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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Knowledge-guided learning with curated prior genetic biomarkers for robust model interpretation

Abstract Motivation Knowledge-guided learning offers effective and robust model training strategies in data-scarce settings by incorporating established domain knowledge, thereby enhancing generalization, robustness, and interpretability. By contrast, conventional deep learning approaches rely purely on data-driven learning, which can limit robust model interpretability, particularly in high-dimensional settings with limited size samples. In computational biology, knowledge-guided learning has primarily leveraged network- and structural-based knowledge, leading to biologically interpretable representations and enhanced predictive performance compared to conventional approaches. However, curated biomarkers, one of the most accessible forms of biological knowledge, remain largely unexplored within knowledge-guided paradigms. Results In this study, we propose a model-agnostic training paradigm, Biomarker-driven Explainable Prior-guided Learning (BioExPL), that can be applied to any neural networks that incorporates curated prior knowledge. BioExPL enforces neural networks to reflect curated biomarker priors in their latent representations through a novel knowledge-alignment loss. BioExPL consistently demonstrated significantly improved predictive performance and enhanced model interpretability with minimized computational overhead in simulation studies and intensive experiments on multiple cancer datasets. BioExPL not only integrates prior curated knowledge into the model but also accurately identifies unknown associated signals additionally. BioExPL is model-agnostic and domain-independent, enabling its integration into diverse neural network architectures. Availability and implementation The open-source is publicly available at: https://github.com/datax-lab/BioExPL.

Baek, Beomsu [Department of Computer Science, Univ↗
DOE OSTI2019

The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases

Model organisms are essential experimental platforms for discovering gene functions, defining protein and genetic networks, uncovering functional consequences of human genome variation, and for modeling human disease. For decades, researchers who use model organisms have relied on Model Organism Databases (MODs) and the Gene Ontology Consortium (GOC) for expertly curated annotations, and for access to integrated genomic and biological information obtained from the scientific literature and public data archives. Through the development and enforcement of data and semantic standards, these genome resources provide rapid access to the collected knowledge of model organisms in human readable and computation-ready formats that would otherwise require countless hours for individual researchers to assemble on their own. Since their inception, the MODs for the predominant biomedical model organisms [Mus sp (laboratory mouse), Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, and Rattus norvegicus] along with the GOC have operated as a network of independent, highly collaborative genome resources. In 2016, these six MODs and the GOC joined forces as the Alliance of Genome Resources (the Alliance). By implementing shared programmatic access methods and data-specific web pages with a unified "look and feel," the Alliance is tackling barriers that have limited the ability of researchers to easily compare common data types and annotations across model organisms. To adapt to the rapidly changing landscape for evaluating and funding core data resources, the Alliance is building a modern, extensible, and operationally efficient "knowledge commons" for model organisms using shared, modular infrastructure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Model-Based Approaches to Generate Knowledge from Data in a Plant Reliability Context

One challenge that nuclear power plant system engineers are facing is that the amount of equipment reliability (ER) data being continuously generated are extremely large. These data elements come in different forms: textual (e.g., condition reports) and numeric (e.g., generated by monitoring systems) and they provide system engineers with valuable insights and information regarding the discovery of anomalous behaviors or degradation trends, the identification of the possible causes behind such behaviors and trends, and the prediction of their direct consequences. This paper directly targets the generation of knowledge from ER data by putting “data into context”. Here, we employ model-based system engineering (MBSE) models of systems and assets to represent and capture their architecture and functional (i.e., cause-effect) relations. ER data elements are processed by identifying first which elements of the developed MBSE elements they are referring to. This task is much harder for textual data since the information contained in issue or maintenance reports needs to “be understood” by a computational tool. Here we called this process “knowledge extraction” where our methods to extract knowledge from textual data. Lastly, once numeric and textual ER data elements have been processed and “understood”, we discover possible cause-effect relations among them. This is performed by observing if a logical connection through the MBSE models exists, and if there is a temporal relation among them. The logic and temporal are the two main ingredients to perform “machine reasoning” from ER data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Model-Based Approaches to Generate Knowledge from Data in a Plant Reliability Context

