Lees et al. [Phys. Rev. Lett. 127, 105001 (2021)], by increasing the complexity of the model space and allowing for coupling between degradation terms. Since the model capacity of DNN SM+ is higher than the model of Lees et al., DNN SM+ can potentially provide an improvement in predictive capability, and we use this model to provide insight into complicated degradation dependencies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Observation of 𝑡⁢𝑊⁢𝑍 Production at the CMS Experiment

The first observation of single top quark production in association with a 𝑊 and a 𝑍 boson in proton-proton collisions is reported. The analysis uses data at center-of-mass energies of 13 and 13.6 TeV recorded with the CMS detector at the CERN LHC, corresponding to a total integrated luminosity of 200 fb −1 . Events with three or four charged leptons, which can be electrons or muons, are selected. Advanced machine-learning algorithms and improved reconstruction methods, compared to an earlier analysis, result in an unprecedented sensitivity to 𝑡⁢𝑊⁢𝑍 production. The measured cross sections for 𝑡⁢𝑊⁢𝑍 production are 248 ± 52 fb and 242 ± 77 fb for $\sqrt{s}$ =13 and 13.6 TeV, respectively. The signal is established with a statistical significance of 5.8 standard deviations, with 3.5 expected, compared to the background-only hypothesis.

Hayrapetyan, Aram [Yerevan Physics Institute]↗

DOE OSTI2024

Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography

The dysfunction of α and β cells in pancreatic islets can lead to diabetes. Many questions remain on the subcellular organization of islet cells during the progression of disease. Existing three-dimensional cellular mapping approaches face challenges such as time-intensive sample sectioning and subjective cellular identification. To address these challenges, we have developed a subcellular feature-based classification approach, which allows us to identify α and β cells and quantify their subcellular structural characteristics using soft X-ray tomography (SXT). We observed significant differences in whole-cell morphological and organelle statistics between the two cell types. Additionally, we characterize subtle biophysical differences between individual insulin and glucagon vesicles by analyzing vesicle size and molecular density distributions, which were not previously possible using other methods. These sub-vesicular parameters enable us to predict cell types systematically using supervised machine learning. We also visualize distinct vesicle and cell subtypes using Uniform Manifold Approximation and Projection (UMAP) embeddings, which provides us with an innovative approach to explore structural heterogeneity in islet cells. This methodology presents an innovative approach for tracking biologically meaningful heterogeneity in cells that can be applied to any cellular system.

3D cell mapping↗

DOE OSTI2024

Comparative study of machine learning techniques for post-combustion carbon capture systems

Computational analysis of countercurrent flows in packed absorption columns, often used in solvent-based post-combustion carbon capture systems (CCSs), is challenging. Typically, computational fluid dynamics (CFD) approaches are used to simulate the interactions between a solvent, gas, and column's packing geometry while accounting for the thermodynamics, kinetics, heat, and mass transfer effects of the absorption process. These simulations can then be used explain a column's hydrodynamic characteristics and evaluate its CO 2 -capture efficiency. However, these approaches are computationally expensive, making it difficult to evaluate numerous designs and operating conditions to improve efficiency at industrial scales. In this work, we comprehensively explore the application of statistical ML methods, convolutional neural networks (CNNs), and graph neural networks (GNNs) to aid and accelerate the scale-up and design optimization of solvent-based post-combustion CCSs. We apply these methods to CFD datasets of countercurrent flows in absorption columns with structured packings characterized by several geometric parameters. We train models to use these parameters, inlet velocity conditions, and other model-specific representations of the column to estimate key determinants of CO 2 -capture efficiency without having to simulate additional CFD datasets. We also evaluate the impact of different input types on the accuracy and generalizability of each model. We discuss the strengths and limitations of each approach to further elucidate the role of CNNs, GNNs, and other machine learning approaches for CO 2 -capture property prediction and design optimization.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

A Method for Producing Hierarchical and Statistically Calibrated Predictions of Nuclear Material Properties from Existing Models

Computer vision-based analysis of micrographs of nuclear materials is an emerging technique for property prediction, synthetic route identification, and other material analysis tasks. These analysis tasks play a pivotal role in many material characterization applications such as signature development for treaty verification, process optimization, etc. The backbone in many of the recent computer vision-based techniques is a deep learning model, which takes a fixed-size set of pixels and provides a class prediction for that set of pixels. For example, previous work developed a deep convolutional neural network (CNN) to predict the synthetic route from a 256 px x 256 px patch taken from a larger image of uranium ore concentrates. In this work, we present several methods for first calibrating these models in a manner that they can provide accurate probabilities of their predictions’ veracity, and several methods of combining these probabilities. Overall, the combination of these two steps into a pipeline allows for full-image and even full-sample (where a sample has many images) predictions with associated confidence values. Finally, we show that one can also use the patch predictions and confidence to produce a visualization to map predicted constituents through the image. Results and examples for predicting and mapping uranium ore concentrates’ synthetic process from imagery will be presented.

artificial intelligence↗