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At least 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually updated as new genes are discovered.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Deep Active Learning for Solvability Prediction in Power Systems

Traditional methods for solvability region analysis can only have inner approximations with inconclusive conservatism and handle limited types of power flow models. In this letter, we propose a deep active learning framework for solvability prediction in power systems. Compared with passive learning where the training is performed after all instances are labeled, active learning selects most informative instances to be labeled and therefore significantly reduces the size of the labeled dataset for training. In the active learning framework, the acquisition functions, which correspond to different sampling strategies, are defined in terms of the on-the-fly posterior probability from the classifier. First, the IEEE 39-bus system is employed to validate the proposed framework, where a two-dimensional case is illustrated to visualize the effectiveness of the sampling method followed by the high-dimensional numerical experiments. Then, the Northeast Power Coordinating Council (NPCC) 140-bus system is used to validate the performance on large-scale power systems.

42 ENGINEERING↗
DOE OSTI2025

NWB Sensors Infrared Cloud Imager Data Products from SGP

NWB Sensors is a company which has developed a commercially available Infrared Cloud Imager (ICI). For more information, consult the company's webpage, https://www.nwbsensors.com/infrared-cloud-imager. To validate the radiometric accuracy of the ICI, NWB Sensors deployed it to the ARM SGP User Facility in 2023. The primary motivation of this deployment was to perform an intercomparison between the ICI and the Atmospheric Emitted Radiance Interferometer (AERI). The AERI spectral radiance data product can be integrated across the response function of the ICI and directly compared to the zenith radiance observed by the ICI. In addition, the ICI uses proprietary models of the downwelling clear-sky radiance in its cloud processing algorithms. They are based on surface meteorology and precipitable water vapor (PWV). These models were validated by comparing their predicted radiances to those derived from radiative transfer models of the ARM radiosondes. Finally, PWV observations derived from the ICI's onboard GNSS-based PWV retrieval system were compared against those from the microwave radiometer. This dataset contains the ICI radiance and cloud data products.

Atmosphere↗
NASA NTRS2005

Creation and testing of an artificial neural network based carbonate detector for Mars rovers

We have developed an artificial neural network (ANN) based carbonate detector capable of running on current and future rover hardware. The detector can identify calcite in visible/NIR (350-2500 nm) spectra of both laboratory specimens covered by ferric dust and rocks in Mars analogue field environments. The ANN was trained using the Backpropagation algorithm with sigmoid activation neurons. For the training dataset, we chose nine carbonate and eight non-carbonate representative mineral spectra from the USGS spectral library. Using these spectra as seeds, we generated 10,000 variants with up to 2% Gaussian noise in each reflectance measurement. We cross-validated several ANN architectures, training on 9,900 spectra and testing on the remaining 100. The best performing ANN correctly detected, with perfect accuracy, the presence (or absence) of carbonate in spectral data taken on field samples from the Mojave desert and clean, pure marbles from CT. Sensitivity experiments with JSC Mars-1 simulant dust suggest the carbonate detector would perform well in aeolian Martian environments.

neural networks↗
NASA NTRS2017

Estimating Evaporative Fraction From Readily Obtainable Variables in Mangrove Forests of the Everglades, U.S.A.

A remote-sensing-based model to estimate evaporative fraction (EF) the ratio of latent heat (LE; energy equivalent of evapotranspiration -ET-) to total available energy from easily obtainable remotely-sensed and meteorological parameters is presented. This research specifically addresses the shortcomings of existing ET retrieval methods such as calibration requirements of extensive accurate in situ micro-meteorological and flux tower observations, or of a large set of coarse-resolution or model-derived input datasets. The trapezoid model is capable of generating spatially varying EF maps from standard products such as land surface temperature [T(sub s)] normalized difference vegetation index (NDVI)and daily maximum air temperature [T(sub a)]. The 2009 model results were validated at an eddy-covariance tower (Fluxnet ID: US-Skr) in the Everglades using T(sub s) and NDVI products from Landsat as well as the Moderate Resolution Imaging Spectroradiometer (MODIS) sensors. Results indicate that the model accuracy is within the range of instrument uncertainty, and is dependent on the spatial resolution and selection of end-members (i.e. wet/dry edge). The most accurate results were achieved with the T(sub s) from Landsat relative to the T(sub s) from the MODIS flown on the Terra and Aqua platforms due to the fine spatial resolution of Landsat (30 m). The bias, mean absolute percentage error and root mean square percentage error were as low as 2.9% (3.0%), 9.8% (13.3%), and 12.1% (16.1%) for Landsat-based (MODIS-based) EF estimates, respectively. Overall, this methodology shows promise for bridging the gap between temporally limited ET estimates at Landsat scales and more complex and difficult to constrain global ET remote-sensing models.