One challenge that nuclear power plant system engineers are facing is continuous generation of an extremely large amount of equipment reliability (ER) data. These data elements come in textual (e.g., condition reports) and numeric (e.g., generated by monitoring systems) forms. They provide system engineers with valuable insights and information by discovering anomalous behaviors or degradation trends, identifying possible causes behind such behaviors and trends, and predicting their direct consequences. This paper directly targets the knowledge generation from ER data by putting “data into context.” We employ model-based system engineering (MBSE) of systems and assets to represent and capture their architecture and functional (i.e., cause-effect) relations. ER data elements are processed by first identifying which of the developed MBSE elements they are referring to. This task is harder for textual data since the information contained in issue or maintenance reports needs to be “understood” by a computational tool. We called this process “knowledge extraction” since our methods extract knowledge from textual data. Last, once numeric and textual ER data elements have been processed and “understood,” we discover possible cause-effect relations among them. This is performed by observing whether a logical connection through the MBSE models exists, and if there is a temporal relationship among them. The logic and temporal are the two main ingredients to perform “machine reasoning” from ER data.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Quantifying microbial control of soil organic matter dynamics at macrosystem scales

Soil organic matter (SOM) stocks, decomposition and persistence are largely the product of controls that act locally. Yet the controls are shaped and interact at multiple spatiotemporal scales, from which macrosystem patterns in SOM emerge. Theory on SOM turnover recognizes the resulting spatial and temporal conditionality in the effect sizes of controls that play out across macrosystems, and couples them through evolutionary and community assembly processes. For example, climate history shapes plant functional traits, which in turn interact with contemporary climate to influence SOM dynamics. Selection and assembly also shape the functional traits of soil decomposer communities, but it is less clear how in turn these traits influence temporal macrosystem patterns in SOM turnover. Here, we review evidence that establishes the expectation that selection and assembly should generate decomposer communities across macrosystems that have distinct functional effects on SOM dynamics. Representation of this knowledge in soil biogeochemical models affects the magnitude and direction of projected SOM responses under global change. Yet there is high uncertainty and low confidence in these projections. To address these issues, we make the case that a coordinated set of empirical practices are required which necessitate (1) greater use of statistical approaches in biogeochemistry that are suited to causative inference; (2) long-term, macrosystem-scale, observational and experimental networks to reveal conditionality in effect sizes, and embedded correlation, in controls on SOM turnover; and (3) use of multiple measurement grains to capture local- and macroscale variation in controls and outcomes, to avoid obscuring causative understanding through data aggregation. Here, when employed together, along with process-based models to synthesize knowledge and guide further empirical work, we believe these practices will rapidly advance understanding of microbial controls on SOM and improve carbon cycle projections that guide policies on climate adaptation and mitigation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

CCSI Toolset 3.19 Release

CCSI Toolset 3.19 Release Highlights A gradient generation tool was developed to support GENN models in FOQUS. Certain machine learning tools train gradient-enhanced neural network (GENN) models which can be more accurate for complex datasets given a priori knowledge of model derivatives. However, the derivatives must be known beforehand and are not often available for process data. This tool automatically predicts the gradients for a training dataset in a form usable by common GENN trainers, such as Surrogate Modeling Toolbox. Support was added for Surrogate Modeling Toolbox GENN models in FOQUS, including updates to the run methods, node properties, test framework, documentation and optional dependencies list. Users can train/save Surrogate Modeling Toolbox gradient-enhanced neural network (GENN) models with custom objects and produce .pkl files compatible with the Machine Learning/Artificial Intelligence Plugin in FOQUS. A simpler implementation of the ordering algorithm in the Sequential Design of Experiments (SDOE) module was included. The SDOE examples documentation was updated. The Optimality-Based Design of Experiments was updated to improve the error handling when the results are None.

