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Application of ML/AI for Identifying Earth Science Datasets in Research Publications

NASA Data Active Archive Centers, or DAACs, ingest, store and distribute data acquired from satellites, ground systems as well as modelling data. These data are organized by the datasets, each presenting collection of files usually associated with the certain mission, instrument, processing level, parameter(s), algorithm and/or model. The number of datasets offered by a single DAAC to the public varies. GES DISC, for example, currently offers for public use approximately ~1,300 datasets. While each publicly offered dataset comes with supporting documentation, it is challenging for novice and even experienced scientists to navigate among the datasets that offer similar parameters to find the datasets for their particular research application. Supplying dataset documentation with the scientific paper citations that refer to that dataset provides means for the dataset users to educate themselves with the application research that dataset is being used in. Collecting citations of the papers that use the datasets for their research yield valuable insights into application areas of those datasets, information about usage of the dataset groups for specific applications and those application topics. It also gives insights into the “deep metrics” of the dataset usage, as opposed to the common metrics of the dataset usage such as number of users who downloaded the dataset files and volumes of downloaded data. Association of a certain scientific paper with the dataset(s) presents a challenge because most of the paper authors do not properly cite the datasets, datasets usually have cryptic names and Digital Object Identifiers (DOIs) that are used for dataset identification were assigned to the datasets only few years ago. Simple Google or online library search do not provide even meaningful fraction of the results when performed by the dataset name or DOI, however they provide too many results when the search is done by more broader terms such as mission and instrument names. Attempts to create an AI system capable to identify dataset in the scientific papers have already been made using neural networks classifiers on the basis of the dataset mission, instrument and variable name. This method was applied to NASA SEDAC, which has 41 datasets in total. In GES DISC there can be as many as ~100 datasets per mission/instrument with some of the datasets consisting of multiple variables so there is a need for more differentiating parameters for dataset identification in the paper. The approach we are currently investigating is creating AI classifiers that are based on multiple dataset features, or keywords, extracted from the NASA Earthdata Common Dataset Repository (CMR). The features are weighted based on how precisely they can identify a dataset. The classifier uses preprocessed paper text as input and searches for the CMR datasets whose feature sets are the closest to the feature sets contained in the paper. The challenges of dataset identification include variety of ways the paper authors describe the datasets in their papers and incomplete tagging of the CMR dataset description (DIFs).

Irina Gerasimov↗

DOE OSTI2025

On the Effectiveness of Neural Operators at Zero-Shot Weather Downscaling [SWR-25-20]

Code repository for the experiments performed in the paper: On the Effectiveness of Neural Operators at Zero-Shot Weather Downscaling (https://doi.org/10.1017/eds.2025.11) Overall, our work investigates the zero-shot downscaling potential of neural operators. To summarize, our contributions are: 1. We provide a comparative analysis based on two challenging weather downscaling problems, between various neural operator and non-neural-operator methods with large upsampling factors (e.g., 8x and 15x) and fine grid resolutions (e.g., 2 km × 2 km wind speed). 2. We examine whether neural operator layers provide unique advantages when testing downscaling models on upsampling factors higher than those seen during training, i.e., zero-shot downscaling. Our results instead show the surprising success of an approach that combines a powerful transformer-based model with a parameter-free interpolation step at zero-shot weather downscaling. 3. We find that this Swin-Transformer-based approach mostly outperforms all neural operator models in terms of average error metrics, whereas an enhanced super-resolution generative adversarial network (ESRGAN)-based approach is better than most models in capturing the physics of the system, and suggests their use in future work as strong baselines. However, these approaches still do not capture variations at smaller spatial scales well, including the physical characteristics of turbulence in the HR data. This suggests a potential for improvement in transformer or GAN-based methods and neural-operator-based methods for zero-shot weather downscaling.

