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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Bayesian D‐Optimal Designs for Gaussian Process Surrogate Models

Computer experiments often employ space-filling strategies to create surrogate models with strong predictive performance. The impact of model parameter estimation for Gaussian process surrogates, however, is often overlooked. Obtaining a better initial estimate of the covariance lengthscale parameter, θ, can greatly improve the resulting Gaussian process fit through more effective sequential acquisitions during active learning. In this work, we propose a novel initial design maximizing the Bayesian D-optimality criterion of the Gaussian process lengthscale parameter. Previously published results have shown the emphasis on lengthscale estimation to be promising, but relied on an empirically driven design creation process. Our Bayesian D-optimal designs are rooted in information theory and lead to more informative sequential acquisitions by improving lengthscale estimation. In many cases, these gains eventually result in better surrogates than those seeded with space-filling initial designs. Furthermore, Bayesian D-optimal designs can be tailored to either isotropic or anisotropic covariance structures, and the Bayesian framework enables the inclusion of prior knowledge in the design process, offering greater flexibility and adaptability. Through several simulation studies, we demonstrate the advantages of Bayesian D-optimal designs in terms of both lengthscale estimation accuracy and predictive performance during active learning.

Bayesian experimental design↗
DOE OSTI2021

Bayesian Estimation of the D(p,γ) 3 He Thermonuclear Reaction Rate

Big bang nucleosynthesis (BBN) is the standard model theory for the production of the light nuclides during the early stages of the universe, taking place for a period of about 20 minutes after the big bang. Deuterium production, in particular, is highly sensitive to the primordial baryon density and the number of neutrino species, and its abundance serves as a sensitive test for the conditions in the early universe. The comparison of observed deuterium abundances with predicted ones requires reliable knowledge of the relevant thermonuclear reaction rates, and their corresponding uncertainties. Recent observations reported the primordial deuterium abundance with percent accuracy, but some theoretical predictions based on BBN are at tension with the measured values because of uncertainties in the cross section of the deuterium-burning reactions. In this work, we analyze the S-factor of the D(p,γ) 3 He reaction using a hierarchical Bayesian model. We take into account the results of eleven experiments, spanning the period of 1955--2021; more than any other study. We also present results for two different fitting functions, a two-parameter function based on microscopic nuclear theory and a four-parameter polynomial. Furthermore, our recommended reaction rates have a 2.2\% uncertainty at 0.8~GK, which is the temperature most important for deuterium BBN. Differences between our rates and previous results are discussed.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Bayesian uncertainty quantification of tristructural isotropic particle fuel silver release: Decomposing model inadequacy plus experimental noise and parametric uncertainties

Tristructural isotropic (TRISO) particle fuel is one of the most promising fuel concepts enabling high temperature and high burnup reactor operation. One dominant source of radioactivity released from the TRISO particles is silver (Ag), which is subject to a high release fraction and long decay life compared to other fission products. Previous modeling efforts using the fuel performance code BISON indicated nonnegligible uncertainties in modeling the diffusion process of fission products in TRISO compared to the Advanced Gas Reactor experiments. The overall uncertainties observed when modeling the fission product diffusion can result from uncertainties in model parameters, noisy experimental measurements, and deficiencies in the developed models. The three types of underlying uncertainties have not yet been properly quantified in open literature. Here, this paper presents the Bayesian uncertainty quantification (UQ) using massively parallelizable Markov chain Monte Carlo samplers. The uncertainties due to model parameters, model inadequacy, and experimental measurement noise are quantified, with the σ term used to represent the sum of the model inadequacy and measurement noise uncertainties. It is worth noting that this is the first time the σ term is inferred for nuclear fuel experiments, as compared to using prescribed values for uncertainty quantification in previous work. The parallelizable Markov chain Monte Carlo samplers efficiently infer the model parameters and the σ term, giving insight into physical parameters like diffusion coefficients and the combined model discrepancy and measurement noise. A subsequent forward uncertainty quantification (UQ) is also performed based on the calibration results to generate more accurate predictions of the Ag release. The model inadequacy plus experimental noise is the most dominant source of uncertainty compared to the parametric uncertainty. All the UQ analyses presented in this work are based on the second series of the irradiation experiments in the Advanced Gas Reactor program.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