AS↗
DOE OSTI2024

Structured information extraction from scientific text with large language models

Extracting structured knowledge from scientific text remains a challenging task for machine learning models. Here, we present a simple approach to joint named entity recognition and relation extraction and demonstrate how pretrained large language models (GPT-3, Llama-2) can be fine-tuned to extract useful records of complex scientific knowledge. We test three representative tasks in materials chemistry: linking dopants and host materials, cataloging metal-organic frameworks, and general composition/phase/morphology/application information extraction. Records are extracted from single sentences or entire paragraphs, and the output can be returned as simple English sentences or a more structured format such as a list of JSON objects. This approach represents a simple, accessible, and highly flexible route to obtaining large databases of structured specialized scientific knowledge extracted from research papers.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

Abstract Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI’s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Measurement of U 238 ( n , n ' γ ) cross section data and their impact on reaction models

A better knowledge of (n,xn) reaction cross sections is important for both reaction modeling and energy applications. This article focuses on inelastic scattering of neutrons off 238 U for which improvements are needed to better constrain evaluations and solve inconsistencies in nuclear power reactor calculations. A new precise measurement of (n,xnγ) reaction cross sections on 238 U has been performed at the GELINA (Geel Electron LINear Accelerator) neutron facility operated by EC-JRC-Geel (Belgium) with the GRAPhEME (GeRmanium array for Actinides PrEcise MEasurements) setup. The prompt γ-ray spectroscopy method coupled to time-of-flight measurements is used to extract (n,xnγ) cross section values which can be further combined to infer the total neutron inelastic scattering cross section. Cross section data for 18 γ transitions (five never measured before) are presented and compared to the data in the literature. Here, emphasis is especially given to the uncertainty determination to produce partial cross section data as accurate as possible. Due to intrinsic limitations of the experimental method, the use of additional nuclear structure information coupled with theoretical modeling is required to determine the total (n, n') cross section over the whole neutron energy range. We have investigated modeling aspects of the 238 U(n,n'γ) cross sections related to the description of compound nucleus and preequilibirum mechanisms as well as the discrete part of nuclear structure. Through comparison between experimental and calculated (n,n'γ) cross sections, we pinpoint inaccuracies in the description of specific reaction mechanisms and challenge recently implemented models. This helps improving the whole modeling of the (n, n') reaction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

The potential role of methanesulfonic acid (MSA) in aerosol formation and growth and the associated radiative forcings