Sinha, Saumya [National Renewable Energy Laborator↗

DOE OSTI2020

Transformation of Ferrihydrite to Goethite and the Fate of Plutonium

Understanding the interactions between plutonium and iron (oxy)hydroxide minerals is necessary to gain a predictive understanding of plutonium environmental mobility and to evaluate long-term performance of nuclear waste repositories. We investigated the fate of plutonium during the formation of ferrihydrite and its subsequent transformation into goethite. Ferrihydrite was synthesized with varying quantities of Pu(IV) following either a sorption or coprecipitation process; the ferrihydrite was then aged hydrothermally to yield goethite. Additionally, the synthesized materials were characterized via extended X-ray absorption fine structure spectroscopy, transmission electron microscopy, and acid leaching to elucidate the nature of plutonium association with ferrihydrite and goethite. In samples prepared following the sorption method, plutonium was identified in two different forms: a PuO 2 precipitate and a surface-sorbed plutonium complex. For the samples prepared via coprecipitation, no PuO 2 formation occurs in the ferrihydrite precursor and in the goethite experiments where plutonium concentration is ≤1000 ppm (mg kg –1 ). In these coprecipitation products, plutonium is strongly bound to the minerals either via formation of an inner sphere complex, or via an incorporation process. In the coprecipitation experiments, PuO 2 formation only occurs at the highest plutonium concentration (3000 ppm), suggesting that during ferrihydrite transformation into goethite, part of the plutonium can be remobilized to form PuO 2 nanoparticles. Collectively, our results demonstrate that the nature of plutonium associated with the precursor ferrihydrite (adsorbed vs coprecipitated) will have a direct impact on the association of plutonium with its alteration product (goethite). Furthermore, the data illustrate that some properties of plutonium association with the precursor ferrihydrite are retained through the transformation into goethite. These findings show that plutonium strongly associates with iron (oxy)hydroxides formed through coprecipitation processes and in these materials, plutonium can be strongly retained by the iron minerals.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

SMC 2021 Data Challenge: Analyzing Resource Utilization and User Behavior on Titan Supercomputer

Resource utilization statistics of submitted jobs on a supercomputer can help us understand how users from various scientific domains use HPC platforms and better design a job scheduler. We explore to generate insight regarding workload distribution and usage pattern domains from job scheduler trace, GPU failure information, and project-specific information collected from Titan supercomputer. Furthermore, we want to know how the scheduler performance varies over time and how the users' scheduling behavior changes following a system failure. These observations have the potential to provide valuable insight, which is helpful to prepare for system failures. These practices will help us develop and apply novel machine learning algorithms in understanding system behavior, requirement, and better scheduling of HPC systems. There are two datasets, RUR and GPU: RUR dataset is the job scheduler traces collected from the Titan supercomputer from 01/01/2015 to 07/31/2019 (2015.csv - 2019.csv). These were collected using resource Utilization Report (RUR), a Cray-developed resource-usage data collection and reporting system. It contains the usage information of its critical resources (CPU, Memory, GPU, and I/O) of each running job on Titan during that period (https://ieeexplore.ieee.org/abstract/document/8891001). It includes ProjectAreas as additional information, every job is associated with a project ID. TheProjectAreas.csv dataset provides a mapping of the project ID to its domain science. GPU dataset has information regarding GPU failure on Titan. There have been some hardware-related issues in the GPUs in Titan that caused some GPUs to fail, sometimes irrecoverably during some job runs. This dataset provides information regarding these failures during the execution of the submitted jobs. GPUs on Titan are uniquely identified by a serial number (SN), and they are installed in a location. A GPU can be installed in a location, then removed from that location following a failure, and then re-installed in a different location after fixing the problem. If the failure can't be recovered, the GPU might be removed entirely from Titan. There are two prominent types of failures that resulted in the removal of GPUs from Titan: Double Bit Error (DBE) and Out of the Bus (OTB). The dataset (gc_full.csv) has seven attributes, we provided a short description of these attributes in the ReadMe file. To learn more about this dataset, please refer to the git repository https://github.com/olcf/TitanGPULife and the related publication (https://ieeexplore.ieee.org/abstract/document/9355319).

42 ENGINEERING↗

DOE OSTI2025

A comparative analysis of numerical approaches for the description of gas flow in clay-based repository systems: From a laboratory to a large-scale gas injection test

