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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally-driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian model (BP-Quant) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern, or the existence of multiple over-expressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab ® and R packages at https://github.com/PNNL-Comp-Mass-Spec/BP-Quant.

Protein Quantitation, proteomics↗
DOE OSTI2015

A Bayesian approach for parameter estimation and prediction using a computationally intensive model

Bayesian methods have been successful in quantifying uncertainty in physics-based problems in parameter estimation and prediction. In these cases, physical measurements y are modeled as the best fit of a physics-based model eta(theta), where theta denotes the uncertain, best input setting. Hence the statistical model is of the form y = eta(theta) + c, where epsilon accounts for measurement, and possibly other, error sources. When nonlinearity is present in eta(center dot), the resulting posterior distribution for the unknown parameters in the Bayesian formulation is typically complex and nonstandard, requiring computationally demanding computational approaches such as Markov chain Monte Carlo (MCMC) to produce multivariate draws from the posterior. Although generally applicable, MCMC requires thousands (or even millions) of evaluations of the physics model eta(center dot). This requirement is problematic if the model takes hours or days to evaluate. To overcome this computational bottleneck, we present an approach adapted from Bayesian model calibration. This approach combines output from an ensemble of computational model runs with physical measurements, within a statistical formulation, to carry out inference. A key component of this approach is a statistical response surface, or emulator, estimated from the ensemble of model runs. We demonstrate this approach with a case study in estimating parameters for a density functional theory model, using experimental mass/binding energy measurements from a collection of atomic nuclei. We also demonstrate how this approach produces uncertainties in predictions for recent mass measurements obtained at Argonne National Laboratory.

Higdon, Dave↗
DOE OSTI2022

Uncertainty quantification in breakup reactions

Breakup reactions are one of the favored probes to study loosely bound nuclei, particularly those in the limit of stability forming a halo. In order to interpret such breakup experiments, the continuum discretized coupled channel method is typically used. In this study, the first Bayesian analysis of a breakup reaction model is performed. Herein we use a combination of statistical methods together with a three-body reaction model (the continuum discretized coupled channel method) to quantify the uncertainties on the breakup observables due to the parameters in the effective potential describing the loosely bound projectile of interest. The combination of tools we develop opens the path for a Bayesian analysis of not only breakup processes, but also a wide array of complex processes that require computationally intensive reaction models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Mass Detection for Heavy-Duty Vehicles using Gaussian Belief Propagation

Predicting vehicle mass is critical to accurately estimate energy use and emissions of commercial trucks. However, data from vehicle telematics is often not at sufficient temporal resolution or accuracy for use in model-based detection methods. In this work, a new statistical mass prediction technique is described for heavy-duty vehicles that incorporates the use Gaussian Belief Propagation (GBP) for probabilistic inference. Similar to Bayesian inference models, the GBP model typically requires less labeled training data than other contemporary machine learning techniques. First, a factor graph is constructed, and a set of Gaussian belief nodes with associated means and variances are fitted to the training data. To better handle noisy input data, the GBP mass prediction model utilizes a k-nearest factors (kNF) algorithm for probabilistic inference on unseen testing data. The proposed method is compared with a classical weighted k-nearest neighbors (kNN) regressor. This statistical kNF-GBP model works even with low-quantity, low-quality initial training data, while being capable of realtime mass estimation. Unlike the kNN regressor, the GBP model produces a measure of uncertainty with its predictions. The proposed method is validated using curve-sampled driving data collected from multiple cloud-connected Class 8 regional haul diesel trucks. Both the kNN regressor and the kNF-GBP mass prediction model were able to predict payload mass with coefficients of determination above 0.97 with minimal data preprocessing.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2019

A Bayesian statistical approach to inferring particle dynamics from in-situ pump POC and chloropigment data from the Mediterranean Sea

Concentrations of chloropigments and particulate organic carbon (POC) in large-volume in-situ pump samples from the Mediterranean Sea were used to estimate rate constants of processes that control the fate of particles, and specifically chloropigments, in the water column. In this paper we introduce a Bayesian statistical inversion method that combines the data with a new box model and has the capacity to infer rate constants for POC respiration/dissolution, chlorophyll and pheopigment degradation, and particle aggregation and disaggregation. We use first-order kinetics to model disaggregation, and use both first-order and second-order kinetics to model aggregation. Using these methods, the estimated small-particle (1–70 μm) POC respiration rate constant was 2.44 -1.00 +1.69 yr -1 (0.41 yr). The estimated disaggregation and second-order aggregation rate constants were 85.6 -36.4 +63.4 yr -1 (1.17×10 -2 yr) and 2.78 -1.17 +2.01 μM -1 yr -1 , respectively. Using the optimal rate constants and the corresponding particle concentrations, disaggregation is ~4.2 times faster than the small-size POC dissolution rate, which indicates that disaggregation is a dominant processes at the time of sampling. More importantly, by comparing our results with those of previous studies, we conclude that sampling methods have less influence than tracers themselves on inferring particle dynamic rate constants. We previously introduced a somewhat similar approach to modeling SV sediment trap data, but large volume pumps are a much more common sample collection method in oceanographic surveys than SV sediment traps, and thus our new model should have a wider applicability.