trapezoid↗
NASA NTRSDate not supplied

Detecting And Characterizing Archetypes of Unintended Consequences in Engineered Systems

When designing engineered systems, the potential for unintended consequences of design policies or design decisions exists despite best intentions. Conditions that might cause the formation of unintended consequences are often known only in hindsight. However, since these conditions are associated with a single event, it is difficult to uncover the general patterns of conditions leading to unintended consequences. In this research, patterns of conditions associated with unintended consequences are learned from historical data and represented in the form of archetypes. While previous work using systems theoretic modeling has identified high-level archetypes, this work leverages a self-organizing map to learn archetypes of unintended consequences from human-tagged risk factors in a large data set of lessons learned from adverse events at NASA. The sixty-six identified archetypes contain patterns of conditions such as complexity and human-machine interaction associated with the formation of unintended consequences. To validate the archetypes, a sample of the archetypes is represented using system dynamics in order to illustrate that the identified archetypes are specialized versions of known high-level archetypes of unintended consequences. While the research is based upon a specific dataset, the archetypes apply to any engineered system and the pattern of leading indicators open a new path to manage unintended consequences and mitigate the magnitude of potentially adverse outcomes.

Hannah S Walsh↗
NASA NTRS2020

Comparison of Raindrop Size Distribution between NASA's S-Band Polarimetric Radar and Two-Dimensional Video Disdrometers

The ground-based-radar-derived raindrop size distribution (DSD) parameters—mass-weighted drop diameter D mass and normalized intercept parameter NW—are the sole resource for direct validation of the National Aeronautics and Space Administration (NASA) Global Precipitation Measurement (GPM ) mission Core Observatory satellite-based retrieved DSD. Both D mass and NW are obtained from radar-measured reflectivity Z Hand differential reflectivity ZDR through empirical relationships. This study uses existing relationships that were determined for the GPM ground validation (GV) program and directly compares the NASA S-band polarimetric radar (NPOL) observables of Z Hand Z DR and derived D mass and NW with those calculated by two-dimensional video disdrometer (2DVD). The joint NPOL and 2DVD datasets were acquired during three GPM GV field campaigns conducted in eastern Iowa, southern Appalachia, and western Washington State. The comparative study quantifies the level of agreement for ZH, ZDR, D mass, and log (NW) at an optimum distance (15–40 km) from the radar as well as at distances greater than 60 km from radar and over mountainous terrain. Interestingly, roughly 10%–15% of the NPOLZH–Z DR pairs were well outside the envelope of 2DVD-estimatedZH–Z DR pairs. The exclusion of these pairs improved the comparisons noticeably.

Ali Tokay↗
NASA NTRSDate not supplied

Using CALIPSO's New Ocean Derived Column Optical Depths

CALIPSO’s Version 4.51 Level 2 data release introduces an all-new group of science data sets containing estimates of total column two-way transmittances and effective optical depths derived from CALIOP ocean surface backscatter measurements and MERRA-2 reanalysis wind speed data. These estimates use data from the standard CALIOP lidar signal but in a passive sensor-like way, thus creating a unique link to passive instrument measurements. These new retrievals are provided for the entire mission, day and night, at 532nm, and are reported at single shot, 1km, and 5km resolutions for all profiles in which a valid lidar ocean surface return is detected. The addition of a total column optical depth constraint on subsequent retrievals of cloud and aerosol optical properties opens the door for many exciting new ways to leverage the already rich and versatile CALIPSO dataset. Following a brief review of the retrieval technique, this talk will focus on quality assurance assessments, estimated uncertainties, and data usage scenarios. We will conclude with examples highlighting some of the exciting work already being done using this new addition to CALIPSO’s already rich data record.

R Ryan↗
DOE OSTI2022

Novel Application of Machine Learning Techniques for Rapid Source Apportionment of Aerosol Mass Spectrometer Datasets

