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DOE OSTI2025

Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification

Accurate metagenomic classification relies on comprehensive, up-to-date, and validated reference databases. While the NCBI BLAST Nucleotide (nt) database, encompassing a vast collection of sequences from all domains of life, represents an invaluable resource, its massive size—currently exceeding 10 12 nucleotides—and exponential growth pose significant challenges for researchers seeking to maintain current nt-based indices for metagenomic classification. Recognizing that no current nt-based indices exist for the widely used Centrifuge classifier, and the last public version currently available was released in 2018, we addressed this critical gap by leveraging advanced high-performance computing resources. We present new Centrifuge-compatible nt databases, meticulously constructed using a novel pipeline incorporating different quality control measures, including reference decontamination and filtering. These measures demonstrably reduce spurious classifications, as shown through our reanalysis of published metagenomic data where Plasmodium annotations were dramatically reduced using our decontaminated database, highlighting how database quality can significantly impact research conclusions. Through temporal comparisons, we also reveal how our approach minimizes inconsistencies in taxonomic assignments stemming from asynchronous updates between public sequence and taxonomy databases. These discrepancies are particularly evident in taxa such as Listeria monocytogenes and Naegleria fowleri, where classification accuracy varied significantly across database versions. These new databases, made available as pre-built Centrifuge indexes, respond to the need for an open, robust, nt-based pipeline for taxonomic classification in metagenomics. Applications such as environmental metagenomics, forensics, and clinical metagenomics, which require comprehensive taxonomic coverage, will benefit from this resource. Our work highlights the importance of treating reference databases as dynamic entities, subject to ongoing quality control and validation akin to software development best practices. This approach is crucial for ensuring accuracy and reliability of metagenomic analysis, especially as databases continue to expand in size and complexity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Semi-Automatic Geographic Information System Framework for Creating Photo-Realistic Digital Twin Cities to Support Autonomous Driving Research

Digital twin cities are frequently used in vehicle and traffic simulations to render realistic on-road driving scenarios under various traffic and environmental conditions. These digital twins provide a high-fidelity replica of the physical world (e.g., buildings, roads, infrastructures, traffic) to create three-dimensional (3D) virtual-physical environments to support various emerging vehicle and transportation technologies such as connected and automated vehicles. These virtual environments provide a cost-effective digital proving ground to evaluate, validate, and test emerging technologies that include control algorithms, localization, perception, and sensors. Replicating a real-world traffic scenario in a digital twin using a traditional 3D modeling approach is a time-consuming and labor-intensive effort. Here this paper presents a semi-automated spatial framework to construct realistic 3D digital twin cities to support autonomous driving research using readily available geographic information system (GIS) data and 3D prefabricated (prefab) models. We start with a comprehensive review of geospatial data sources of essential digital entities required in a 3D digital twin city and present an integrated GIS-3D modeling pipeline using customized QGIS/GDAL and Blender scripting in Python. The pipeline outputs are realistic 3D digital twin cities compatible with common vehicle simulation software, such as CARLA and IPG CarMaker. The paper closes with a showcase to demonstrate the quality and usability of a digital twin city created to replicate the Shallowford Road corridor in Chattanooga in both Unity and Unreal engine-based virtual environment. The generated digital twin city can be applied to a hardware-in-the-loop simulation environment with an actual testing vehicle to facilitate autonomous driving research.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2023

Building a Computational and Experimental Rapid Response Pipeline to Counter the Coronavirus Disease 2019 Outbreak and Emerging Biothreats