Atmospheric marine aerosol particles impact Earth's albedo and climate. These particles can be primary or secondary and come from a variety of sources, including sea salt, dissolved organic matter, volatile organic compounds, and sulfur-containing compounds. Dimethylsulfide (DMS) marine emissions contribute greatly to the global biogenic sulfur budget, and its oxidation products can contribute to aerosol mass, specifically as sulfuric acid and methanesulfonic acid (MSA). Further, sulfuric acid is a known nucleating compound, and MSA may be able to participate in nucleation when bases are available. As DMS emissions, and thus MSA and sulfuric acid from DMS oxidation, may have changed since pre-industrial times and may change in a warming climate, it is important to characterize and constrain the climate impacts of both species. Currently, global models that simulate aerosol size distributions include contributions of sulfate and sulfuric acid from DMS oxidation, but to our knowledge, global models typically neglect the impact of MSA on size distributions. In this study, we use the GEOS-Chem-TOMAS (GC-TOMAS) global aerosol microphysics model to determine the impact on aerosol size distributions and subsequent aerosol radiative effects from including MSA in the size-resolved portion of the model. The effective equilibrium vapor pressure of MSA is currently uncertain, and we use the Extended Aerosol Inorganics Model (E-AIM) to build a parameterization for GC-TOMAS of MSA's effective volatility as a function of temperature, relative humidity, and available gas-phase bases, allowing MSA to condense as an ideally nonvolatile or semivolatile species or too volatile to condense. We also present two limiting cases for MSA's volatility, assuming that MSA is always ideally nonvolatile (irreversible condensation) or that MSA is always ideally semivolatile (quasi-equilibrium condensation but still irreversible condensation). We further present simulations in which MSA participates in binary and ternary nucleation with the same efficacy as sulfuric acid whenever MSA is treated as ideally nonvolatile. When using the volatility parameterization described above (both with and without nucleation), including MSA in the model changes the global annual averages at 900 hPa of submicron aerosol mass by 1.2 %, N3 (number concentration of particles greater than 3 nm in diameter) by -3.9 % (non-nucleating) or 112.5 % (nucleating), N80 by 0.8 % (non-nucleating) or 2.1 % (nucleating), the cloud-albedo aerosol indirect effect (AIE) by -8.6 mW m -2 (non-nucleating) or -26 mW m -2 (nucleating), and the direct radiative effect (DRE) by -15 mW m -2 (non-nucleating) or -14  mW m -2 (nucleating). The sulfate and sulfuric acid from DMS oxidation produces 4–6 times more submicron mass than MSA does, leading to an ~10 times stronger cooling effect in the DRE. But the changes in N80 are comparable between the contributions from MSA and from DMS-derived sulfate/sulfuric acid, leading to comparable changes in the cloud-albedo AIE. Model–measurement comparisons with the Heintzenberg et al. (2000) dataset over the Southern Ocean indicate that the default model has a missing source or sources of ultrafine particles: the cases in which MSA participates in nucleation (thus increasing ultrafine number) most closely match the Heintzenberg distributions, but we cannot conclude nucleation from MSA is the correct reason for improvement. Model–measurement comparisons with particle-phase MSA observed with a customized Aerodyne high-resolution time-of-flight aerosol mass spectrometer (AMS) from the ATom campaign show that cases with the MSA volatility parameterizations (both with and without nucleation) tend to fit the measurements the best (as this is the first use of MSA measurements from ATom, we provide a detailed description of these measurements and their calibration). However, no one model sensitivity case shows the best model–measurement agreement for both Heintzenberg and the ATom campaigns. As there are uncertainties in both MSA's behavior (nucleation and condensation) and the DMS emissions inventory, further studies on both fronts are needed to better constrain MSA's past, current, and future impacts upon the global aerosol size distribution and radiative forcing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Machine learning-based surrogate models and transfer learning for derivative free optimization of HT-PEM fuel cells

Widespread adoption of high-temperature polymer electrolyte membrane electrochemical systems, such as fuel cells (HT-PEMFCs), requires models and computational tools for accurate optimization and guiding new materials for enhancing performance and durability. In this contribution, knowledge-based modelling and data-driven modelling are combined using Few-Shot Learning and implementing an Automated Machine Learning framework for the generation of Machine Learning-based surrogate models. Applicability of the resulting model for derivative-free optimization is demonstrated. Additionally, a way of considering extrapolation in the optimization task is presented. Results show that although extrapolation is needed to achieve better solutions during optimization, it can be monitored and managed. As a result, tuning the electrode ionomer binder's properties, such as ionic conductivity, in the fuel cell represents a promising pathway for improving HT-PEMFC performance.

08 HYDROGEN↗
DOE OSTI2018

Development of a Kalman filter estimator for simulation and control of particulate matter distribution of a diesel catalyzed particulate filter

The knowledge of the temperature and particulate matter mass distribution is essential for monitoring the performance and durability of a catalyzed particulate filter. A catalyzed particulate filter model was developed, and it showed capability to accurately predict temperature and particulate matter mass distribution and pressure drop across the catalyzed particulate filter. However, the high-fidelity model is computationally demanding. Therefore, a reduced order multi-zone particulate filter model was developed to reduce computational complexity with an acceptable level of accuracy. In order to develop a reduced order model, a parametric study was carried out to determine the number of zones necessary for aftertreatment control applications. The catalyzed particulate filter model was further reduced by carrying out a sensitivity study of the selected model assumptions. The reduced order multi-zone particulate filter model with 5 × 5 zones was selected to develop a catalyzed particulate filter state estimator considering its computational time and accuracy. Next, a Kalman filter–based catalyzed particulate filter estimator was developed to estimate unknown states of the catalyzed particulate filter such as temperature and particulate matter mass distribution and pressure drop (Δ P) using the sensor inputs to the engine electronic control unit and the reduced order multi-zone particulate filter model. A diesel oxidation catalyst estimator was also integrated with the catalyzed particulate filter estimator in order to provide estimates of diesel oxidation catalyst outlet concentrations of NO 2 and hydrocarbons and inlet temperature for the catalyzed particulate filter estimator. The combined diesel oxidation catalyst–catalyzed particulate filter estimator was validated for an active regeneration experiment. The validation results for catalyzed particulate filter temperature distribution showed that the root mean square temperature error by using the diesel oxidation catalyst–catalyzed particulate filter estimator is within 3.2 °C compared to the experimental data. Similarly, the Δ P estimator closely simulated the measured total Δ P and the estimated cake pressure drop error is within 0.2 kPa compared to the high-fidelity catalyzed particulate filter model.