There is nowadays a consensus among many countries that geological disposal is a favourable solution for the long-term management. Although different host formations and different barrier systems are under consideration around the world, clay-based materials form an important component for waste isolation in most national programmes. Hence, a good comprehension of the effect of gas flow on the hydro-mechanical behaviour of clay-based soils is essential, both at laboratory and field scale. Task B under the international cooperative project DECOVALEX-2023 has recently shown that, after some enhancement, models can be employed to reproduce laboratory scale tests, even with different sample geometries 37 . However, further work is required to understand whether they can be applied to simulate a large-scale experiment. Up-scaling of models for the advective transport of gas through clay-based low permeable material presents a number of problems related to the difficulty in obtaining consistent hydrogeological parameters and constitutive relationships at both laboratory and field scale. Based on a unique dataset from a large-scale gas injection test (Lasgit) performed at the Äspö Hard Rock Laboratory (Sweden), Task B within DECOVALEX-2023 has explored the refinement of these numerical strategies applied to the simulation of gas flow. Work performed within the task reveals that codes do not need to be substantially modified from the laboratory models to reproduce full-scale tests: indeed, model parameters calibrated and validated at laboratory scale have been applied to predict field scale gas flow at Lasgit, including peak gas pressure and injected cumulative gas volume. By means of (1) the introduction of interfaces between blocks to reflect the experimental configuration and the (2) adjustment of some parameters (e.g., higher permeability), the updated models are able to represent most of the key features observed in the experimental data, even at a large scale.

Tamayo-Mas, E↗

DOE OSTI2025

An Overview of the Molten Salt Thermal Properties Database–Thermophysical, Version 4.0 (MSTDB-TP V.4.0)

A central repository of thermophysical and thermochemical properties of molten salt compositions of relevance to molten salt reactors (MSRs) is vital in supporting the broad community of MSR developers, who are at various stages of developing and deploying their reactor designs. In general, these MSR designs differ significantly from developer to developer (e.g., with respect to the hardness of the neutron spectra, level of fissile loading, target multicomponent temperatures and power levels, and moderating capabilities). Therefore, the fuel and coolant salts being considered vary greatly: they may be chlorides or fluorides, they utilize different actinides at different ratios, and the cations in the melt are selected based on perceived advantages and disadvantages. Considering the general need for thermal properties, and the vastness of the array of potential candidate salt mixtures, the Molten Salt Thermal Properties Database (MSTDB) was initiated in 2018 with the goal of providing thermophysical and thermochemical characterization of key molten salt compounds and mixtures across their temperature and compositional domains. The MSTDB is thus divided into the thermophysical arm (MSTDB-TP) and the thermochemical arm (MSTDB-TC). The MSTDB is an effort funded by the Department of Energy, Office of Nuclear Energy (DOE-NE) Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, and the MSR Campaign. This report provides an overview of the MSTDB-TP v4.0 in terms of the data contained within, the state of the tools used to access the data, the availability of predictive models that leverage the raw data in the database, the preliminary status of developmental efforts that are currently underway, and an account of future goals for MSTDB-TP. The primary goal for the update from MSTDB-TP v.3.1 to v4.0 was the incorporation of surface tension data into the database; this property is important for thermal hydraulics modeling and species transport in other tools that have been developed under the NEAMS program. A breakdown of the surface tension data that have been added into MSTDB-TP v4.0 is provided herein, and the manner in which the quality of the data has been assessed is also documented. For MSTDB-TP v4.0, newly published thermophysical property data—primarily from collaborative experimental efforts under the MSR Campaign—have been incorporated into the database, and the resulting expansion is documented here. Because of the size to which MSTDB-TP has grown, the raw data format has now been recast into JavaScript Object Notation (JSON) format for easier connection with the MSTDB-TP application programming interface (API). Saline; the pre-existing comma-separated value (CSV) format has been deprecated but is still maintained, accessible, and up to date. As a final effort in packaging the MSTDB-TP v4.0 update, the graphical user interface (GUI) for MSTDB has been updated to allow full accessibility to the density and viscosity predictive models, which are based on Redlich-Kister expansions of MSTDB-TP raw data. Some other major aspects of this report, in terms of preliminary and future work, include: (1) documentation of the formalism and preliminary testing of a kinetic theory model that may act as a predictive model for thermal conductivity; (2) documentation of the candidate predictive models that may be considered in the future for surface tension, making use of the surface tension data now in MSTDB-TP v4.0; (3) a preliminary account of a data collection process that will enable the filling of additional gaps within MSTDB-TP, namely with data which have been collected computationally (e.g., through ab initio molecular dynamics).