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

Predicting fusion ignition at the National Ignition Facility with physics-informed deep learning

Here, an inertial confinement fusion experiment, carried out at the National Ignition Facility, has achieved ignition by generating fusion energy exceeding the laser energy that drove the experiment. Prior to the experiment, a generative machine learning model that combines radiation hydrodynamics simulations, deep learning, experimental data, and Bayesian statistics was used to predict, with a probability greater than 70%, that ignition was the most likely outcome for this shot.

Spears, Brian K. [Lawrence Livermore National Labo↗
DOE OSTI2019

sitoolbox: A package for Bayesian estimation of the isotropy violation in the CMB sky

ABSTRACT The standard model of cosmology predicts a statistically isotropic (SI) cosmic microwave background (CMB) sky. However, the SI violation signals are always present in an observed sky-map. Different cosmological artefacts, measurement effects, and unavoidable effects during data analysis, etc. may lead to isotropy violation in an otherwise SI sky. Therefore, a proper data analysis technique should calculate all these SI violation signals, so that they can be matched with SI violation signals from the known sources, and then conclude if there is any intrinsic SI violation in the CMB sky. In one of our recent works, we presented a general Bayesian formalism for measuring the isotropy violation signals in the CMB sky in the presence of an idealized isotropic noise. In this paper, we have extended the mechanism and develop a software package, sitoolbox, for measuring SI violation in presence of anisotropic noise and masking.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

Hierarchical Bayesian estimation for adsorption isotherm parameter determination

Estimation of isotherm model parameters from experimental data is necessary in adsorption process modeling. To facilitate isotherm modeling, databases that store experimental data exist. Nevertheless, data inconsistency among different researchers must be resolved to find a single set of isotherm parameters from multiple data sets. Herein, we propose a hierarchical Bayesian estimation method to quantify the discrepancy by a multiplicative factor while simultaneously obtaining the probability distributions of a single set of isotherm parameters. This approach also allows us to identify outliers, which are data sets that are not in agreement with other sets. The proposed approach is demonstrated for the case of CO 2 adsorption in the metal-organic framework UiO-66.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Active Subspace Methods for Data-Intensive Inverse Problems

Fostered by advances in computing, simulation and data science have emerged as the third and fourth paradigms enabling scientific discovery. Many mathematical challenges arise when integrating these paradigms to produce new knowledge. One of the most important challenges is the inverse or calibration problem: find the inputs of a simulation such that its outputs agree with a given set of measurements. As both the cost of the complex simulations and the volume of measurement data sets increase, intuition-driven trial-and-error methods for calibration quickly become untenable; modern scientists need more computationally efficient and mathematically rigorous methods. When measurements and simulated predictions contain uncertainty, the Bayesian perspective on statistical inference provides a popular mathematical framework for developing computational methods to solve inverse problems. Markov chain Monte Carlo (MCMC) methods are a mainstay of this framework; they characterize a probability distribution on the space of model inputs that is conditioned on the given measurements. However, despite recent advances, MCMC methods remain impractical for expensive simulations with more than a handful of inputs. At its heart, MCMC searches the space of inputs for corresponding outputs that match measurements, and so it is afflicted with the curse of dimensionality. Additionally, MCMC methods become less efficient as the volume of the measurement data increases, particularly if the measurements are redundant. To make MCMC—and Bayesian methods, in general—amenable to today’s computer models with millions of inputs and terabytes of measurement data, one must devise methods to reduce the dimension of both the simulation inputs and the measurements. For many models used in practice, the outputs vary primarily on a low-dimensional manifold of the nominally high-dimensional input space. Recently developed active subspace methods discover this low-dimensional manifold and exploit it to enable analyses typically suited for low-dimensional settings (e.g., statistical inversion of complex systems). We hypothesize that active subspace methods can provide the necessary dimension reduction, enabling existing Bayesian methods to find solutions for a large class of otherwise intractable statistical inverse problems. We will test the hypothesis with a series of mathematical analyses and computational experiments that will proceed along three research veins: (i) integrating active subspace methods into methods for statistical inversion, (ii) addressing current challenges in active subspace methods, and (iii) incorporating methods for nonlinear dimensionality reduction into active subspace methods. We will apply the methods we develop to real inverse problems in chemical kinetics and turbulent flame modeling. Our team combines expertise in methods for inverse problems, dimension reduction, and reduced order modeling. With a history of active collaboration and thoughtful engagement, we bring enthusiasm and fresh perspectives to a well studied subject. We are excited by the potential opportunity to work together to extend and apply active subspace methods to data-intensive inverse problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Active Subspace Methods for Data-Intensive Inverse Problems (Final Report)

