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At least 1,801 records · Page 100
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Metabolome of human gut microbiome is predictive of host dysbiosis

Background: Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome’s interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on its community metabolome; an emergent property of the microbiome. Results: Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles. Conclusions: Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome–host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.

human microbiome↗
NASA NTRSDate not supplied

Designing Molten Salt Eutectics

Designing stable electrolytes with target properties is an important challenge in realizing next generation energy storage devices. Molten salt eutectics-based electrolytes are known for their stability with minimal parasitic reactions when compared to traditional organic electrolytes and are an attractive option for different battery chemistries. The operating temperature of the molten salt batteries depends on the melting temperature of the eutectic and hence there is a necessity to discover novel low melting temperature molten salt eutectic mixtures for energy storage applications. In this work we develop a high throughput computational screening approach for molten salt mixtures using thermodynamic modeling and machine learning (ML). COSMO-SAC model and ML approaches were independently developed based on the existing experimental data and these models were further used to predict the eutectic melting temperature and composition of several new binary, ternary, and quaternary mixtures. We show that combining ML and thermodynamic modeling strategies is effective in exploring the vast design space of molten salt mixtures.

Ashwin Ravichandran↗
DOE OSTI2019

A machine learning approach to thermal conductivity modeling: A case study on irradiated uranium-molybdenum nuclear fuels

A deep neural network was developed for the purpose of predicting thermal conductivity with a case study performed on irradiated nuclear fuel. Traditional thermal conductivity modeling approaches rely on existing theoretical frameworks that describe known, relevant phenomena that govern the microstructural evolution processes during neutron irradiation (such as recrystallization, and pore size, distribution and morphology). Current empirical modeling approaches, however, do not represent all irradiation test data well. We develop a machine learning approach to thermal conductivity modeling that does not require a priori knowledge of a specific material microstructure and system of interest. Our approach allows re-searchers to probe dependency of thermal conductivity on a variety of reactor operating and material conditions. The purpose of building such a model is to allow for improved predictive capabilities linking structure-property-processing-performance relationships in the system of interest (here, irradiated nuclear fuel), which could lead to improved experimental test planning and characterization. The uranium-molybdenum system is the fuel system studied in this work, and historic irradiation test data is leveraged for model development. Our model achieved a mean absolute percent error of approximately 10%. Results indicate our model generalizes well to never before seen data, and thus use of deep learning methods for material property predictions from limited, historic irradiation data is a viable approach. This work challenges the current paradigm in materials science, where material property models are based on limited experimental data fitted to low-dimensionality phenomenological models, or by simulations in which fundamental equations are explicitly solved. The work presented here aims to demonstrate the potential and limitations of machine learning in the field of materials science and material property modeling.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS2018

Application of Machine-Learning Algorithms for On-Board Asteroid Shape Model Determination

The Application of Machine-learning Algorithms for On-board Asteroid Shape Model Determination project will develop an innovative system for spacecraft navigation to expand the capability of small spacecraft to meet the critical challenges associated with small-body exploration. Such challenges include accurate navigation in a microgravity environment and precision targeting of particular locations on an asteroid surface for sample collection. This on-board system will cut the computational "umbilical" back to Earth-currently necessary for the generation of a global shape model that requires thousands of images with sufficient resolution and adequate variation of incidence and emission angles, processed manually by a team of experts on Earth for several months. Small satellites have limited bandwidth and are unable to downlink the data volume required for this processing, restricting their ability to perform deep-space asteroid exploration.

Machine learning algorithms↗
DOE OSTI2024

Building an ab initio solvated DNA model using Euclidean neural networks

Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Physics-Reinforced Machine Learning Algorithms for Multiscale Closure Model Discovery

The central objective of this project was to address the challenge of modeling and simulating complex multiscale turbulence phenomena by leveraging physics-guided machine learning (PGML) and hybrid modeling approaches. By integrating physics-based methods with data-driven models, the research focused on achieving robust and scalable solutions for geophysical turbulence, enhancing numerical weather prediction and climate research tools. The project resulted in significant advancements in computational modeling paradigms, predictive tools for reduced-order modeling, and innovative algorithms for fluid dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Machine learning prediction of incidence of Alzheimer’s disease using large-scale administrative health data