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NASA NTRS2014

Humic Acid Complexation of Th, Hf and Zr in Ligand Competition Experiments: Metal Loading and Ph Effects

The mobility of metals in soils and subsurface aquifers is strongly affected by sorption and complexation with dissolved organic matter, oxyhydroxides, clay minerals, and inorganic ligands. Humic substances (HS) are organic macromolecules with functional groups that have a strong affinity for binding metals, such as actinides. Thorium, often studied as an analog for tetravalent actinides, has also been shown to strongly associate with dissolved and colloidal HS in natural waters. The effects of HS on the mobilization dynamics of actinides are of particular interest in risk assessment of nuclear waste repositories. Here, we present conditional equilibrium binding constants (Kc, MHA) of thorium, hafnium, and zirconium-humic acid complexes from ligand competition experiments using capillary electrophoresis coupled with ICP-MS (CE- ICP-MS). Equilibrium dialysis ligand exchange (EDLE) experiments using size exclusion via a 1000 Damembrane were also performed to validate the CE-ICP-MS analysis. Experiments were performed at pH 3.5-7 with solutions containing one tetravalent metal (Th, Hf, or Zr), Elliot soil humic acid (EHA) or Pahokee peat humic acid (PHA), and EDTA. CE-ICP-MS and EDLE experiments yielded nearly identical binding constants for the metal- humic acid complexes, indicating that both methods are appropriate for examining metal speciation at conditions lower than neutral pH. We find that tetravalent metals form strong complexes with humic acids, with Kc, MHA several orders of magnitude above REE-humic complexes. Experiments were conducted at a range of dissolved HA concentrations to examine the effect of [HA]/[Th] molar ratio on Kc, MHA. At low metal loading conditions (i.e. elevated [HA]/[Th] ratios) the ThHA binding constant reached values that were not affected by the relative abundance of humic acid and thorium. The importance of [HA]/[Th] molar ratios on constraining the equilibrium of MHA complexation is apparent when our estimated Kc, MHA values attained at very low metal loading conditions are compared to existing literature data. Overall, experimental data suggest that the tetravalent transition metal/-actinide-humic acid complexation is important over a wide range of pH values, including mildly acidic conditions, and thus, these complexes should be included in speciation models.

humic acid↗

DOE OSTI2026

Xanthos-Lake Model Source Code

This repository contains the source code for Xanthos-Lake, a lake-modeling extension of the Xanthos framework that introduces a coupled lake component comprising the Xanthos-Lake Snow and Ice Model (xLSIM) and the Xanthos-Lake Water Balance Model (xLWBM). xLSIM is a basin-aware machine-learning model for lake snow, ice, and thermal conditions. It predicts monthly lake ice thickness, snow depth, snow-cover fraction, mixing-layer temperature, and lake ice fraction from meteorological forcing and lake surface-area information. It uses sequence-based deep-learning architectures, including Transformer and hybrid Long Short-Term Memory–Transformer (LSTM–Transformer) models, together with seasonal encoding, multi-lake learning, physical masking, and basin-level cryospheric and non-cryospheric classification. The training workflow uses Ray for scalable execution and includes optional Ray Tune hyperparameter optimization. Model predictions, observations, diagnostics, and feature-importance outputs are written in NetCDF. xLWBM is the water-balance component of the new lake framework. It simulates monthly lake storage, surface area, evaporation, inflow, outflow, and lake–groundwater exchange. It combines physical water-balance equations with calibrated bathymetric relationships, weir-based outlet flow, modified Penman open-water evaporation, groundwater head relaxation, Penman–Monteith snow and ice sublimation, and snow, ice, and thermal conditions supplied by xLSIM. The model calibrates lake parameters against satellite-derived surface-area data, using evaporation-based calibration where surface-area data are unavailable, and supports small, medium, and large lake classes. For large lakes, xLWBM is integrated with the managed-routing workflow so that lake storage and outflow interact directly with downstream river routing and reservoir operations. Together, xLSIM and xLWBM provide Xanthos with a coupled lake-modeling capability. xLSIM supplies the snow, ice, and thermal conditions that affect lake evaporation and snow- and ice-related water exchanges, while xLWBM translates those conditions into dynamic lake storage, surface area, evaporation, and discharge. In return, xLWBM supplies evolving lake surface area to xLSIM. This coupling enables Xanthos to represent lakes as active hydrologic components within basin-scale water-availability and routing simulations.