In this work, we apply machine learning approaches sparse multinomial logistic regression to classify aerosol mass spectrometer (AMS) unit mass resolution (UMR) data followed by an ensemble regression technique for source apportionment of organic aerosols (OA). The classifier was trained on 60 well characterized laboratory and positive matrix factorization (PMF) deconvolved reference spectra to identify eight OA types. These include four laboratory-derived secondary organic aerosol (SOA) spectra, which include isoprene photooxidation SOA, isoprene epoxydiols (IEPOX) SOA, a monoterpene SOA type that includes a-pinene and ß-pinene SOA, and aromatic SOA from oxidation of naphthalene and m-xylene precursors, as well as PMF deconvolved spectra for three primary organic aerosol (POA) types, namely, hydrocarbon-like organic aerosol (HOA), biomass burning organic aerosol (BBOA), and cooking OA (COA), and a more oxidized oxygenated OA type (MO-OOA). A 5-fold cross-validation strategy, repeated 10 times, was used to assess the classifier’s performance. The classifier had high classification accuracy for COA, aromatic SOA, and isoprene SOA spectra but incorrectly classified ~9% by number of MO-OOA spectra as BBOA, 12% of BBOA spectra as HOA (and vice versa), and 18% of IEPOX-SOA spectra as aromatic SOA. Next, an ensemble regression model was trained on an artificially generated dataset consisting of mixtures of different OA types to assess its ability to predict fractional mass abundances from classification probabilities of various OA species obtained from the multinomial logistic regression classifier trained on the reference spectra. Ultimately, the proposed approach was applied for source apportionment of aircraft-based AMS measurements of OA UMR spectra during the HI-SCALE field campaign. On two representative days (May 6th and 18th, 2016), the algorithm determined that ~50-60% of OA by mass was MO-OOA, which represented a highly aged organic aerosol mixture from different sources. On both days, BBOA was determined to contribute less than 10% to OA by mass. However, on May 18th, the aromatic SOA fraction was higher compared to that on May 6th. The proposed approach is capable of rapidly analyzing AMS data in real time, making it suitable for applications where rapid source apportionment of AMS OA spectra is desirable.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Mapping wall-to-wall fractional cover of Arctic tundra plant functional types in Alaska using 20-m spatial resolution satellite imagery and harmonized plot observations

Estimates of fractional cover (fCover) across given land surfaces are used to assess, and often model, vegetation composition and diversity, which are crucial for understanding the health and functioning of terrestrial ecosystems. Remote sensing provides a useful means for scaling local, plot-measured fCover estimates to regional scales. Leveraging a recently synthesized and harmonized plot database, this study generated wall-to-wall maps of fCover for six Alaskan-Arctic plant functional types (PFT), including non-vascular plants, forbs, graminoids, and deciduous and evergreen shrubs, using 20-m satellite data (Sentinel-1, Sentinel-2, ArcticDEM) using a machine learning regression approach, specifically the random forest (RF) algorithm, which is well-suited for handling nonlinear relationships and high-dimensional satellite datasets. This study additionally addressed the spatio-temporal inconsistencies e.g., sampling scale, plot size, and collection year in plot measured fCover by adopting a multivariate outlier detection approach—Cook’s distance—to identify high-quality plots for model training and validation. Our approach achieves high accuracy (R 2 = 0.59–0.93, root mean squared errors = 0.02–0.10 for all PFTs) between plot-observed and satellite-derived fCover when using high-quality plot samples. The mapped fCover characterizes the spatial patterns of different PFTs across the tundra biome at a 20-m resolution, providing key information needed for improved representation of Arctic tundra vegetation in terrestrial biosphere models to better understand climate-vegetation feedback across the Arctic tundra.

Arctic tundra↗
DOE OSTI2023

Guided construction of single cell reference for human and mouse lung

Accurate cell type identification is a key and rate-limiting step in single-cell data analysis. Single-cell references with comprehensive cell types, reproducible and functionally validated cell identities, and common nomenclatures are much needed by the research community for automated cell type annotation, data integration, and data sharing. Here, we develop a computational pipeline utilizing the LungMAP CellCards as a dictionary to consolidate single-cell transcriptomic datasets of 104 human lungs and 17 mouse lung samples to construct LungMAP single-cell reference (CellRef) for both normal human and mouse lungs. CellRefs define 48 human and 40 mouse lung cell types catalogued from diverse anatomic locations and developmental time points. We demonstrate the accuracy and stability of LungMAP CellRefs and their utility for automated cell type annotation of both normal and diseased lungs using multiple independent methods and testing data. We develop user-friendly web interfaces for easy access and maximal utilization of the LungMAP CellRefs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A foundation model for atomistic materials chemistry