Nationwide population-based cohort provides a new opportunity to build an automated risk prediction model based on individuals’ history of health and healthcare beyond existing risk prediction models. We tested the possibility of machine learning models to predict future incidence of Alzheimer’s disease (AD) using large-scale administrative health data. From the Korean National Health Insurance Service database between 2002 and 2010, we obtained de-identified health data in elders above 65 years (N = 40,736) containing 4,894 unique clinical features including ICD-10 codes, medication codes, laboratory values, history of personal and family illness and socio-demographics. To define incident AD we considered two operational definitions: “definite AD” with diagnostic codes and dementia medication (n = 614) and “probable AD” with only diagnosis (n = 2026). We trained and validated random forest, support vector machine and logistic regression to predict incident AD in 1, 2, 3, and 4 subsequent years. For predicting future incidence of AD in balanced samples (bootstrapping), the machine learning models showed reasonable performance in 1-year prediction with AUC of 0.775 and 0.759, based on “definite AD” and “probable AD” outcomes, respectively; in 2-year, 0.730 and 0.693; in 3-year, 0.677 and 0.644; in 4-year, 0.725 and 0.683. The results were similar when the entire (unbalanced) samples were used. Important clinical features selected in logistic regression included hemoglobin level, age and urine protein level. This study may shed a light on the utility of the data-driven machine learning model based on large-scale administrative health data in AD risk prediction, which may enable better selection of individuals at risk for AD in clinical trials or early detection in clinical settings.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Findings on Subtask 3.1 - Bakken Rich Gas Enhanced Oil Recovery Project

