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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Estimating uncertainty: A Bayesian approach to modelling photosynthesis in C3 leaves

The Farquhar-von Caemmerer-Berry (FvCB) model is extensively used to model pho-tosynthesis from gas exchange measurements. Since its publication, many methods have been developed to measure, or more accurately estimate, parameters of this model. Here, we have created a tool that uses Bayesian statistics to fit photosyn-thetic parameters using concurrent gas exchange and chlorophyll fluorescence mea-surements whilst evaluating the reliability of the parameter estimation. We have tested this tool on synthetic data and experimental data from rice leaves. Our results indicate that reliable parameter estimation can be achieved whilst only keeping one parameter, Km, that is, Michaelis constant for CO2 by Rubisco, prefixed. Additionally, we show that including detailed low CO2 measurements at low light levels increases reliability and suggests this as a new standard measurement protocol. By providing an estimated distribution of parameter values, the tool can be used to evaluate the quality of data from gas exchange and chlorophyll fluorescence measurement proto-cols. Compared to earlier model fitting methods, the use of a Bayesian statistics-based tool minimizes human interaction during fitting, reducing the subjectivity which is essential to most existing tools. A user friendly, interactive Bayesian tool script is provided.

Bayesian statistics, leaf photosynthesis, mesophyl↗
DOE OSTI2022

A Bayesian Approach for In-Situ Stress Prediction and Uncertainty Quantification for Subsurface Engineering

Many subsurface engineering applications require accurate knowledge of the in-situ state of stress for their safe design and operation. Existing methods to meet this need primarily include field measurements for estimating one or more of the principal stresses from a borehole, or optimization methods for constructing a 3D geomechanical model in terms of geophysical measurements. These methods, however, often contain considerable uncertainty in estimating the state of stress. Here, in this paper, we build on a Bayesian approach to quantify uncertainty in stress estimations for subsurface engineering applications. This approach can provide an estimate of the 3D distribution of stress throughout the volume of interest and provide an estimate of the uncertainty arising from the stress measurement, the rheology parameters, and a paucity of measurements. The value of this approach is demonstrated using stress measurements from the In Salah carbon storage site, which was one of the world’s first industrial carbon capture and storage projects. This demonstration shows the application of this Bayesian approach for estimating the initial state of stress for In Salah and quantifying the uncertainty in the estimated stress. Also, an assessment of a maximum injection pressure to prevent geomechanical risks from CO 2 injection pressures is provided in terms of the probability distribution of the minimum principal stress quantified by the approach. With the In Salah case study, this paper demonstrates that using the Bayesian approach can provide additional insights for site explorations and/or project operations to make informed-site decisions for subsurface engineering applications.

58 GEOSCIENCES↗
DOE OSTI2021

Uncertainty quantification for Multiphase-CFD simulations of bubbly flows: a machine learning-based Bayesian approach supported by high-resolution experiments

In this paper, we developed a machine learning-based Bayesian approach to inversely quantify and reduce the uncertainties of multiphase computational fluid dynamics (MCFD) simulations for bubbly flows. The proposed approach is supported by high-resolution two-phase flow measurements, including those by double-sensor conductivity probes, high-speed imaging, and particle image velocimetry. Local distributions of key physical quantities of interest (QoIs), including the void fraction and phasic velocities, are obtained to support the Bayesian inference. In the process, the epistemic uncertainties of the closure relations are inversely quantified while the aleatory uncertainties from stochastic fluctuations of the system are evaluated based on experimental uncertainty analysis. The combined uncertainties are then propagated through the MCFD solver to obtain uncertainties of the QoIs, based on which probability-boxes are constructed for validation. The proposed approach relies on three machine learning methods: feedforward neural networks and principal component analysis for surrogate modeling, and Gaussian processes for model form uncertainty modeling. The whole process is implemented within the framework of an open-source deep learning library PyTorch with graphics processing unit (GPU) acceleration, thus ensuring the efficiency of the computation. The results demonstrate that with the support of high-resolution data, the uncertainties of MCFD simulations can be significantly reduced. The proposed approach has the potential for other applications that involve numerical models with empirical parameters.