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs, especially where protective candidates can be rapidly identified or developed for emerging biothreats and escape variants. Current cutting-edge technologies for this purpose still rely on pathogen-exposed convalescent volunteers and a large screening effort to find a proverbial needle in a haystack. Computational design of protective antibodies based on pre-existing templates skips those requirements and allows for greater control over the breadth and target epitope, while also co-optimizing for potency and developability or other biophysical characteristics. We approached this problem by building and expanding an in vitro experimental rapid antibody production and characterization pipeline to support development of an autonomous, closed loop, active learning software system based on structural simulation and ground truth experimental data to design and evaluate antibody antigen interactions. Starting from early in the pandemic, we targeted SARS-CoV-2, the causative agent of COVID-19, by re-purposing neutralizing antibodies against SARS-CoV-1 that had been identified in the wake of that outbreak in the early 2000’s. We successfully re-targeted three different anti-SARS-CoV-1 antibodies to neutralize SARS-CoV-2 in vitro, where the antibodies were generated externally and tested through conventional binding and neutralization assays internally or with collaborators. As antibodies were identified from the blood of humans infected with SARS-CoV-2, we shifted to collaborate with academic partners to develop improved versions of their human-derived antibodies. This work reached its most important stage in rapid response to the emergence of the Omicron variant of concern (VOC) in late 2021. In a matter of weeks, enabled by on demand innovation to our screening pipeline, we computationally designed and experimentally characterized derivative antibodies of COV2-2130, one of two antibodies from Vanderbilt that form the basis of the AstraZeneca Evusheld prophylactic drug product. This drug product suffers a serious loss of efficacy against Omicron BA.1 and BA.1.1, the first Omicron strains. Due to tight integration of computational design and experimental evaluation, we were able to identify a pair of designs with potent neutralization of the main targets Omicron BA.1 and BA.1.1; but also the earlier Delta variant, and subsequent Omicron strains including BA.2, BA.4, BA.5, and BA.2.75, demonstrating that our multi-target design process can, by its nature, produce robust antibody designs that strictly improve over the parental antibody. These results, recognized by a 2022 Director’s Science and Technology award, have enabled the follow-on GUIDE program, to commence in FY23. While earlier design campaigns were substantially outsourced, we have engineered better and faster processes internally to better compliment, calibrate, and speed computational designs. As part of the follow-on GUIDE program, we will stand up a rapid and high-throughput antibody production and characterization facility staffed with the expertise and capabilities to foster our current collaboration across PLS and ENG as well as other partnerships toward computational design of biologics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Alabama Carbon Storage: Bringing Data to the People

The Gulf Coastal Plain of Alabama has proven potential for geologic carbon storage and current interest in the area for large carbon capture and storage (CCS) projects is high. Extensive CCS relevant data exist in the records of the Geological Survey of Alabama and State Oil and Gas Board of Alabama, however, most of this data is not publicly available or is scattered in separate databases, file cabinets, and tables in publications. The “Alabama Carbon Storage: Data Sharing and Engagement” (ACS-DSE) project seeks to accelerate the responsible development of large CCS projects in the Gulf Coastal Plain of Alabama and offshore in state waters through a publicly accessible database of geologic carbon storage models and data across the region. The ACS-DSE draws on the over 150 years of geologic research and over 20 years of experience in CCS research to place relevant geologic, geophysical, and infrastructure data on a single web platform. Datasets available will include formation depths and elevations, geologic structures, reservoir properties, digital well logs (LAS files), existing penetrations, and geologic models. In addition to downloadable datasets, links to CCS related regulatory agencies and other sources of information will be included (for example, Class VI UIC permitting regulations and pipeline regulations). By making these datasets and models available in commonly used formats on a public website, the project will increase transparency in decision making and decrease the data acquisition time for industry.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2026

Final technical report for DE-SC0022255: Discovering Physically Meaningful Structures from Climate Extreme Data

The past two decades have witnessed natural disasters and extreme weather events that affect millions of people. At the same time, the data volume from high-resolution climate models, satellite, in-situ and ground-based measurements have substantially increased to petabyte scales. These new and readily accessible datasets create the previously missing pipeline required for scientific machine learning (ML) and therefore new opportunities for improved understanding and prediction capability of climate extreme events. This project developed a deep latent variable model framework to discover physically meaningful hidden structures from high-dimensional, spatiotemporal climate extreme data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Two-stage formation-energy correction (NbZr, TaZr, VZr)