The eROSITA Final Equatorial-Depth Survey (eFEDS): The AGN catalog and its X-ray spectral properties

The eROSITA Final Equatorial Depth Survey (eFEDS), observed with eROSITA ahead of its planned 4-yr all-sky survey, is the largest contiguous-field X-ray survey at present. It yielded a large sample of X-ray sources with very rich multiband photometric and spectroscopic coverage. We present here the eFEDS active galactic nuclei (AGN) catalog and the eROSITA X-ray spectral properties of the eFEDS sources. Using a Bayesian method, we performed a systematic X-ray spectral analysis for all the eFEDS sources. We adopted multiple spectral models, including single-component power-law or hot-plasma models and double-component models of a power law plus soft excess. We investigated the capacity of eROSITA X-ray spectra for constraining AGN spectral shapes through a detailed analysis of the posterior parameter probability distribution functions. Hierarchical Bayesian modeling was used to recover the spectral parameter distribution of the sample. The source fluxes and luminosities were measured from the posterior of the spectral fitting. The eFEDS AGN catalog (22 079 sources) comprises ~80% of the eFEDS point sources. Despite a large number of faint sources, our spectral fitting provides reasonable measurements of spectral shapes and intrinsic luminosities for a majority of the sources. Because of sample selection bias, this AGN catalog is dominated by X-ray unobscured sources, with an obscured (logN H > 21.5) fraction of 8%; the power-law emission of the hot corona is also relatively soft, with a typical slope of 2.0. For type-I AGN, the X-ray emission is well correlated with the UV emission with the usual anticorrelation between the X-ray to UV spectral slope α OX and the UV luminosity. The X-ray spectral properties measured with various models are presented for all the eFEDS sources.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A deep learning-based Bayesian framework for high-resolution calibration of building energy models

Calibrating building energy models (BEMs), i.e., closing discrepancy between modeling and field measurements, is of significance to support its applications in building sustainability and resilience analysis. However, as being widely used in practice, current Bayesian calibration is mostly performed in low-resolution (annual or monthly), instead of high-resolution (hourly or sub-hourly), which is crucial to support emerging BEM applications, such as building-renewable energy integration (demand response) and smart control. This is attributable to the gaps in current Bayesian calibration process, including (1) difficulty in supporting reliable high-resolution calibration with over-parameterization and multi-solution issues, (2) inadequacy of meta-model to capture temporal building dynamics in high-resolution, and (3) excessive computational burdens of covariance matrix calculation in Bayesian inference. Therefore, to close these gaps, this research proposes a novel deep learning-based Bayesian calibration framework, involving pre-calibration mechanism, Long Short-Term Memory as surrogate models, and simplified covariance matrix calculation, to calibrate BEMs in high temporal resolution (i.e., hourly) with enhanced accuracy and computational efficiency. Finally, the case study demonstrates its effectiveness to match modeling outcomes with measurements and realize CV-RMSE of < 30 % and NMBE of < 6 % in hourly resolution, as well as a significant reduction of calibration time (by > 99 %, from > 600 h to ~ 1.5 h).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Optimal Bayesian supervised domain adaptation for RNA sequencing data

Abstract Motivation When learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited. Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success. But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all. Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks. Results In this article, we develop a generative optimal Bayesian supervised domain adaptation (OBSDA) model that can integrate RNA sequencing (RNA-Seq) data from different domains along with their labels for improving prediction accuracy in the target domain. Our model can be applied in cases where different domains share the same labels or have different ones. OBSDA is based on a hierarchical Bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters. We first provide an efficient Gibbs sampler for parameter inference in OBSDA. Then, we leverage the gene-gene network prior information and construct an informed and flexible variational family to infer the posterior distributions of model parameters. Comprehensive experiments on real-world RNA-Seq data demonstrate the superior performance of OBSDA, in terms of accuracy in identifying cancer subtypes by utilizing data from different domains. Moreover, we show that by taking advantage of the prior network information we can further improve the performance. Availability and implementation The source code for implementations of OBSDA and SI-OBSDA are available at the following link. https://github.com/SHBLK/BSDA. Supplementary information Supplementary data are available at Bioinformatics online.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Automated Bayesian high-throughput estimation of plasma temperature and density from emission spectroscopy

Here, this paper introduces a novel approach for automated high-throughput estimation of plasma temperature and density using atomic emission spectroscopy, integrating Bayesian inference with sophisticated physical models. We provide an in-depth examination of Bayesian methods applied to the complexities of plasma diagnostics, supported by a robust framework of physical and measurement models. Our methodology is demonstrated using experimental observations in the field of magneto-inertial fusion, focusing on individual and sequential shot analyses of the Plasma Liner Experiment at LANL. The results demonstrate the effectiveness of our approach in enhancing the accuracy and reliability of plasma parameter estimation and in using the analysis to reveal the deep hidden structure in the data. This study not only offers a new perspective of plasma analysis but also paves the way for further research and applications in nuclear instrumentation and related domains.