Atomistic simulations of matter, especially those that leverage first-principles (ab initio) electronic structure theory, provide a microscopic view of the world, underpinning much of our understanding of chemistry and materials science. Over the last decade or so, machine-learned force fields have transformed atomistic modeling by enabling simulations of ab initio quality over unprecedented time and length scales. However, early machine-learning (ML) force fields have largely been limited by (i) the substantial computational and human effort required to develop and validate potentials for each particular system of interest and (ii) a general lack of transferability from one chemical system to the next. Here, we show that it is possible to create a general-purpose atomistic ML model, trained on a public dataset of moderate size, that is capable of running stable molecular dynamics for a wide range of molecules and materials. We demonstrate the power of the MACE-MP-0 model-and its qualitative and at times quantitative accuracy-on a diverse set of problems in the physical sciences, including properties of solids, liquids, gases, chemical reactions, interfaces, and even the dynamics of a small protein. The model can be applied out of the box as a starting or "foundation" model for any atomistic system of interest and, when desired, can be fine-tuned on just a handful of application-specific data points to reach ab initio accuracy. Establishing that a stable force-field model can cover almost all materials changes atomistic modeling in a fundamental way: experienced users obtain reliable results much faster, and beginners face a lower barrier to entry. Foundation models thus represent a step toward democratizing the revolution in atomic-scale modeling that has been brought about by ML force fields.

Batatia, Ilyes↗
DOE OSTI2024

A Provably Accurate Randomized Sampling Algorithm for Logistic Regression

In statistics and machine learning, logistic regression is a widely-used supervised learning technique primarily employed for binary classification tasks. When the number of observations greatly exceeds the number of predictor variables, we present a simple, randomized sampling-based algorithm for logistic regression problem that guarantees high-quality approximations to both the estimated probabilities and the overall discrepancy of the model. Our analysis builds upon two simple structural conditions that boil down to randomized matrix multiplication, a fundamental and well-understood primitive of randomized numerical linear algebra. We analyze the properties of estimated probabilities of logistic regression when leverage scores are used to sample observations, and prove that accurate approximations can be achieved with a sample whose size is much smaller than the total number of observations. To further validate our theoretical findings, we conduct comprehensive empirical evaluations. Overall, our work sheds light on the potential of using randomized sampling approaches to efficiently approximate the estimated probabilities in logistic regression, offering a practical and computationally efficient solution for large-scale datasets.

Chowdhury, Agniva↗
DOE OSTI2022

Machine Learning for Automated Metadata Assignment in Buildings: Cooperative Research and Development (Final Report, CRADA Number CRD-18-00767)

RealTerm Energy and NREL have identified a shared vision to evaluate opportunities to facilitate the organization and assignment of metadata to building control system (BCS) data via industry-informed machine learning (ML). Manual metadata assignment is labor intensive and costly, slowing down any Energy Management and Information System (EMIS) deployment in the building space. This project aims to develop methodologies to accurately assign this metadata and significantly decrease the level of effort associated with deploying EMIS. The objective of this project is to identify/design methodologies to assign metadata to HVAC control points automatically. The identified methodologies will be programmed in analytics algorithms so they can ingest a list of points and produce a detailed tagging following the Haystack classification nomenclature. To validate the efficacy of each methodology, tagging results will be compared utilizing a list of points extracted from RealTerm's building database-as well as data extracted from the NREL campus via the Intelligent Campus program-enabling testing against large datasets with real world challenges. The developed methodologies may leverage building manager/operator input on a limited basis to add context to the classifying algorithms. The partnership aims to advance global efforts in areas related to the DOE missions through improving operational performance of commercial buildings. It is well documented that buildings fall out of commission after they are occupied, wasting significant energy and incurring associated costs simply due to poor operational performance. Emerging EMIS technologies that perform continuous commissioning help to address this issue, yet integration of these systems can be labor intensive both for the technology vendor and the building owner/operator. This project will enable more efficient and cost-effective analytics for buildings, enabling improvement in building operations at lower cost points.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

Conceptual Design of Engineering-Scale Molten Salt Spill Tests to Support Molten Salt Reactor Licensing

Nuclear accident progression analysis codes for reactor licensing must be validated using experimental data that was generated at a large enough scale so that the results are representative of full-scale accidents. This report describes a conceptual design of engineering-scale molten salt spill tests that will provide the necessary datasets to support molten salt reactor (MSR) licensing. Design considerations, salt compositions, test variables, processes to be quantified, and suitable measurement techniques are presented and discussed. Aspects of the conceptual engineering-scale molten salt spill test design presented in this report were made using insights from recent laboratory-scale molten salt spill tests conducted at Argonne. Additional input from model developers, MSR vendors, and technical experts will benefit the design of the proposed engineering-scale molten salt spill tests.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Development and Evaluation of a General Drag Model for Gas-Solid Flows via Deep Learning