Machine Learning↗

DOE OSTI2020

Using Radioiodine Speciation to Address Environmental Remediation and Waste Stream Sequestration Problems at the Fukushima Daiichi Nuclear Power Plant and a DOE Site

Iodine-129 ( 129 I), with a half-life of half-life of 16 million years, is commonly considered the single greatest risk driver in high-level and low-level nuclear repositories. This risk stems from several basic properties of 129 I, and under many geochemical conditions, it can move as an anion at nearly the rate of water through the subsurface environment. 129 I is also extremely radiologically toxic because over 90% of body burden accumulates in the thyroid, which weighs only about 14g in an adult. There is also a large worldwide inventory of radioiodine as a result of its high fission yield and this inventory is rapidly increasing as a result of nuclear energy production. Radioiodine is produced at a rate of 40 GBq (1 Ci) per gigawatt of electricity produced by nuclear power. To illustrate how the properties of 129 I magnify its risk, 129 I accounts for only 0.00002% of the radiation released from the Savannah River Site in Aiken, South Carolina, but contributes 13% of the population dose, a six orders of magnitude magnification of risk with respect to its radioactivity. The currently favored solid phase for LLW immobilization is cement, while HLW immobilization is the incorporation of waste into glass (vitrification). However, so far, the incorporation into cement and subsequent leaching of only iodide has been seriously investigated. The major problem with this approach is that it ignores the complex speciation of iodine, i.e., it ignores iodate and organo-iodine which have different chemistries. Most of the past research was devoted to the mechanism of iodide uptake in cement hydrate phases that is sorption and/or incorporation. Very few data exist on iodate and organo-iodine incorporation in cement, even though large quantities of liquid waste containing also radioiodine have already been solidified in cement Iodine-129 from low-level waste is commonly disposed of in cementitious materials. Grout, a dense cementitious fluid, mixed with a reducing slag, is often used to immobilize radionuclides. However, the reducing environment might not be conducive to immobilize iodine. For example, the silver based immobilization technologies (e.g., AgCl, Ag-impregnated granular activated carbon, Ag-mordenite) remove iodine from the aqueous phase by promoting the formation of Ag-iodide precipitates. The solubility of AgI is eight orders of magnitude lower than it is for AgIO 3 . Similarly, coprecipitation of iodine into calcium carbonate phases occurs only with IO 3 - and not with I - and org-I. If one would want to immobilize iodine more effectively, different engineering approaches would need to be used to promote binding of I - , IO 3 - , or organo-I. Using laboratory experiments with grout, slag, and silver-based adsorbents, and GC-MS and I K-edge XANES and EXAFS and C K-edge XANES spectroscopy for identifying iodine speciation, the major problems with these methods have been identified as focused too much on just one of the iodine species for immobilization, while others, especially organo-I, remained mobile. Finally, we established that most of the adsorbents that are used contain sufficient amounts of organic matter to create organo-I . It is anticipated that increased attention directed at understanding and quantifying the speciation of radioiodine, as opposed to simply total radioiodine, will lead to improved remediation results to be used for long-term radioiodine disposal in cementitious waste forms.

129-Iodine↗

NASA NTRS1997

Risk Management of NASA Projects

Various NASA Langley Research Center and other center projects were attempted for analysis to obtain historical data comparing pre-phase A study and the final outcome for each project. This attempt, however, was abandoned once it became clear that very little documentation was available. Next, extensive literature search was conducted on the role of risk and reliability concepts in project management. Probabilistic risk assessment (PRA) techniques are being used with increasing regularity both in and outside of NASA. The value and the usage of PRA techniques were reviewed for large projects. It was found that both civilian and military branches of the space industry have traditionally refrained from using PRA, which was developed and expanded by nuclear industry. Although much has changed with the end of the cold war and the Challenger disaster, it was found that ingrained anti-PRA culture is hard to stop. Examples of skepticism against the use of risk management and assessment techniques were found both in the literature and in conversations with some technical staff. Program and project managers need to be convinced that the applicability and use of risk management and risk assessment techniques is much broader than just in the traditional safety-related areas of application. The time has come to begin to uniformly apply these techniques. The whole idea of risk-based system can maximize the 'return on investment' that the public demands. Also, it would be very useful if all project documents of NASA Langley Research Center, pre-phase A through final report, are carefully stored in a central repository preferably in electronic format.

Sarper, Hueseyin↗

DOE OSTI2025

Supporting Information - How Can Crop Production Adapt to growing groundwater restrictions in the West?