Fostered by advances in computing, simulation and data science have emerged as the third and fourth paradigms enabling scientific discovery. Many mathematical challenges arise when integrating these paradigms to produce new knowledge. One of the most important challenges is the inverse or calibration problem: find the inputs of a simulation such that its outputs agree with a given set of measurements. As both the cost of the complex simulations and the volume of measurement data sets increase, intuition-driven trial-and-error methods for calibration quickly become untenable; modern scientists need more computationally efficient and mathematically rigorous methods. When measurements and simulated predictions contain uncertainty, the Bayesian perspective on statistical inference provides a popular mathematical framework for developing computational methods to solve inverse problems. Markov chain Monte Carlo (MCMC) methods are a mainstay of this framework; they characterize a probability distribution on the space of model inputs that is conditioned on the given measurements. However, despite recent advances, MCMC methods remain impractical for expensive simulations with more than a handful of inputs. At its heart, MCMC searches the space of inputs for corresponding outputs that match measurements, and so it is afflicted with the curse of dimensionality. Additionally, MCMC methods become less efficient as the volume of the measurement data increases, particularly if the measurements are redundant. To make MCMC—and Bayesian methods, in general—amenable to today’s computer models with millions of inputs and terabytes of measurement data, one must devise methods to reduce the dimension of both the simulation inputs and the measurements. For many models used in practice, the outputs vary primarily on a low-dimensional manifold of the nominally high-dimensional input space. Recently developed active subspace methods discover this low-dimensional manifold and exploit it to enable analyses typically suited for low-dimensional settings (e.g., statistical inversion of complex systems). We hypothesize that active subspace methods can provide the necessary dimension reduction, enabling existing Bayesian methods to find solutions for a large class of otherwise intractable statistical inverse problems. We will test the hypothesis with a series of mathematical analyses and computational experiments that will proceed along three research veins: (i) integrating active subspace methods into methods for statistical inversion, (ii) addressing current challenges in active subspace methods, and (iii) incorporating methods for nonlinear dimensionality reduction into active subspace methods. We will apply the methods we develop to real inverse problems in chemical kinetics and turbulent flame modeling. Our team combines expertise in methods for inverse problems, dimension reduction, and reduced order modeling. With a history of active collaboration and thoughtful engagement, we bring enthusiasm and fresh perspectives to a well studied subject. We are excited by the potential opportunity to work together to extend and apply active subspace methods to data-intensive inverse problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Evaluating the Benefits of Bayesian Hierarchical Methods for Analyzing Heterogeneous Environmental Datasets: A Case Study of Marine Organic Carbon Fluxes

Large compilations of heterogeneous environmental observations are increasingly available as public databases, allowing researchers to test hypotheses across datasets. Statistical complexities arise when analyzing compiled data due to unbalanced spatial sampling, variable environmental context, mixed measurement techniques, and other reasons. Hierarchical Bayesian modeling is increasingly used in environmental science to describe these complexities, however few studies explicitly compare the utility of hierarchical Bayesian models to simpler and more commonly applied methods. Here we demonstrate the utility of the hierarchical Bayesian approach with application to a large compiled environmental dataset consisting of 5,741 marine vertical organic carbon flux observations from 407 sampling locations spanning eight biomes across the global ocean. We fit a global scale Bayesian hierarchical model that describes the vertical profile of organic carbon flux with depth. Profile parameters within a particular biome are assumed to share a common deviation from the global mean profile. Individual station-level parameters are then modeled as deviations from the common biome-level profile. The hierarchical approach is shown to have several benefits over simpler and more common data aggregation methods. First, the hierarchical approach avoids statistical complexities introduced due to unbalanced sampling and allows for flexible incorporation of spatial heterogeneitites in model parameters. Second, the hierarchical approach uses the whole dataset simultaneously to fit the model parameters which shares information across datasets and reduces the uncertainty up to 95% in individual profiles. Third, the Bayesian approach incorporates prior scientific information about model parameters; for example, the non-negativity of chemical concentrations or mass-balance, which we apply here. We explicitly quantify each of these properties in turn. We emphasize the generality of the hierarchical Bayesian approach for diverse environmental applications and its increasing feasibility for large datasets due to recent developments in Markov Chain Monte Carlo algorithms and easy-to-use high-level software implementations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