Total in-place oil for the Bakken petroleum system (BPS) (which includes the Bakken and Three Forks Formations) has been estimated to be 600 billion barrels (bbl). However, BPS wells have decline rates as high as 85% over the first 3 years of their lives, and primary recovery factors typically range from 3% to 10% of original oil in place. Given the low initial recovery rates, even small incremental productivity improvements could dramatically increase technically recoverable oil in the BPS. One potential solution is enhanced oil recovery (EOR) using gas injection, such as carbon dioxide (CO2) or hydrocarbon (HC) gases. While commonly used in conventional reservoirs, CO2 EOR in unconventional tight oil reservoirs has been limited to pilot tests. EOR using rich gas (mixture of methane, ethane, and propane) has also been employed in numerous pilots in several unconventional plays and has recently been successfully applied in the Eagle Ford play. If successful, large-scale gas-based EOR in the BPS could dramatically increase oil productivity and recovery factors and extend the life of the play for decades. While CO2 may be a technically suitable working fluid for EOR in the BPS, supplies are limited and costs for using CO2 in EOR pilots are prohibitively high. Meanwhile, produced gas flaring has presented challenges for BPS operators in North Dakota. Analysis conducted by the North Dakota Pipeline Authority indicates that the current gas-gathering infrastructure in North Dakota is insufficient to accommodate all of the associated gas that is produced from the BPS. The geographically isolated location of North Dakota relative to large natural gas markets, combined with suppressed natural gas prices, has made it economically challenging for industry to invest capital in expanding gas-gathering infrastructure in the state. These circumstances led to a research program conducted by the Energy & Environmental Research Center (EERC) in partnership with Liberty Resources Management Company LLC (LR) to examine the potential to use rich gas injection for EOR and mitigate flaring. A rich gas EOR pilot test was designed and executed by LR at its Stomping Horse development area in Williams County, North Dakota. From July 2018 through May 2019, a total of 160 million standard cubic feet (MMscf) of rich produced gas was injected into the BPS using five different wells in a sequential injection strategy. LR’s Leon–Gohrick drill spacing unit (DSU) was used as the test site. Regulatory oversight was provided by the North Dakota Industrial Commission (NDIC). Technical support was provided by the EERC through a series of laboratory, modeling, and field-based activities, and additional post-pilot research activities incorporated learnings from the test, developed new laboratory data, improved fracture modeling methods, and developed machine learning and big data analytics. The results from the Stomping Horse rich gas EOR pilot activities indicate that developing an effective, economical EOR approach for the BPS will require more field tests. Another key lesson learned from the Stomping Horse tests is that detailed pre- and posttest data on reservoir conditions and fluids production are essential. Robust reservoir characterization provides information that is crucial to creating realistic geomodels and conducting valid dynamic simulations of potential EOR scenarios. A detailed understanding of the completions and production history of offset wells is also necessary for valid test result interpretations. This knowledge is essential to designing the operational parameters of injectivity tests and interpreting the results. A conformance control strategy is also essential to success. Laboratory-based examinations of rich gas interactions with reservoir fluids and rocks were conducted, with an emphasis on determining the ability to mobilize oil in the tight reservoir rocks and shales of the BPS. Injection fluid composition was shown to have a positive impact on reducing reservoir oil minimum miscibility pressure (MMP), reducing interfacial tension (IFT), and altering wettability. IFT and contact angle measurements demonstrated that wettability can be altered in the presence of rich gas, suggesting the potential to improve oil recovery. Iterative modeling of surface infrastructure and reservoir performance using data generated by the various project activities was conducted. A geologic model of the Stomping Horse area was built; history-matched oil, gas, and water production was used in simulations of various EOR scenarios. Early programmatic modeling results were used to support LR’s design and operation of the EOR pilot and to provide insight regarding optimization of future commercial-scale BPS EOR design and operations. Post-pilot modeling focused on alternative methods of understanding complex fracture networks and accelerating simulation time. These led to improved simulation run times and provide excellent history-matching results. Several of these iterative models were used as the bases for developing algorithms into machine learning and big data analytics. History matching in reservoir simulation is time-consuming and computer processing-intensive. Machine learning algorithms were created, and an automated history-matching tool was developed. A large set of synthetic reservoir simulations were created to generate well responses (oil, gas, and water production, well bottomhole pressure [BHP], and tracer or propane breakthrough) for a set of EOR operating parameters that included offset well status (open or closed), injectate (rich gas or propane), injection rate, and injection well BHP. A user interface was developed to provide real-time visualization. Machine learning-based models were developed to provide rapid forecasting of well performance given a set of user-defined EOR operating parameters. These predictive models allow the user to modify the offset well status, injection rate, and injection well BHP and rapidly forecast future production performance. The combination of real-time visualization tools with real-time forecasting tools provides a framework for real-time control—operational changes that the EOR site operator can enact (e.g., changing gas injection rates) to affect the observed performance and potentially improve the EOR outcome. There is great reason to be optimistic about the future of EOR in the Bakken. The results of the laboratory studies suggest significant potential for high rates of oil mobilization using produced field gas injection under the right conditions. The results of the lab studies, combined with rigorous statistical analysis of well production data and associated modeling efforts, confirm the notion that fluid mobility within the reservoir is controlled by fractures. As more knowledge is gained about the nature and distribution of fracture networks in the Bakken, the industry will be in a better position to predict and, ultimately, influence fluid mobility. New field tests are necessary to develop a more complete understanding of those conditions. Thoughtful and creatively engineered field tests within a well-characterized geologic setting will yield the fundamental knowledge needed to take Bakken oil production to the next level. This subtask was cofunded through the EERC–U.S. Department of Energy Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FE0024233. Nonfederal funding was provided by the North Dakota Industrial Commission’s Oil and Gas Research Program and Computer Modelling Group.

04 OIL SHALES AND TAR SANDS↗
NASA NTRS2018

Machine Learning Application to Atmospheric Chemistry Modeling

Atmospheric chemistry is a high-dimensionality, large-data problem and thus may be suited to machine-learning algorithms. We show here the potential of a random forest regression algorithm to replace the gas-phase chemistry solver in the GEOS-Chem chemistry model. In this proof-of-concept study, we used one month of model output to train random forest regression models to predict the concentrations of each long-lived chemical species after integration based upon the physical and chemical conditions before the chemical integration. The choice of prediction type has a strong impact on the skill of the regression model. We find best results from predicting the change in concentration for very long-lived species and the absolute concentration for shorter lived species. The skill of the machine learning algorithm is further improved by using a family approach for NO and NO2 rather than treating them independently.By replacing the numerical integrator with the random forest algorithm and running this model for one month, we find that the model is able to reproduce many of the features of the reference chemistry simulation. Replacing the integration methodology with a machine learning algorithm has the potential to be substantially faster. There are a wide range of applications for such an approach, e.g. to generate boundary conditions, for use in air quality forecasts or chemical data assimilation systems, etc.