42 ENGINEERING↗
DOE OSTI2024

Expanding neutrino oscillation parameter measurements in NOvA using a Bayesian approach

NOvA is a long-baseline neutrino oscillation experiment that measures oscillations in charged-current ν μ → ν μ (disappearance) and ν μ → ν e (appearance) channels, and their antineutrino counterparts, using neutrinos of energies around 2 GeV over a distance of 810 km. In this work we reanalyze the dataset first examined in our previous paper [] using an alternative statistical approach based on Bayesian Markov chain Monte Carlo. We measure oscillation parameters consistent with the previous results. We also extend our inferences to include the first NOvA measurements of the reactor mixing angle θ 13 , where we find 0.071 ≤ sin 2 2 θ 13 ≤ 0.107 , and the Jarlskog invariant, where we observe no significant preference for the C P -conserving value J = 0 over values favoring C P violation. We use these results to examine the effects of constraints from short-baseline measurements of θ 13 using antineutrinos from nuclear reactors when making NOvA measurements of θ 23 . Our long-baseline measurement of θ 13 is shown to be consistent with the reactor measurements, supporting the general applicability and robustness of the Pontecorvo-Maki-Nakagawa-Sakata framework for neutrino oscillations. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

A Bayesian approach to evaluation of soil biogeochemical models

Abstract. To make predictions about the carbon cycling consequences of rising global surface temperatures, Earth system scientists rely on mathematical soil biogeochemical models (SBMs). However, it is not clear which models have better predictive accuracy, and a rigorous quantitative approach for comparing and validating the predictions has yet to be established. In this study, we present a Bayesian approach to SBM comparison that can be incorporated into a statistical model selection framework. We compared the fits of linear and nonlinear SBMs to soil respiration data compiled in a recent meta-analysis of soil warming field experiments. Fit quality was quantified using Bayesian goodness-of-fit metrics, including the widely applicable information criterion (WAIC) and leave-one-out cross validation (LOO). We found that the linear model generally outperformed the nonlinear model at fitting the meta-analysis data set. Both WAIC and LOO computed higher overfitting risk and effective numbers of parameters for the nonlinear model compared to the linear model, conditional on the data set. Goodness of fit for both models generally improved when they were initialized with lower and more realistic steady-state soil organic carbon densities. Still, testing whether linear models offer definitively superior predictive performance over nonlinear models on a global scale will require comparisons with additional site-specific data sets of suitable size and dimensionality. Such comparisons can build upon the approach defined in this study to make more rigorous statistical determinations about model accuracy while leveraging emerging data sets, such as those from long-term ecological research experiments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A Bayesian approach to time-domain photonic Doppler velocimetry analysis

Photonic Doppler velocimetry (PDV) is an established technique for measuring the velocities of fast-moving surfaces in high-energy-density experiments. In the standard approach to PDV analysis, the short-time Fourier transform (STFT) is used to generate a spectrogram from which the velocity history of the target is inferred. The user chooses the form, duration, and separation of the window function. Here, in this study, we present a Bayesian approach to infer the velocity directly from the PDV oscilloscope trace, without using the spectrogram for analysis. This is clearly a difficult inference problem due to the highly periodic nature of the data, but we find that with carefully chosen prior distributions for the model parameters, we can accurately recover the injected velocity from synthetic data. We validate this method using PDV data collected at the STAR two-stage light gas gun at Sandia National Laboratories, recovering shock-front velocities in quartz that are consistent with those inferred using the STFT-based approach and are interpolated across regions of low signal-to-noise data. Although this method does not rely on the same user choices as the STFT, we caution that it can be prone to misspecification if the chosen model is not sufficient to capture the velocity behavior. Analysis using posterior predictive checks can be used to establish whether a better model is required, although more complex models come with additional computational cost, often taking more than several hours to converge when sampling the Bayesian posterior. We, therefore, recommend it be viewed as a complementary method to that of the STFT-based approach.