Bayesian inference↗
DOE OSTI2021

A Markov framework for generalized post-event systems recovery modeling: From single to multihazards

State-dependent models can be used to represent the system recovery process as a series of stochastic transitions from lower to higher functional states. However, the applications of these models have been limited in scope and there is a lack of a generalized recovery modeling framework. A generalized framework would permit a robust forecasting of systems and system-of-systems recovery under multiple hazards, and more broadly, would contribute to community disaster preparedness. This paper develops a generalized post hazard-event recovery modeling framework based on state-dependent Markov-type processes. We then apply the proposed framework to solve a spectrum of problems that range from hind-casting single-system recovery following a single hazard event to forecasting post-event trajectories under multiple hazards and modeling the recovery of a system-of-systems. First, Markov chains are used to hind-cast the observed recovery for a portfolio of buildings affected by the 2014 South Napa, California, earthquake. Next, Markov processes are used to formulate a parametric post hazard-event recovery model, which can be updated using Bayesian statistics when relevant datasets become available. Semi-Markov processes are then used to develop a more general model of single hazard recovery, which accounts for the intensity of the loading and level of damage caused by the event. Semi-Markov processes with non-renewal features are then used to account for multihazard interactions in a post-event recovery model, and applied to a case study that involves a community in Charleston, South Carolina. Lastly, Markov-type processes are combined with Bayesian networks to model the recovery of residential, commercial, educational, and industrial buildings (system-of-systems) following a hazard event. Overall, these applications demonstrate the versatility of the Markov framework towards handling recovery problems with varying levels of complexity.

42 ENGINEERING↗
DOE OSTI2024

A general Bayesian algorithm for the autonomous alignment of beamlines

Autonomous methods to align beamlines can decrease the amount of time spent on diagnostics, and also uncover better global optima leading to better beam quality. The alignment of these beamlines is a high-dimensional expensive-to-sample optimization problem involving the simultaneous treatment of many optical elements with correlated and nonlinear dynamics. Bayesian optimization is a strategy of efficient global optimization that has proved successful in similar regimes in a wide variety of beamline alignment applications, though it has typically been implemented for particular beamlines and optimization tasks. In this paper, we present a basic formulation of Bayesian inference and Gaussian process models as they relate to multi-objective Bayesian optimization, as well as the practical challenges presented by beamline alignment. We show that the same general implementation of Bayesian optimization with special consideration for beamline alignment can quickly learn the dynamics of particular beamlines in an online fashion through hyperparameter fitting with no prior information. We present the implementation of a concise software framework for beamline alignment and test it on four different optimization problems for experiments on X-ray beamlines at the National Synchrotron Light Source II and the Advanced Light Source, and an electron beam at the Accelerator Test Facility, along with benchmarking on a simulated digital twin. We discuss new applications of the framework, and the potential for a unified approach to beamline alignment at synchrotron facilities.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Encoding nonlinear and unsteady aerodynamics of limit cycle oscillations using nonlinear sparse Bayesian learning