Keller, Christoph A.↗
DOE OSTI2022

FutureTense

Protective vaccines and reliable diagnostics are essential tools for controlling viral diseases. However, the efficacy of these tools can be diminished by mutations in viral genomes. The delay between the emergence of new viral strains and the redesign of vaccines and diagnostics allows for continued viral transmission. Is it possible to address this challenge by computationally predicting viral genome sequence evolution? Can we “future-proof” vaccines and diagnostics by targeting both current and anticipated future sequence variants? While predicting viral evolution is still an unsolved, “grand challenge” problem in biology, the large, and rapidly growing, number of SARS-CoV-2 genome sequences provide an opportunity to quantify the ability of machine learning to predict viral genome sequence evolution. Towards this end, we have developed a simple computational model for predicting viral evolution at the level of individual nucleotides. The key metric for quantifying the per-base, prediction accuracy for viral evolution is the Mann-Whitney U statistic (or, equivalently, the area under the receiver operator curve). Since the Mann-Whitney U statistic is not a differentiable function, existing deep leaning packages (like Pytorch and Keras/TensorFlow) are not useful, as they require that the accuracy metric/objective function be analytically differentiable with respect to the model parameters. To overcome this challenge, we have implemented custom software, “FutureTense”, that can train a machine learning model by maximizing the non-differentiable Mann-Whitney U statistic. This software trains a machine learning model by exploring along the direction of the discrete gradient of the Mann-Whitney U statistic in the model parameter space. Parallel computing and genome sequence-specific optimizations are used to accelerate model training. The resulting machine learning model learns the observed high C->U mutation rates in the SARS-CoV-2 genome (which are potentially induced by host defenses) and provides prediction accuracies that are significantly better than one would expect from random chance. While predicting viral evolution is still quite far from a solved problem, the surprising performance of this simple model gives hope that the accuracy of predicting viral genome evolution can be further increased by more sophisticated approaches.

Gans, Jason↗
NASA NTRS2024

Augmenting RANS Turbulence Models Guided by Field Inversion and Machine Learning

This report investigates the use of a data-driven approach, viz., Field Inversion and Machine Learning (FIML), to improve conventional RANS turbulence models like the Spalart-Allmaras model and the Menter SST k-ω model. One of the crucial aspects of using an ML-based approach with limited training data to produce corrections that are generalizable to a large range of flow configurations is to design appropriate “features” (inputs to the ML model). A model, based on guidance from the FIML methodology, is presented in analytical form. An additional list of potential features is provided. Although these were not used in the present correction, they were considered in the course of its development, and are included to fully document the complete process employed in the present work.

turbulence modeling↗
DOE OSTI2022

Spatial Transferability of Machine Learning Based Volume Estimation Models

High-quality traffic volume data is essential for efficient transportation planning and operations. However, such high-quality data is expensive to collect, owing primarily to the high capital cost of installing and maintaining continuous counting stations (CCSs). Recent availability of probe-based vehicle data offers a cost-effective solution for increasing the observability of traffic volumes. However, having ample ground truth traffic data is a prerequisite for developing robust volume estimation models. Though this might not be a big issue in many states, states with scarce CCS data might be able to benefit from robust volume estimation models developed in (adjacent) data-rich states. While there is a reasonable amount of spatial transferability research in the transportation domain, there is a dearth of knowledge on the spatial transferability of probe-based volume estimation models. To address this gap, this paper explores spatial transferability of volume estimation models developed from data in three states (Colorado, North Carolina, and Pennsylvania). Results indicate that it is extremely important to maintain temporal consistency when attempting spatial transferability of volume estimation models. It was also found that models trained on regions with lower peak traffic volumes will limit the performance of models transferred to states with higher peak hourly traffic volumes. Corroborating findings from existing spatial transferability research on other topics, it was found that a meta-model (developed using data from multiple states) performs better than volume estimation models developed within any one of the states.

ADVANCED PROPULSION SYSTEMS↗
NASA NTRSDate not supplied

NASA Earth: Synthetic Spectranomics - Deep Learning of Surface 3-D Geometry, Chemistry, and Hyperspectra to Inform Next-generation Land Models

Machine and deep learning (ML/DL) have transformed our approach to Earth observation and system modeling (EOSM), unifying both in view of ML/DL models as a form of data assimilation (DA). Trained on diverse Earth observation records, detailed physical models, or hybrids of both in physics-informed machine learning, ML/DL may improve upon existing Earth system model (ESM) formulations while creating entirely new classes of models. One important application of deep learning is observation synthesis, allowing ESM developers to prepare for the increased spatial, temporal, and spectral/polar resolution of proposed future observing systems. This may involve the retrospective application of learning algorithms to existing observational records, with or without physical radiative transfer models, to co-inform mission planning and ESM development while providing a degree of data continuity for new missions.