Abstract This data plan outlines the structure and content of datasets generated and utilized in the research presented in the manuscript abstract. Groundwater overdraft has led to serious water supply issues in the US West. Most western states manage groundwater use through a permitting system, but California has only recently begun to restrict groundwater use statewide with the 2014 passage of groundwater restrictions which target the elimination of groundwater overdraft practices by 2042. With groundwater extraction curtailed, crop production in the US West (a $95 billion industry annually) will be affected, and appropriate response strategies will be needed to ensure minimal disruption to food production and the regional economy. In this paper, we explore the adoption of alternative adaptive responses: (a) deficit irrigation; (b) switching to less water-intensive crops; (c) changing the extent of irrigated land (including fallowing); and (d) geographically shifting crop production. Employing an integrated modeling approach, we explicitly capture the interactions and feedbacks between local hydrology, changes in crop yields, crop and land use decision-making, changes in crop prices, and regional shifts in crop production. We find that the optimal adaptive response is spatially heterogeneous and comprises a portfolio of strategies. Southwestern states and California will be the most impacted by groundwater restrictions. The optimal responses in these states are to both adopt deficit irrigation strategies and reduce a portion of their irrigated croplands, resulting in a shift in crop production to northwestern states with a larger supply of water. The datasets detailed in this repository represent the output from these integrated models, specifically designed to support the analysis and visualization presented in the manuscript and supplemental information. These datasets, used in conjunction with the scripts available at our associated GitHub repository (https://github.com/pches/Femeena_etal_How_can_crop_production_adapt), enable the reproduction of figures and facilitate a comprehensive understanding of the optimal adaptive strategies in agriculture for mitigating water stress under varying groundwater extraction scenarios, as outlined in the abstract.

DNDCe↗

DOE OSTI2025

Supporting Information - How Can Crop Production Adapt to growing groundwater restrictions in the West?

DNDCe↗

DOE OSTI2025

Supporting Information - How Can Crop Production Adapt to growing groundwater restrictions in the West?

DNDCe↗

DOE OSTI2025

Automation of Vulnerability and Patch Management: Information Extraction, Association, and Optimization

Vulnerability and patch management is an integral part of a robust cybersecurity program, yet it grows increasingly complex due to the sheer amount of data that must be analyzed. Particularly in Operational Technology (OT) environments, analysis must be done manually because of the lack of automated solutions. Additionally, there are many steps in this process, from the initial discovery of the vulnerability to the implementation of its remediation, and each step in the process requires different data in order to be performed effectively. In this work, we provide approaches and strategies to assist operators in industrial or OT environments throughout the vulnerability management cycle. Security advisories provide key information about mitigation strategies, or actions that can be taken when a patch is unavailable or cannot be installed. Details of these strategies are not shared in public vulnerability databases and must be found manually. We approach this problem by designing a solution to automatically identify that information within vendor security advisories and retrieve it for operator use. We start with an approach that requires domain-specific knowledge of certain frequently-seen reference websites. Next, an approach that can work on an arbitrary website but relies on certain keywords. Finally, an approach that uses Natural Language Processing (NLP) methods and does not require specific knowledge or keywords. Each of these approaches is more general than its predecessor; we demonstrate high accuracy for all approaches Advisories also often contain details of affected products in non-standard or natural language formats. While this information can be easily understood when read by an operator, the non-standard format acts as a barrier to effective automation. We provide an approach for the first step in this process: identifying vendors in security advisories and mapping them to a standard framework for representing digital assets and software products. We evaluate five established string similarity algorithms, plus one of our own design that combines string similarity and information theory, on the task of mapping vendors to their corresponding entries in the Common Platform Enumeration (CPE) repository. Our results show that our proposed metric outperforms all others. Due to the constraints on time, finances, and personnel for organizations, Large Language Models (LLMs) may seem like attractive opportunities for security operators to speed up information gathering; however, it is still not clear whether LLMs can handle vulnerability management tasks well. To answer this question, we perform an empirical study of LLMs’ ability to provide consistent, accurate information about vulnerabilities in order to guide organizations in their adoption of LLMs. We observe poor performance for all models tested, suggesting that these models are not well-suited to the consistent retrieval of accurate vulnerability information. Finally, once vulnerabilities have been identified and any additional information has been obtained, operators must decide which remediation actions to implement based on their available resources. This already-complex problem becomes even more so when we consider that a vulnerability may have multiple avenues for remediation. We formulate this scenario as two knapsack problems and provide solutions, which we then compare against several existing strategies for vulnerability prioritization seen in real operational environments.