This project presents the development and evaluation of a general drag model for gas–solid multiphase flows using deep learning techniques. A comprehensive database of more than 4,000 experimental and numerical data points for spherical and non spherical particles was compiled, incorporating geometric features such as sphericity, aspect ratio, and orientation. Several predictive approaches—including traditional em pirical correlations, machine learning, and deep neural networks—were benchmarked, with the proposed Drag Coefficient Correlation-aided Deep Neural Network (DCC DNN) demonstrating superior accuracy. To account for particle–particle interactions, additional drag data were generated using CFD-based simulations of packed and flu idized beds, leading to the development of a retrained model capable of incorporat ing volume fraction effects. Integration of the trained model with the MFiX CFD solver was achieved using FTorch, enabling drag predictions during discrete element method (DEM) simulations. Validation against experimental data for single particles and fluidized beds confirmed the model’s improved predictive ability, particularly for non-spherical geometries. While the model performed strongly under fluidized con ditions, limitations remained in unfluidized regimes, suggesting a need for expanded datasets. Overall, this study demonstrates the feasibility of combining deep learning with physics-informed CFD to improve drag modeling for gas–solid flows, with promis ing implications for scaling multiphase simulations in industrial applications.

42 ENGINEERING↗
DOE OSTI2022

Estimation of Corn Latent Heat Flux from High Resolution Thermal Imagery

Crop evapotranspiration (ET), which is directly related to latent heat flux, is also a key indicator in determining the water status of crops. In order to estimate the latent heat flux, two-source energy balance (TSEB) models have been developed for thermal imagery from satellite platforms. However, because of the coarse resolution of thermal sensors on the satellite, distinguishing soil and vegetation is difficult which complicates the calculation process and introduces errors in latent heat estimates. In this research, high-resolution thermal datasets (0.05 m) and corresponding RGB datasets (0.03 m) were used for calculating crop latent heat flux using an adapted TSEB model. The RGB datasets were used for supervised classification of soil and vegetation, and the classification results were then used to filter the thermal mosaics to separate vegetation and soil temperatures. The vegetation temperature is used for calculating latent heat flux and the results are validated against the ground reference measurements of latent heat using a handheld porometer. The objective of this research is to introduce a workflow including an adapted TSEB model which is customized for high resolution thermal images from unmanned aircraft systems (UAS) to estimate the latent heat flux of row crops in agricultural fields. Nine dates of data collection in 2018 and 2020 have been evaluated and the root mean square error (RMSE) varies between 16 to 106 W/m2 depending on the days after planting (DAP) and the time of measurement for each day. The results indicate that the workflow introduced here is able to provide estimates of instantaneous latent heat flux (evapotranspiration) measurements for row crops in agricultural fields which will enable people to make reliable decisions related to irrigation scheduling.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRSDate not supplied

Developing Open-Source Training Materials for AI/ML and Space Biological Sciences Using NASA Cloud-Based Data

Artificial Intelligence (AI) and Machine Learning (ML) has gained significant traction in the biological and biomedical research fields in the last two decades, in part thanks to an increasing culture of open data sharing and reuse. Due to its capability for identifying complex relationships and patterns, AI/ML methodology is particularly well suited to recognize and predict biological patterns from high-dimensional next-generation sequencing data (e.g. whole genome sequencing, transcriptomic sequencing), as well as from biological or medical imaging data (e.g. microscopy, computed tomography, ultrasound, magnetic resonance imaging, radiography). These methodologies hold particular promise for space biosciences research and automated space health monitoring systems. However, there are many key considerations for properly training, validating, and testing a machine learning model in biological research or clinical application. Even with the positive culture of Open Science and data sharing, inexperienced researchers working quickly without proper checks can produce models that perform poorly outside of the immediate training dataset. Lessons learned from biological AI/ML research indicate that Open Science principles such as data sharing and open-source code must go hand-in-hand with publicly available, high-quality training curricula in best practices, with modules centered on real-life scientific use cases and data so future AI/ML practitioners gain experience on real problems. Here we present the development of open-source training materials for AI/ML and space biosciences, as part of the NASA Transform to Open Science Training (TOPST) initiative. We develop 4 independent training programs, focused on the following topics: 1) Fundamentals of Machine Learning and Space Biosciences Domain, 2) Open Science, Artificial Intelligence, and Ethical Best Practices for Data Sharing and Analysis, 3) Using AI/ML Classification to Identify Gene Networks Affected By Space Exposure in Mouse Liver, and 4) Using Neural Networks to Find DNA Damage Patterns in Immune Cells after Radiation. All programs leverage cloud-based NASA biological datasets. The curriculum we present will enable worldwide access to training in AI/ML and scientific analysis.

James Andrew Casaletto↗