Adam Erickson↗
DOE OSTI2021

Uncertainty quantification for deep learning in particle accelerator applications

With the advent of increased computational resources and improved algorithms, machine learning-based models are being increasingly applied to complex problems in particle accelerators. However, such data-driven models may provide overly confident predictions with unknown errors and uncertainties. For reliable deployment of machine learning models in high-regret and safety-critical systems such as particle accelerators, estimates of prediction uncertainty are needed along with accurate point predictions. In this investigation, we evaluate Bayesian neural networks (BNN) as an approach that can provide accurate predictions along with reliably quantified uncertainties for particle accelerator problems, and compare their performance with bootstrapped ensembles of neural networks. We select three accelerator setups for this evaluation: a storage ring, a photoinjector, and a linac. The problems span different data volumes and dimensionalities (e.g., scalar predictions as well as image outputs). It is found that BNN provide accurate predictions of the mean along with reliable estimates of predictive uncertainty across the test cases. In this vein, BNN may offer an attractive alternative to deterministic deep learning tools to generate accurate predictions with quantified uncertainties in particle accelerator applications.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

An interpretable machine learning framework to understand bikeshare demand before and during the COVID-19 pandemic in New York City

In recent years, bikesharing systems have become increasingly popular as affordable and sustainable micromobility solutions. Advanced mathematical models such as machine learning are required to generate good forecasts for bikeshare demand. Here, this study proposes a machine learning modeling framework to estimate hourly demand in a large-scale bikesharing system. Two Extreme Gradient Boosting models were developed: one using data from before the COVID-19 pandemic (March 2019 to February 2020) and the other using data from during the pandemic (March 2020 to February 2021). Furthermore, a model interpretation framework based on SHapley Additive exPlanations was implemented. Based on the relative importance of the explanatory variables considered in this study, share of female users and hour of day were the two most important explanatory variables in both models. However, the month variable had higher importance in the pandemic model than in the pre-pandemic model.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Golden Eagle Behavioral Modeling Enabled by High-Fidelity Atmospheric Models

The DOE-funded Golden Eagle Behavioral Modeling project combines knowledge of eagle behavior, eagle telemetry data, high-fidelity atmospheric and wind power plant flow models, and machine learning to develop tools that predict behavior and risk around wind power plants. This presentation provides background on the project and modeling approaches, as well as recent modeling and validation results from the region around the Top of the World wind plant in Wyoming.

49 EE - Wind and Water Power Program - Wind (EE-4W↗
DOE OSTI2026

Machine Learning Interatomic Potentials for Modeling Framework Flexibility and Water Uptake in NbOFFIVE-1-Ni Metal–Organic Framework

Metal–organic frameworks (MOFs), with their distinctive porous structures and tunable chemical properties, have shown immense promise in the separation and storage of gases. Currently, the accurate simulation of their adsorptive properties remains challenging, especially for systems where the molecules fit very tightly into the pores. Traditional simulation methods often approximate the frameworks as rigid and do not account for the framework flexibility seen in materials such as NbOFFIVE-1-Ni. First-principles molecular dynamics (FPMD) simulations offer the desired accuracy in modeling this flexibility but are limited by their extensive computational demands, rendering them impractical for long simulations. Conversely, classical force field-based simulations offer computational efficiency but lack the necessary accuracy. Here, to break this accuracy-efficiency trade-off, we have developed machine learning interatomic potentials trained on energies and forces from FPMD to model the framework flexibility of NbOFFIVE-1-Ni in the presence of water over nanosecond time scales. Furthermore, by integrating MLIP-driven molecular dynamics (MLIP-MD) with grand canonical Monte Carlo (GCMC) simulations, we further incorporated framework flexibility into adsorption predictions, yielding water adsorption isotherms that better align with experimental data compared to those of conventional GCMC simulations. These advances offer new opportunities for the design and optimization of MOFs in gas storage and separation applications.

adsorption↗

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