McClanahan, Kylie↗

DOE OSTI2022

Improvement of eukaryotic protein predictions from soil metagenomes

During the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI’s IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗

DOE OSTI2022

DIVA/DeviceEditor (DIVA) v6.0.0

The DIVA software interfaces a process in which researchers design their DNA with a web-based graphical user interface (DeviceEditor), submit their designs to a central queue, and a few weeks later receive their sequence-verified clonal constructs. Each researcher independently designs the DNA to be constructed with a web-based BioCAD tool, and presses a button to submit their designs to a central queue. Researchers have web-based access to their DNA design queues, and can track the progress of their submitted designs as they progress from "evaluation", to "waiting for reagents", to "in progress", to "complete". Researchers access their completed constructs through the central DNA repository. Along the way, all DNA construction success/failure rates are captured in a central database. Once a design has been submitted to the queue, a small number of dedicated staff evaluate the design for feasibility and provide feedback to the responsible researcher if the design is either unreasonable (e.g., encompasses a combinatorial library of a billion constructs) or small design changes could significantly facilitate the downstream implementation process. The dedicated staff then use DNA assembly design automation software to optimize the DNA construction process for the design, leveraging existing parts from the DNA repository where possible and ordering synthetic DNA where necessary. Once all requisite process inputs are available, the design progresses from "waiting for reagents" to "in progress" in the design queue. Human-readable and machine-parseable DNA construction protocols output by the DNA assembly design automation software are then executed by the dedicated staff exploiting lab automation devices wherever possible. Since the all employed DNA construction methods are sequence-agnostic, standardized (utilize the same enzymatic master mixes and reaction conditions), completely independent DNA construction tasks can be aggregated into the same multi-well plates and pursued in parallel. The resulting sets of cloned constructs can then be screened by high-throughput next-gen sequencing platforms for sequence correctness. A combination of long read-length (e.g., PacBio) and paired-end read platforms (e.g., Illumina) would be exploited depending the particular task at hand (e.g., PacBio might be sufficient to screen a set of pooled constructs with significant gene divergence). Post sequence verification, designs for which at least one correct clone was identified will progress to a "complete" status, while designs for which no correct clones were identified will progress to a "failure" status. Depending on the failure mode (e.g., no transformants), and how many prior attempts/variations of assembly protocol have been already made for a given design, subsequent attempts may be made or the design can progress to a "permanent failure" state. All success and failure rate information will be captured during the process, including at which stage a given clonal construction procedure failed (e.g., no PCR product) and what the exact failure was (e.g. assembly piece 2 missing). This success/failure rate data can be leveraged to refine the DNA assembly design process.

Plahar, Hector↗

DOE OSTI2024

A digital twin solution for floating offshore wind turbines validated using a full-scale prototype

Abstract. In this work, we implement, verify, and validate a physics-based digital twin solution applied to a floating offshore wind turbine. The digital twin is validated using measurement data from the full-scale TetraSpar prototype. We focus on the estimation of the aerodynamic loads, wind speed, and section loads along the tower, with the aim of estimating the fatigue lifetime of the tower. Our digital twin solution integrates (1) a Kalman filter to estimate the structural states based on a linear model of the structure and measurements from the turbine, (2) an aerodynamic estimator, and (3) a physics-based virtual sensing procedure to obtain the loads along the tower. The digital twin relies on a set of measurements that are expected to be available on any existing wind turbine (power, pitch, rotor speed, and tower acceleration) and motion sensors that are likely to be standard measurements for a floating platform (inclinometers and GPS sensors). We explore two different pathways to obtain physics-based models: a suite of dedicated Python tools implemented as part of this work and the OpenFAST linearization feature. In our final version of the digital twin, we use components from both approaches. We perform different numerical experiments to verify the individual models of the digital twin. In this simulation realm, we obtain estimated damage equivalent loads of the tower fore–aft bending moment with an accuracy of approximately 5 % to 10 %. When comparing the digital twin estimations with the measurements from the TetraSpar prototype, the errors increased to 10 %–15 % on average. Overall, the accuracy of the results is promising and demonstrates the possibility of using digital twin solutions to estimate fatigue loads on floating offshore wind turbines. A natural continuation of this work would be to implement the monitoring and diagnostics aspect of the digital twin to inform operation and maintenance decisions. The digital twin solution is provided with examples as part of an open-source repository.

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