Allison, James R. [First Light Fusion Ltd., Yarnto↗
DOE OSTI2021

A Bayesian Approach to the Eagar–Tsai Model for Melt Pool Geometry Prediction with Implications in Additive Manufacturing of Metals

Here, this paper focuses on improving the melt pool geometry predictions and quantifying uncertainties using an adapted version of the Eagar–Tsai (E–T) model that incorporates temperature-dependent properties of the material as well as powder conditions. Additionally, Bayesian inference is employed to predict distributions for the E–T model input parameters of laser absorptivity and powder bed porosity by incorporating experimental results into the analysis. Monte Carlo uncertainty propagation is then used with these parameter distributions to estimate the melt pool depth and associated uncertainty. Our results for the 316L stainless steel suggest that both the absorptivity and powder bed porosity are strongly influenced by the laser power. In contrast, the scanning speed has only a marginal effect on both the absorptivity and powder bed porosity. We constructed a printability map using the Bayesian E–T model based on power-dependent input parameter values to demonstrate the merit of the approach. The Bayesian approach improved the accuracy in predicting the keyhole regions in the laser power-scan speed parameter space for the 316L stainless steel. Although applied to a specific adaptation of the E–T model, the method put forth can be extended to quantify uncertainties in other numerical models as well as in the estimation of unknown parameters.

316L Stainless Steel (SS).↗
DOE OSTI2020

Comparing traditional and Bayesian approaches to ecological meta‐analysis

Abstract Despite the wide application of meta‐analysis in ecology, some of the traditional methods used for meta‐analysis may not perform well given the type of data characteristic of ecological meta‐analyses. We reviewed published meta‐analyses on the ecological impacts of global climate change, evaluating the number of replicates used in the primary studies ( n i ) and the number of studies or records ( k ) that were aggregated to calculate a mean effect size. We used the results of the review in a simulation experiment to assess the performance of conventional frequentist and Bayesian meta‐analysis methods for estimating a mean effect size and its uncertainty interval. Our literature review showed that n i and k were highly variable, distributions were right‐skewed and were generally small (median n i = 5, median k = 44). Our simulations show that the choice of method for calculating uncertainty intervals was critical for obtaining appropriate coverage (close to the nominal value of 0.95). When k was low (<40), 95% coverage was achieved by a confidence interval (CI) based on the t distribution that uses an adjusted standard error (the Hartung–Knapp–Sidik–Jonkman, HKSJ), or by a Bayesian credible interval, whereas bootstrap or z distribution CIs had lower coverage. Despite the importance of the method to calculate the uncertainty interval, 39% of the meta‐analyses reviewed did not report the method used, and of the 61% that did, 94% used a potentially problematic method, which may be a consequence of software defaults. In general, for a simple random‐effects meta‐analysis, the performance of the best frequentist and Bayesian methods was similar for the same combinations of factors ( k and mean replication), though the Bayesian approach had higher than nominal (>95%) coverage for the mean effect when k was very low ( k < 15). Our literature review suggests that many meta‐analyses that used z distribution or bootstrapping CIs may have overestimated the statistical significance of their results when the number of studies was low; more appropriate methods need to be adopted in ecological meta‐analyses.

Pappalardo, Paula↗
DOE OSTI2020

Data from: Comparing traditional and Bayesian approaches to ecological meta-analysis

Despite the wide application of meta-analysis in ecology, some of the traditional methods used for meta-analysis may not perform well given the type of data characteristic of ecological meta-analyses. We reviewed published meta-analyses on the ecological impacts of global climate change, evaluating the number of replicates used in the primary studies (ni) and the number of studies or records (k) that were aggregated to calculate a mean effect size. We used the results of the review in a simulation experiment to assess the performance of conventional frequentist and Bayesian meta-analysis methods for estimating a mean effect size and its uncertainty interval. Our literature review showed that ni and k were highly variable, distributions were right-skewed, and were generally small (median ni =5, median k=44). Our simulations show that the choice of method for calculating uncertainty intervals was critical for obtaining appropriate coverage (close to the nominal value of 0.95). When k was low (<40), 95% coverage was achieved by a confidence interval based on the t-distribution that uses an adjusted standard error (the Hartung-Knapp-Sidik-Jonkman, HKSJ), or by a Bayesian credible interval, whereas bootstrap or z-distribution confidence intervals had lower coverage. Despite the importance of the method to calculate the uncertainty interval, 39% of the meta-analyses reviewed did not report the method used, and of the 61% that did, 94% used a potentially problematic method, which may be a consequence of software defaults. In general, for a simple random-effects meta-analysis, the performance of the best frequentist and Bayesian methods were similar for the same combinations of factors (k and mean replication), though the Bayesian approaches had higher than nominal (>95%) coverage for the mean effect when k was very low (k<15). Our literature review suggests that many meta-analyses that used z-distribution or bootstrapping confidence intervals may have over-estimated the statistical significance of their results when the number of studies was low; more appropriate methods need to be adopted in ecological meta-analyses.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A Data-Fusion Method using Bayesian Approach to Enhance Raw Data Accuracy of Position and Distance Measurements for Connected Vehicles