This article investigates the applicability of a recently proposed, nonlinear sparse Bayesian learning (NSBL) algorithm to identify and estimate the complex aerodynamics of limit cycle oscillations. NSBL provides a semi-analytical framework for determining the data-optimal sparse model nested within a (potentially) over-parameterized model. This is particularly relevant to nonlinear dynamical systems where modelling approaches involve the use of physics-based and data-driven components. In such cases, the data-driven components, where analytical descriptions of the physical processes are not readily available, are often prone to overfitting, meaning that the empirical aspects of these models will often involve the calibration of an unnecessarily large number of parameters. While an overparameterized model may fit the observed data well, such models may be inadequate for making predictions in regimes that are different from those wherein the data were recorded. In view of this, it is desirable to not only calibrate the model parameters, but also identify the optimal compromise between data fit and model complexity. In this article, we exhibit the optimal model discovery for an aeroelastic system wherein the structural dynamics are well-known and described by a differential equation model, coupled with a semi-empirical aerodynamic model for laminar separation flutter, resulting in low-amplitude limit cycle oscillations (LCO). To illustrate the performance of the algorithm, in this article, we use synthetic data and demonstrate the ability of the algorithm to correctly rediscover the optimal model and model parameters, given a known data-generating model. The synthetic data are generated from a forward simulation of a known differential equation model with parameters selected so as to mimic the dynamics observed in wind-tunnel experiments. Subsequently, we demonstrate the performance of the algorithm for model selection using noisy LCO data from wind tunnel experiments. As there is no ground truth available for the experimental data case, we provide a comparison between NSBL and Bayesian model selection to validate the results, and demonstrate the use of NSBL as an efficient alternative to traditional methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

The Effect of Embedded Nanoparticles on the Phonon Spectrum of Ice: An Inelastic X-ray Scattering Study

As a contribution to the ongoing effort toward high-frequency sound manipulation in composite materials, we use Inelastic X-ray Scattering to probe the phonon spectrum of ice, either in a pure form or with a sparse amount of nanoparticles embedded in it. The study aims at elucidating the ability of nanocolloids to condition the collective atomic vibrations of the surrounding environment. We observe that a nanoparticle concentration of about 1 % in volume is sufficient to visibly affect the phonon spectrum of the icy substrate, mainly canceling its optical modes and adding nanoparticle phonon excitations to it. We highlight this phenomenon thanks to the lineshape modeling based on a Bayesian inference, which enables us to capture the finest detail of the scattering signal. The results of this study can empower new routes toward the shaping of sound propagation in materials through the control of their structural heterogeneity.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Unpacking model inadequacy: The quantification of silver release from TRISO fuel by considering empirical and mechanistic approaches

Increasing adoption of the proposed tristructural isotropic (TRISO) particle fuel for both advanced and existing reactors makes it critical to assess and address any uncertainties and inadequacies of TRISO fission product release models. Model inadequacy stems from simplifications made to the computational model when compared to the experiments. The modeling and simulation efforts conducted using the BISON fuel performance code, along with the experimental campaigns carried out under the Advanced Gas Reactor Fuel Development and Qualification Program, afford a unique opportunity to conduct a rigorous modeling inadequacy assessment within the Bayesian uncertainty quantification (UQ) framework. Here, this study compares the standard Bayesian framework against the Kennedy-O'Hagan (KOH) framework, which explicitly represents modeling inadequacy, in regard to UQ for TRISO silver release models. For this purpose, both the traditional Arrhenius equation fitted to experimental data and the more advanced lower-length-scale (LLS)-informed model, which considers microstructure information, are independently considered. Applying the inverse UQ process on the AGR-2 and -3/4 datasets revealed modeling inadequacy to be the most dominant source of uncertainty. Experimental noise uncertainty is also significant; however, model parameter uncertainty can be considered negligible. Interestingly, both the Arrhenius equation and the LLS-informed model demonstrated similar levels of modeling inadequacy. For the forward predictive UQ, the KOH framework improved both the accuracy and quality of quantified uncertainties in comparison to the standard Bayesian framework. This is true for both the Arrhenius equation and the LLS-informed model. In comparing these modeling approaches, both demonstrated similar performance at the engineering scale, while the LLS-informed model expectedly outperformed the Arrhenius equation at the mesoscale. These conclusions highlight the importance of explicitly accounting for modeling inadequacy in the UQ process, and reinforce the need for continuous refinement of physics-based models in order to address the modeling inadequacy.