This bundle contains the scripts, the raw and corrected per-structure data, and the manuscript plots for the NbZr / TaZr / VZr BCC binary formation energies and the associated RMSDs. Why a two-stage correction is necessary: The "raw" formation energy of every relaxed VASP configuration is computed in the usual way, FE_raw(c) = E_alloy(c) - sum_i x_i * E_pure_i , where E_pure_i are the per-atom total energies of the pure-element reference structures (Nb, Ta, V, Zr in the same BCC supercell, with identical INCAR / KPOINTS / PAW choices). With perfectly consistent reference runs the raw FE should vanish at the two pure-element endpoints (x = 0 and x = 1) by construction. In practice this does not hold for two reasons that are present in our dataset: 1. Reference-energy inconsistency (composition-dependent bias). Even with identical input parameters, the pure-element runs (stored in `corrected_DFT_pure_element_runs/`) differ slightly from the values that would be implied by the alloy runs at near-pure compositions (a few meV/atom). This bias is approximately linear in concentration, because the residual error in E_pure_Nb (or E_pure_Ta / E_pure_V) propagates into FE_raw(c) as (1 - x) * dE_pure_1, and the corresponding error in E_pure_Zr propagates as x * dE_pure_2. Left uncorrected, this produces a non-physical "tilt" of FE_raw(x) and shifts the entire FE-vs-x cloud away from zero at the endpoints. 2. Endpoint anchoring against the audited true endpoints. The strict endpoint values (FE_x0_meVatom, FE_x1_meVatom in `corrected_fe_strict_endpoints_20260518/strict_endpoint_check_20260518.csv`) were re-derived from an independent cross-check of the pure-element runs. After stage 1 removes the linear bias, the near-pure compositions in the alloy dataset still extrapolate to values that differ slightly from these audited endpoints — because stage 1 is fit from a few near-end alloy bins, not from the audited pure-element references themselves. The README.txt file discusses how these issues are addressed by the two-stage correction, and describes folder layout, pipeline summary, and how to re-run.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Automated electrosynthesis reaction mining with multimodal large language models (MLLMs)

Leveraging the chemical data available in legacy formats such as publications and patents is a significant challenge for the community. Automated reaction mining offers a promising solution to unleash this knowledge into a learnable digital form and therefore help expedite materials and reaction discovery. However, existing reaction mining toolkits are limited to single input modalities (text or images) and cannot effectively integrate heterogeneous data that is scattered across text, tables, and figures. In this work, we go beyond single input modalities and explore multimodal large language models (MLLMs) for the analysis of diverse data inputs for automated electrosynthesis reaction mining. We compiled a test dataset of 65 articles (MERMES-T24 set) and employed it to benchmark five prominent MLLMs against two critical tasks: (i) reaction diagram parsing and (ii) resolving cross-modality data interdependencies. The frontrunner MLLM achieved ≥96% accuracy in both tasks, with the strategic integration of single-shot visual prompts and image pre-processing techniques. We integrate this capability into a toolkit named MERMES (multimodal reaction mining pipeline for electrosynthesis). Our toolkit functions as an end-to-end MLLM-powered pipeline that integrates article retrieval, information extraction and multimodal analysis for streamlining and automating knowledge extraction. This work lays the groundwork for the increased utilization of MLLMs to accelerate the digitization of chemistry knowledge for data-driven research.

Leong, Shi Xuan↗

DOE OSTI2024

Reduced Order Model for Guided Wave Propagation on Gas Pipelines to Enable Real-Time Simulation

Reduced order model for simulation of Guided wave propagation is presented here. The utilization of reduced order models ensures efficient data generation for a variety of parameters where it takes huge computational effort to simulate, crucial for timely monitoring and decision-making. Autoencoder based reduced order models are proposed here, which are trained on simulated data from open-source finite element framework, Firedrake.

Bukka, Sandeep Reddy↗

DOE OSTI2024

Reduced Order Model for Guided Wave Propagation on Gas Pipelines to Enable Real-Time Simulation

Bukka, Sandeep Reddy↗

DOE OSTI2020

Policy Considerations When Federating Facilities for Experimental and Observational Data Analysis

Today’s computational, experimental, and observational facilities afford us tremendous opportunities to couple theory and experiment at increasingly large scales. Empirical sensing capabilities are growing dramatically with beam line and detector improvements, and with advances in our ability to deploy large-scale data gathering observations of the natural world. The coupling of computational simulations and analysis to process the data from experimental and observational facilities is giving rise to cross-facility workflows. Such federations of facilities are in fact becoming an explicit requirement for large-scale scientific discovery. As we scale up these pipelines of scientific discovery, each participating facility needs to establish and align policies so that the federation can work seamlessly in an end-to-end manner. This chapter outlines specific policy considerations in enabling the federation of facilities for data analysis. Design choices and vital policy decisions cover the areas of data acquisition and storage, data transfer, computational resource allocation and co-scheduling, seamless federated user access, and cross-cutting governance. By highlighting the explicit and implicit interdependencies between facilities, we aim to provide facility designers and policymakers the information on policy issues to address early in a facility’s operations, thus enabling successful cross-facility federation and improved experimental and observational data analysis outcomes.