Accurate positioning of vehicles is a critical element of autonomous and connected vehicle systems. Most of other studies heavily focused on enhancing simultaneous localization and mapping (SLAM) methods, i.e., constructing or updating a map of an unknown environment and tracking an object within the map. This paper provides a method that can, in addition to existing SLAM or relevant methods, enhance the raw measurements of position and distance. The basic idea of this study is to identify and update the error distribution of each data source by combining all available information. A Bayesian approach was incorporated to estimate and update the error distribution of individual data sources or sensors. The proposed method can be conducted in real-time environments, and a self-learning scheme determines whether enough data has been collected to further improve the accuracy of such measurements. The simulated experiments show that the proposed model noticeably improves the accuracy of position and distance measurements. Especially, the estimated biases of position coordinates and distance measures are very close to the biases of true error distributions, with the R-squared over 0.98. A similar approach can also be utilized to enhance accuracy of other sensors or measurements in connected vehicle or relevant systems, where multi-data sources are available.

Lim, Hyeonsup↗
DOE OSTI2022

Technical note: Modeling spatial fields of extreme precipitation – a hierarchical Bayesian approach

Abstract. We introduce a hierarchical Bayesian model for the spatial distribution of rainfall corresponding to an extreme event of a specified duration that could be used with regional hydrologic models to perform a regional hydrologic risk analysis. An extreme event is defined if any gaging site in the watershed experiences an annual maximum rainfall event and the spatial field of rainfall at all sites corresponding to that occurrence is modeled. Applications to data from New York City demonstrate the effectiveness of the model for providing spatial scenarios that could be used for simulating loadings into the urban drainage system. Insights as to the homogeneity in spatial rainfall and its implications for modeling are provided by considering partial pooling in the hierarchical Bayesian framework.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

A Bayesian approach to the long-baseline neutrino oscillation sensitivity of DUNE

The sensitivity of the Deep Underground Neutrino Experiment (DUNE) to neutrino oscillation is evaluated using a Bayesian Markov Chain Monte Carlo (MCMC) approach. This analysis uses the same underlying sensitivity inputs as previous DUNE studies [Eur. Phys. J. C 80, 978 (2020)], and therefore does not present updated DUNE sensitivities, but instead explores the additional inferences accessible using a Bayesian approach. We present four-dimensional posterior probability distributions of the oscillation parameters, highlighting the breadth of correlation in the parameter space of interest, especially between $\sin^2 θ_{23}$ and $\sin^2 θ_{13}$. We exploit the flexibility of the Bayesian framework to incorporate parameter constraints post hoc and assess the impact of applying a reactor short-baseline $θ_{13}$ constraint. A significant increase in the sensitivity to the $θ_{23}$ octant is found when including the constraint. Posterior distributions of derived quantities can be easily constructed from MCMC results. This work presents the first study of DUNE's sensitivity to the Jarlskog invariant, $J$, a quantity that provides a parametrisation-independent measure of charge-parity violation in the leptonic sector.

Abbaslu, Saeed [IPM, Tehran] (ORCID:00000003356771↗
DOE OSTI2023

A Bayesian Approach for Characterizing and Mitigating Gate and Measurement Errors

Various noise models have been developed in quantum computing study to describe the propagation and effect of the noise that is caused by imperfect implementation of hardware. Identifying parameters such as gate and readout error rates is critical to these models. We use a Bayesian inference approach to identify posterior distributions of these parameters such that they can be characterized more elaborately. By characterizing the device errors in this way, we can further improve the accuracy of quantum error mitigation. Experiments conducted on IBM’s quantum computing devices suggest that our approach provides better error mitigation performance than existing techniques used by the vendor. Also, our approach outperforms the standard Bayesian inference method in some scenarios.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