PROVABGS: The Probabilistic Stellar Mass Function of the BGS One-percent Survey

We present the probabilistic stellar mass function (pSMF) of galaxies in the DESI Bright Galaxy Survey (BGS), observed during the One-percent Survey. The One-percent Survey was one of DESI's survey validation programs conducted from 2021 April to May, before the start of the main survey. It used the same target selection and similar observing strategy as the main survey and successfully observed the spectra and redshifts of 143,017 galaxies in the r < 19.5 magnitude-limited BGS Bright sample and 95,499 galaxies in the fainter surface-brightness- and color-selected BGS Faint sample over z < 0.6. We derive pSMFs from posteriors of stellar mass, M*, inferred from DESI photometry and spectroscopy using the Hahn et al. PRObabilistic Value-Added BGS (PROVABGS) Bayesian spectral energy distribution modeling framework. We use a hierarchical population inference framework that statistically and rigorously propagates the M* uncertainties. Furthermore, we include correction weights that account for the selection effects and incompleteness of the BGS observations. We present the redshift evolution of the pSMF in BGS, as well as the pSMFs of star-forming and quiescent galaxies classified using average specific star formation rates from PROVABGS. Overall, the pSMFs show good agreement with previous stellar mass function measurements in the literature. Our pSMFs showcase the potential and statistical power of BGS, which in its main survey will observe >100 × more galaxies. Moreover, we present the statistical framework for subsequent population statistics measurements using BGS, which will characterize the global galaxy population and scaling relations at low redshifts with unprecedented precision.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Bayesian inference for plasmonic nanometrology

Here, we introduce a Bayesian method for the characterization of plasmonic nanoparticles, which is applicable to both near- and far-field problems. Designed to combine data generated from any photon-plasmon interaction experiment with physically motivated theoretical models, our approach leverages state-of-the-art Markov chain Monte Carlo sampling techniques and returns parameter estimates on nanometric scales. Simulated spectral data sets, describing resonant scattering of photons from ellipsoidal and toroidal nanoparticles, are explored as concrete examples of our approach, with the resulting Bayesian estimates showing excellent agreement with the ground truth, even under conditions of high statistical noise. By incorporating Bayes factors into the method as well, we reveal how model selection can determine which one of competing geometric shapes better explains the observed data. Our comprehensive nanometrology procedure can be tailored to a variety of light-particle interaction models, and its reliance on Bayesian inference furnishes automatic uncertainty quantification. In addition to applicability to a host of plasmonic configurations such as nanoparticle dimers, trimers, and array studies, it is proposed that the presented analysis can be extended to the quantum regime, where nonclassical photon statistics may provide additional insight for inference of scatterer properties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

ROSE: A reduced-order scattering emulator for optical models

A new generation of phenomenological optical potentials requires robust calibration and uncertainty quantification, motivating the use of Bayesian statistical methods. These Bayesian methods usually require calculating observables for thousands or even millions of parameter sets, making fast and accurate emulators highly desirable or even essential. Emulating scattering across different energies or with interactions such as optical potentials is challenging because of the nonaffine parameter dependence, meaning the parameters do not all factorize from individual operators. Here we introduce and demonstrate the reduced-order scattering emulator ( ROSE ) framework, a reduced basis emulator that can handle nonaffine problems. ROSE is fully extensible and works within the publicly available band framework software suite for calibration, model mixing, and experimental design. As a demonstration problem, we use ROSE to calibrate a realistic nucleon-target scattering model through the calculation of elastic cross sections. This problem shows the practical value of the ROSE framework for Bayesian uncertainty quantification with controlled trade-offs between emulator speed and accuracy as compared to high-fidelity solvers. Finally, planned extensions of ROSE are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS2015