Shankar, Mallikarjun (Arjun)↗

DOE OSTI2022

A multi-modal scanning system to digitize CBRNE emergency response scenes

A handheld system developed to digitize a contextual understanding of the scene at a chemical, biological, radiological, nuclear and/or explosives (CBRNE) events is described. The system uses LiDAR and cameras to create a colorized 3D model of the environment, which helps domain experts that are supporting responders in the field. To generate the digitized model, a responder scans any suspicious objects and the surroundings by carrying the system through the scene. The scanning system provides a real-time user interface to inform the user about scanning progress and to indicate any areas that may have been missed either by the LiDAR sensors or the cameras. Currently, the collected data are post-processed on a different device, building a colorized triangular mesh of the encountered scene, with the intention of moving this pipeline to the scanner at a later point. The mesh is sufficiently compressed to be sent over a reduced bandwidth connection to a remote analyst. Furthermore, the system tracks fiducial markers attached to diagnostic equipment that is placed around the suspicious object. The resulting tracking information can be transmitted to remote analysts to further facilitate their supporting efforts. The paper will discuss the system's design, software components, the user interface used for scanning a scene, the necessary procedures for calibration of the sensors, and the processing steps of the resulting data. The discussion will close by evaluating the system's performance on 11 scenes.

Salathe, Marco↗

DOE OSTI2022

A multi-modal scanning system to digitize CBRNE emergency response scenes

Prins, Nicholas↗

DOE OSTI2022

Computational models of direct and indirect X‐ray breast imaging detectors for in silico trials

Abstract Background To facilitate in silico studies that investigate digital mammography (DM) and breast tomosynthesis (DBT), models replicating the variety in imaging performance of the DM and DBT systems, observed across manufacturers are needed. Purpose The main purpose of this work is to develop generic physics models for direct and indirect detector technology used in commercially available systems, with the goal of making them available open source to manufacturers to further tweak and develop the exact in silico replicas of their systems. Methods We recently reported on an in silico version of the SIEMENS Mammomat Inspiration DM/DBT system using an open‐source GPU‐accelerated Monte Carlo x‐ray imaging simulation code (MC‐GPU). We build on the previous version of the MC‐GPU codes to mimic the imaging performances of two other Food and Drug Administration (FDA)‐approved DM/DBT systems, such as Hologic Selenia Dimensions (HSD) and the General Electric Senographe Pristina (GSP) systems. In this work, we developed a hybrid technique to model the optical spread and signal crosstalk observed in the GSP and HSD systems. MC simulations are used to track each x‐ray photon till its first interaction within the x‐ray detector. On the other hand, the signal spread in the x‐ray detectors is modeled using previously developed analytical equations. This approach allows us to preserve the modeling accuracy offered by MC methods in the patient body, while speeding up secondary carrier transport (either electron–hole pairs or optical photons) using analytical equations in the detector. The analytical optical spread model for the indirect detector includes the depth‐dependent spread and collection of optical photons and relies on a pre‐computed set of point response functions that describe the optical spread as a function of depth. To understand the capabilities of the computational x‐ray detector models, we compared image quality metrics like modulation transfer function (MTF), normalized noise power spectrum (NNPS), and detective quantum efficiency (DQE), simulated with our models against measured data. Please note that the purpose of these comparisons with measured data would be to gauge if the model developed as part of this work could replicate commercially used direct and indirect technology in general and not to achieve perfect fits with measured data. Results We found that the simulated image quality metrics such as MTF, NNPS, and DQE were in reasonable agreement with experimental data. To demonstrate the imaging performance of the three DM/DBT systems, we integrated the detector models with the VICTRE pipeline and simulated DM images of a fatty breast model containing a spiculated mass and a calcium oxalate cluster. In general, we found that the images generated using the indirect model appeared more blurred with a different noise texture and contrast as compared to the systems with direct detectors. Conclusions We have presented computational models of three commercially available FDA‐approved DM/DBT systems, which implement both direct and indirect detector technology. The updated versions of the MC‐GPU codes that can be used to replicate three systems are available in open source format through GitHub.