Engineering↗
DOE OSTI2023

Nitrogen fixing shrubs advance the pace of tall-shrub expansion in low-Arctic tundra

Abstract Tall deciduous shrubs are critically important to carbon and nutrient cycling in high-latitude ecosystems. As Arctic regions warm, shrubs expand heterogeneously across their ranges, including within unburned terrain experiencing isometric gradients of warming. To constrain the effects of widespread shrub expansion in terrestrial and Earth System Models, improved knowledge of local-to-regional scale patterns, rates, and controls on decadal shrub expansion is required. Using fine-scale remote sensing, we modeled the drivers of patch-scale tall-shrub expansion over 68 years across the central Seward Peninsula of Alaska. Models show the heterogeneous patterns of tall-shrub expansion are not only predictable but have an upper limit defined by permafrost, climate, and edaphic gradients, two-thirds of which have yet to be colonized. These observations suggest that increased nitrogen inputs from nitrogen-fixing alders contributed to a positive feedback that advanced overall tall-shrub expansion. These findings will be useful for constraining and projecting vegetation-climate feedbacks in the Arctic.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Posterior Regularized Bayesian Neural Network

Traditional NNs often lack the ability for uncertainty quantification. Bayesian NNs(BNNs) could help measure the confidence level by using distributions in NNs modeling. Besides, knowledge is commonly available and could improve the performance of BNNs if it can be properly incorporated. In this work, we propose a novel Posterior-Regularized BNN(PR-BNN) model by incorporating soft and hard constraints as a posterior regularization term. We also propose an augmented Lagrangian method and stochastic optimization algorithm for efficient updating via Monte Carlo sampling. The simulations and case studies for solar PV plants have shown the performance improvement of the proposed model over traditional BNNs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Kinetics Modeling for Design of Continuous Enzymatic Hydrolysis

Enzymatic hydrolysis of cellulose to monomeric sugars continues to be a limiting step in cost-effectively producing sugar and fermentation-based biofuels from biomass. In particular, the high cost of enzymes coupled with the long time-scale of reaction pose challenges to economic viability. Performing enzymatic hydrolysis in a continuous mode with enzyme recycle may provide a path towards substantially reduced costs for sugar production, but design and analysis are complicated by a lack of suitable kinetics models. Computationally attainable models, such as fractal-based models, require knowledge of the reaction-history of the biomass, and are thus only suitable for describing the batch reactions from which they are derived. Fundamental models, while potentially more generalizable, are often too computationally intensive to use in process or reactor modeling. In this work, a phenomenological rate model is proposed based on a two-phase substrate representation. Good agreement is seen between batch and continuous enzymatic hydrolysis (CEH) experiment data, which validates the model and enables us to solve for reactor design parameters, such as CEH reactor size and stream flow rates, based on process variables like yield. This model is integrated with techno-economic analysis software to explore economic sensitivities. Important design optimizations and tradeoffs are identified and quantified, including the relative cost imposed by rate slowdown from sugar inhibition versus the cost to remove and concentrate sugars at a lower concentration. It also identifies, high-leverage avenues for further exploration, such as increasing the maximum feasible solids concentration, and sustaining high membrane flux and reliability.

09 BIOMASS FUELS↗