A Bayesian Approach to Real-Time Dynamic Parameter Estimation Using Phasor Measurement Unit Measurement

Here, we develop a polynomial-chaos-expansion (PCE)-based approach for decentralized dynamic parameter estimation through Bayesian inference. Using this approach, the non-Gaussian distribution of the inverted parameters is obtained. More specifically, we first represent the decentralized generator model with the PCE-based surrogate. This surrogate allows us to efficiently evaluate the time-consuming dynamic solver at parameter values through Metropolis-Hastings (M-H)-based Markov chain Monte Carlo (MCMC). Then, we propose a two-stage hybrid Markov chain Monte Carlo (MCMC) to recover a posteriori distribution of the decentralized generator model parameters. In the first stage, we use the gradient-enhanced Langevin MCMC algorithm to characterize an intermediate posterior parameter distribution. This algorithm is computationally scalable to the high-dimensional parameter space. Based on the intermediate posterior distribution, during the second stage, we use the adaptive MCMC algorithm to fine-tune the strong correlations between the parameters. Finally, the fully recovered a posterior distribution is obtained in the end. The simulation results show that the proposed PCE-based hybrid MCMC algorithm can accurately and efficiently estimate the high-dimensional generator dynamic model parameters with full probabilistic distribution provided.

42 ENGINEERING↗
DOE OSTI2022

A Bayesian approach to nanoparticle characterization

We introduce and numerically validate a Bayesian method for plasmonic nanometrology. Applicable to any system described by a scattering cross section, our approach quantifies uncertainty automatically and enables model comparison through Bayes factors.

Lukens, Joseph↗
DOE OSTI2021

A consistent, Bayesian, approach to the cross section probability distribution in the unresolved resonance region

The cross sections of neutron-induced reactions can be divided into three energy ranges: the resolved resonance region (RRR), the unresolved resonance region (URR), and the fast region. In general, the cross sections in the URR show significant fluctuations that cannot be predicted and cannot be experimentally resolved, thus, it is commonly assumed that the cross section at a specific energy is given by a probability distribution function (PDF) over a range of values that can span several orders of magnitude. The current methodology used to describe such behavior is to construct the PDF by stochastically generating resonance ladders and numerically measuring the PDF. The resonance ladders are sampled using known resonance statistical properties and average resonance widths and spacings extrapolated from the RRR. Although this is a standard and widely used technique, it is computationally very expensive, therefore, an alternative, analytical, approach would be preferable due to the considerable speed up of the computational time in real life applications. Moreover, the current methodology does not take into account existing experimental data, such for total and capture cross sections, that are available for many nuclei. Finally, this approach was developed to be used in reactor-scale applications and it is not suited for use in single-event applications. In this work we will rethink the entire approach to the PDF construction using a Bayesian mindset. This will allow us to provide a different definition of the PDF that allows a much faster calculation of the higher-temperature PDFs and a proper combination of theoretical and experimental PDFs following the probability theory. We will also show that our definition is well suited for single-event applications and we will make an explicit connection between our method and the standard approach. We do this by showing that the central limit theorem applies and our method leads to the same PDF obtained with the standard methodology, for a large number of events per history.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

A Logarithmic Bayesian Approach to Quantum Error Detection

We consider the problem of continuous quantum error correction from a Bayesian perspective, proposing a pair of digital filters using logarithmic probabilities that are able to achieve near-optimal performance on a three-qubit bit-flip code, while still being reasonable to implement on low-latency hardware. These practical filters are approximations of an optimal filter that we derive explicitly for finite time steps, in contrast with previous work that has relied on stochastic differential equations such as the Wonham filter. By utilizing logarithmic probabilities, we are able to eliminate the need for explicit normalization and can reduce the Gaussian noise distribution to a simple quadratic expression. The state transitions induced by the bit-flip errors are modeled using a Markov chain, which for log-probabilities must be evaluated using a LogSumExp function. We develop the two versions of our filter by constraining this LogSumExp to have either one or two inputs, which favors either simplicity or accuracy, respectively. Using simulated data, we demonstrate that the single-term and two-term filters are able to significantly outperform both a double threshold scheme and a linearized version of the Wonham filter in tests of error detection under a wide variety of error rates and time steps.

97 MATHEMATICS AND COMPUTING↗