Sengupta, Aunnasha↗

DOE OSTI2022

Photometric redshift-aided classification using ensemble learning

We present SHEEP, a new machine learning approach to the classic problem of astronomical source classification, which combines the outputs from the XGBoost, LightGBM, and CatBoost learning algorithms to create stronger classifiers. A novel step in our pipeline is that prior to performing the classification, SHEEP first estimates photometric redshifts, which are then placed into the data set as an additional feature for classification model training; this results in significant improvements in the subsequent classification performance. SHEEP contains two distinct classification methodologies: (i) Multi-class and (ii) one versus all with correction by a meta-learner. We demonstrate the performance of SHEEP for the classification of stars, galaxies, and quasars using a data set composed of SDSS and WISE photometry of 3.5 million astronomical sources. The resulting F1 -scores are as follows: 0.992 for galaxies; 0.967 for quasars; and 0.985 for stars. In terms of the F1-scores for the three classes, SHEEP is found to outperform a recent RandomForest-based classification approach using an essentially identical data set. Our methodology also facilitates model and data set explainability via feature importances; it also allows the selection of sources whose uncertain classifications may make them interesting sources for follow-up observations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Accelerating Advanced Light Source Science Through Multi-Facility HPC Workflows

Synchrotron light sources support a wide array of techniques to investigate materials, often producing complex, high-volume data that challenge traditional workflows. At the Advanced Light Source (ALS), we developed infrastructure to move microtomography data over ESnet to ALCF and NERSC, where CPU- and GPU-based algorithms generate 3D reconstructed volumes of experimental samples. We employ two data movement and reconstruction models: real-time processing as data streams directly to NERSC compute nodes, and automated file transfer to NERSC and ALCF file systems. The streaming pipeline provides users with feedback in under ten seconds, while the file-based workflow produces high-quality reconstructions suitable for deeper analysis in 20-30 minutes. This infrastructure enables users to utilize HPC resources without direct access to backend systems. We plan to extend this architecture to more endstations, supporting our beamline scientists and users.

Abramov, David↗

DOE OSTI2024

Machine Learning Automation Pipeline

Machine Learning Automation Pipeline (MLAP) is a package to perform machine learning (ML) analysis in a step by step manner, starting with data extraction until analysis and prediction. The scripts provide the users option to chose an action such as "Extract", "Prep", and "Train" and numerous cases can be launched with just a single command. The inputs for each case are provided using a JSON file. The simulation results of several cases can be assessed using an automated process and analyzed for various metrics pertinent to ML analysis.

Jha, Pankaj↗

DOE OSTI2023

The Dark Energy Survey Six-Year Calibration Star Catalog

This Technical Note presents a catalog of calibrated reference stars that was generated by the Forward Calibration Method (FGCM) pipeline (arXiv:1706.01542) as part of the FGCM photometric calibration of the full Dark Energy Survey (DES) 6-Year data set (Y6). This catalog provides DES grizY magnitudes for 17 million stars with i-band magnitudes mostly in the range 16 < i < 21 spread over the full DES footprint covering 5000 square degrees over the Southern Galactic Cap at galactic latitudes b < -20 degrees (plus a few outlying fields disconnected from the main survey footprint). These stars are calibrated to a uniformity of better than 1.8 milli-mag (0.18%) RMS over the survey area. The absolute calibration of the catalog is computed with reference to the STISNIC.007 spectrum of the Hubble Space Telescope CalSpec standard star C26202; including systematic errors, the absolute flux system is known at the approximately 1% level. As such, these stars provide a useful reference catalog for calibrating grizY-band or grizY-like band photometry in the Southern Hemisphere, particularly for observations within the DES footprint.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Using Large Language Models to help customers monitor global threat data

Large Language Models have proven adept at answering general knowledge questions. To make these generative AI tools useful to our mission customers for monitoring global threats, the data sciences team at Sandia is utilizing retrieval augmented generation (RAG) techniques to customize these models with local data. The local data we use consists of data such as research articles and patent abstracts that we've collected over the last several years using automated pipelines.

Herzer, John Andrew [Sandia National Laboratories ↗