Hazard Assessment from Storm Tides and Rainfall on a Tidal River Estuary

Here, we report on methods and results for a model-based flood hazard assessment we have conducted for the Hudson River from New York City to Troy/Albany at the head of tide. Our recent work showed that neglecting freshwater flows leads to underestimation of peak water levels at up-river sites and neglecting stratification (typical with two-dimensional modeling) leads to underestimation all along the Hudson. As a result, we use a three-dimensional hydrodynamic model and merge streamflows and storm tides from tropical and extratropical cyclones (TCs, ETCs), as well as wet extratropical cyclone (WETC) floods (e.g. freshets, rain-on-snow events). We validate the modeled flood levels and quantify error with comparisons to 76 historical events. A Bayesian statistical method is developed for tropical cyclone streamflows using historical data and consisting in the evaluation of (1) the peak discharge and its pdf as a function of TC characteristics, and (2) the temporal trend of the hydrograph as a function of temporal evolution of the cyclone track, its intensity and the response characteristics of the specific basin. A k-nearest-neighbors method is employed to determine the hydrograph shape. Out of sample validation tests demonstrate the effectiveness of the method. Thus, the combined effects of storm surge and runoff produced by tropical cyclones hitting the New York area can be included in flood hazard assessment. Results for the upper Hudson (Albany) suggest a dominance of WETCs, for the lower Hudson (at New York Harbor) a case where ETCs are dominant for shorter return periods and TCs are more important for longer return periods (over 150 years), and for the middle-Hudson (Poughkeepsie) a mix of all three flood events types is important. However, a possible low-bias for TC flood levels is inferred from a lower importance in the assessment results, versus historical event top-20 lists, and this will be further evaluated as these preliminary methods and results are finalized. Future funded work will quantify the influences of sea level rise and flood adaptation plans (e.g. surge barriers). It would also be valuable to examine how streamflows from tropical cyclones and wet cool-season storms will change, as this factor will dominate at upriver locations.

Hazard assessment↗
DOE OSTI2013

Collaborative Research: Using ARM Observations to Evaluate GCM Cloud Statistics for Development of Stochastic Cloud-Radiation Parameterizations

The long-range goal of several past and current projects in our DOE-supported research has been the development of new and improved parameterizations of cloud-radiation effects and related processes, using ARM data, and the implementation and testing of these parameterizations in global models. The main objective of the present project being reported on here has been to develop and apply advanced statistical techniques, including Bayesian posterior estimates, to diagnose and evaluate features of both observed and simulated clouds. The research carried out under this project has been novel in two important ways. The first is that it is a key step in the development of practical stochastic cloud-radiation parameterizations, a new category of parameterizations that offers great promise for overcoming many shortcomings of conventional schemes. The second is that this work has brought powerful new tools to bear on the problem, because it has been an interdisciplinary collaboration between a meteorologist with long experience in ARM research (Somerville) and a mathematician who is an expert on a class of advanced statistical techniques that are well-suited for diagnosing model cloud simulations using ARM observations (Shen). The motivation and long-term goal underlying this work is the utilization of stochastic radiative transfer theory (Lane-Veron and Somerville, 2004; Lane et al., 2002) to develop a new class of parametric representations of cloud-radiation interactions and closely related processes for atmospheric models. The theoretical advantage of the stochastic approach is that it can accurately calculate the radiative heating rates through a broken cloud layer without requiring an exact description of the cloud geometry.

58 GEOSCIENCES↗
DOE OSTI2019

Joint Bayesian analysis of large angular scale CMB temperature anomalies

Cosmic microwave background measurements show an agreement with the concordance cosmology model except for a few notable anomalies: Power Suppression , the lack of large scale power in the temperature data compared to what is expected in the concordance model, and Cosmic Hemispherical Asymmetry , a dipolar breakdown of statistical isotropy. An expansion of the CMB covariance in Bipolar Spherical Harmonics naturally parametrizes both these large-scale anomalies, allowing us to perform an exhaustive, fully Bayesian joint analysis of the power spectrum and violations of statistical isotropy up to the dipole level. Our analysis sheds light on the scale dependence of the Cosmic Hemispherical Asymmetry. Assuming a scale-dependent dipole modulation model with a two-parameter power law form, we explore the posterior pdf of amplitude A($l$ = 16) and the power law index α and find the maximum a posteriori values A * (l = 16) = 0.064 ± 0.022 and $α_*$ = -0.92 ± 0.22. The maximum a posteriori direction associated with the Cosmic Hemispherical Asymmetry is ($l,b$) = (247.8 o , -19.6 o ) in Galactic coordinates, consistent with previous analyses. We evaluate the Bayes factor BSI-DM to compare the Cosmic Hemispherical Asymmetry model with the isotropic model. The data prefer but do not substantially favor the anisotropic model (BSI-DM=0.4). We consider several priors and find that this evidence ratio is robust to prior choice. The large-scale power suppression does not soften when jointly inferring both the isotropic power spectrum and the parameters of the asymmetric model, indicating no evidence that these anomalies are coupled.

79 ASTRONOMY AND ASTROPHYSICS↗