Advanced reactors↗
DOE OSTI2023

Sequential Bayesian Experimental Design for Calibration of Expensive Simulation Models

Simulation models of critical systems often have parameters that need to be calibrated using observed data. For expensive simulation models, calibration is done using an emulator of the simulation model built on simulation output at different parameter settings. Using intelligent and adaptive selection of parameters to build the emulator can drastically improve the efficiency of the calibration process. The article proposes a sequential framework with a novel criterion for parameter selection that targets learning the posterior density of the parameters. The emergent behavior from this criterion is that exploration happens by selecting parameters in uncertain posterior regions while simultaneously exploitation happens by selecting parameters in regions of high posterior density. Furthermore, the advantages of the proposed method are illustrated using several simulation experiments and a nuclear physics reaction model.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A Spatiotemporal Prediction Model for Regional Scheduling of Shared Bicycles Based on the INLA Method

Dock-less bicycle-sharing programs have been widely accepted as an efficient mode to benefit health and reduce congestions. And modeling and prediction has always been a core proposition in the field of transportation. Most of the existing demand prediction models for shared bikes take regions as research objects; therefore, a POI-based method can be a beneficial complement to existing research, including zone-level, OD-level, and station-level techniques. Point of interest (POI) is the location description of spatial entities, which can reflect the cycling route characteristics for both commuting and noncommuting trips to a certain extent, and is also the main generating point and attraction point of shared-bike travel flow. In this study, we make an effort to model a POI-level cycling demand with a Bayesian hierarchical method. The proposed model combines the integrated nested Laplace approximation (INLA) and random partial differential equation (SPDE) to cope with the huge computation in the modeling process. In particular, we have adopted the dock-less bicycle-sharing rental records of Mobike as a case study to validate our method; the study area was one of the fastest growing urban districts in Shanghai in August 2016. The operation results show that the method can help better understand, measure, and characterize spatiotemporal patterns of bike-share ridership at the POI level and quantify the impact of the spatiotemporal effect on bicycle-sharing use.

Yu, Zhuoran↗
DOE OSTI2020

BASS: An R Package for Fitting and Performing Sensitivity Analysis of Bayesian Adaptive Spline Surfaces

In this work, we present the R package BASS as a tool for nonparametric regression. The primary focus of the package is fitting fully Bayesian adaptive spline surface (BASS) models and performing global sensitivity analyses of these models. The BASS framework is similar to that of Bayesian multivariate adaptive regression splines (BMARS) from Denison, Mallick, and Smith (1998), but with many added features. The software is built to efficiently handle significant amounts of data with many continuous or categorical predictors and with functional response. Under our Bayesian framework, most priors are automatic but these can be modified by the user to focus on parsimony and the avoidance of overfitting. If directed to do so, the software uses parallel tempering to improve the reversible jump Markov chain Monte Carlo (RJMCMC) methods used to perform inference. We discuss the implementation of these features and present the performance of BASS in a number of analyses of simulated and real data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Does the leaf economic spectrum hold within plant functional types? A Bayesian multivariate trait meta-analysis

The leaf economic spectrum is a widely-studied axis of plant trait variability that defines a trade-off between leaf longevity and productivity. While this has been investigated at the global scale, where it is robust, and at local scales, where deviations from it are common, it has received less attention at the intermediate scale of PFTs. We investigated whether global leaf economic relationships are also present within the scale of plant functional types (PFTs) commonly used by Earth System models, and the extent to which this global-PFT hierarchy can be used to constrain trait estimates. We developed a hierarchical multivariate Bayesian model that assumes separate means and covariance structures within and across PFTs and fit this model to seven leaf traits from the TRY database related to leaf longevity, morphology, biochemistry, and photosynthetic metabolism. Although patterns of trait covariation were generally consistent with the leaf economic spectrum, we found three approximate tiers to this consistency. Relationships among morphological and biochemical traits (SLA, N, P) were the most robust within and across PFTs, suggesting that covariation in these traits is driven by universal leaf construction trade-offs and stoichiometry. Relationships among metabolic traits (R_d, V_{c,max}, J_max) were slightly less consistent, reflecting in part their much sparser sampling (especially for high-latitude PFTs), but also pointing to more flexible plasticity in plant metabolistm. Finally, relationships involving leaf lifespan were the least consistent, indicating that leaf economic relationships related to leaf lifespan are dominated by across-PFT differences and that within-PFT variation in leaf lifespan is more complex and idiosyncratic. Across all traits, these covariance were an important source of information, as evidenced by the improved imputation accuracy and reduced predictive uncertainty in multivariate models compared to univariate models. Ultimately, our study reaffirms the value of studying not just individual traits but the multivariate trait space and the utility of hierarchical modeling for studying the scale dependence of trait relationships.

biodiversity, ecological modeling, ecology, leaf b↗