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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Quantifying the propagation of parametric uncertainty on flux balance analysis

Flux balance analysis (FBA) and associated techniques operating on stoichiometric genome-scale metabolic models play a central role in quantifying metabolic flows and constraining feasible phenotypes. At the heart of these methods lie two important assumptions: (i) the biomass precursors and energy requirements neither change in response to growth conditions nor environmental/genetic perturbations, and (ii) metabolite production and consumption rates are equal at all times (i.e., steady-state). Despite the stringency of these two assumptions, FBA has been shown to be surprisingly robust at predicting cellular phenotypes. In this paper, we formally assess the impact of these two assumptions on FBA results by quantifying how uncertainty in biomass reaction coefficients, and departures from steady-state due to temporal fluctuations could propagate to FBA results. In the first case, conditional sampling of parameter space is required to re-weigh the biomass reaction so as the molecular weight remains equal to 1 g mmol –1 , and in the second case, metabolite (and elemental) pool conservation must be imposed under temporally varying conditions. Results confirm the importance of enforcing the aforementioned constraints and explain the robustness of FBA biomass yield predictions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Uncertainty Quantification Framework for Predicting Material Response with Large Number of Parameters: Application to Creep Prediction in Ferritic-Martensitic Steels Using Combined Crystal Plasticity and Grain Boundary Models

This paper presents an uncertainty quantification (UQ) framework for the physics-based model prediction of material response with a large number of parameters. The application problem presented in this work is that of predicting creep in Grade 91 steel at 600°C. The material response is defined with a physically based microstructural model with constitutive equations emulating several observed phenomena in Grade 91 and embodied into an explicit geometry mesoscale finite element model for prior austenite grains and grain boundaries. Creep within the grains and in grain boundaries are represented by crystal plasticity for dislocation motion and a physics-based model for cavity growth and nucleation, respectively. The creep behavior of this material is influenced by several parameters, some of which have a wide range of variation based on experimental data. UQ combined with microstructural modeling can discover the core microstructural causes of experimental variability, leading to improved materials with lower variability in critical long-term material properties. In this study, we investigate the model's uncertainty to identify material properties that may be modified during production to increase creep life and analyze different components of the crystal plasticity model for improvements. For this purpose, a quantity of interest is defined as time to minimum creep rate, which correlates well to the creep failure of the material. A deep neural network model was trained and validated to be used as a surrogate for the finite element model. Then, a variance-based sensitivity analysis is performed on the surrogate model to find the Sobol indices of the input parameters in respect to the output quantity of interest. The Sobol indices are used to reduce the dimensionality of the model. Generalized polynomial chaos expansion is used on the reduced basis models to propagate the uncertainty from the input parameters to the quantity of interest using the deep neural network surrogate model. These results are benchmarked against uncertainty propagation using Monte Carlo simulations. In conclusion, the UQ performed through the reduced basis model captures almost all the uncertainty in the model with significantly fewer simulations, making it possible to perform the UQ directly via simulations with the finite element model rather than surrogate machine-learned models.

36 MATERIALS SCIENCE↗
DOE OSTI2020

UQ Toolkit v 2.0

The Uncertainty Quantification (UQ) Toolkit is a software library for the characterizaton and propagation of uncertainties in computational models. For the characterization of uncertainties, Bayesian inference tools are provided to infer uncertain model parameters, as well as Bayesian compressive sensing methods for discovering sparse representations of high-dimensional input-output response surfaces, and also Karhunen-Loève expansions for representing stochastic processes. Uncertain parameters are treated as random variables and represented with Polynomial Chaos expansions (PCEs). The library implements several spectral basis function types (e.g. Hermite basis functions in terms of Gaussian random variables or Legendre basis functions in terms of uniform random variables) that can be used to represent random variables with PCEs. For propagation of uncertainty, tools are provided to propagate PCEs that describe the input uncertainty through the computational model using either intrusive methods (Galerkin projection of equations onto basis functions) or non-intrusive methods (perform deterministic operation at sampled values of the random values and project the obtained results onto basis functions).

Safta, Cosmin↗
DOE OSTI2025

Uncertainty quantification for misspecified machine learned interatomic potentials

The use of high-dimensional regression techniques from machine learning has significantly improved the quantitative accuracy of interatomic potentials. Atomic simulations can now plausibly target quantitative predictions in a variety of settings, which has brought renewed interest in robust means to quantify uncertainties. In many practical settings where model complexity is constrained (e.g., due to performance considerations), misspecification — the inability of any one choice of model parameters to exactly match all training data — is a key contributor to errors that is often disregarded. Here, we employ a recent misspecification-aware regression technique to quantify parameter uncertainties, which is then propagated to a broad range of phase and defect properties in tungsten. The propagation is performed through both brute-force resampling and implicit Taylor expansion. The propagated misspecification uncertainties robustly quantify and bound errors on a broad range of material properties. We demonstrate application to recent foundational machine learning interatomic potentials, accurately predicting and bounding errors in MACE-MPA-0 energy predictions across the diverse materials project database.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Unbinned extraction of $γ$ from $B\to DK$ with normalizing flows

We introduce an unbinned method for extracting the CKM angle $γ$ from the decay chain $B^\pm \to (D \to K_S π^+ π^-) K^\pm$ using normalizing flows (NFs). The NFs, trained on $D$ decay data, learn a faithful continuous representation of the amplitude and strong phase variation over the $D\to K_Sπ^+π^-$ Dalitz plot whose fidelity improves with increased data sample sizes. With this input, the $B$ decay data can be used to extract the parameters $r_B$, $δ_B$, and $γ$. We test the method on Monte Carlo generated data, where it successfully recovers the injected value of $γ$ within uncertainties. The present implementation propagates statistical uncertainties from finite training data via an ensemble of independently trained flows, and does not attempt to capture the effects of systematic experimental errors. We explore two versions of the method that differ in how the trigonometric constraint on phase variation is encoded, and comment on the possible extension to Bayesian NFs, which would provide direct uncertainty estimates on the learned densities without requiring ensemble training.

Grossman, Yuval [Cornell U., LEPP]↗
DOE OSTI2024

Uncertainty Quantification via Stable Distribution Propagation

We propose a new approach for propagating stable probability distributions through neural networks. Our method is based on local linearization, which we show to be an optimal approximation in terms of total variation distance for the ReLU non-linearity. This allows propagating Gaussian and Cauchy input uncertainties through neural networks to quantify their output uncertainties. To demonstrate the utility of propagating distributions, we apply the proposed method to predicting calibrated confidence intervals and selective prediction on out-of-distribution data. The results demonstrate a broad applicability of propagating distributions and show the advantages of our method over other approaches such as moment matching.

Artificial Intelligence (cs.AI)↗
DOE OSTI2021

A minimally invasive, efficient method for propagation of full-field uncertainty in solid dynamics

In this work, we present a minimally invasive method for forward propagation of material property uncertainty to full-field quantities of interest in solid dynamics. Full-field uncertainty quantification enables the design of complex systems where quantities of interest, such as failure points, are not known a priori. The method, motivated by the well-known probability density function (PDF) propagation method of turbulence modeling, uses an ensemble of solutions to provide the joint PDF of desired quantities at every point in the domain. A small subset of the ensemble is computed exactly, and the remainder of the samples are computed with approximation of the evolution equations based on those exact solutions. Although the proposed method has commonalities with traditional interpolatory stochastic collocation methods applied directly to quantities of interest, it is distinct and exploits the parameter dependence and smoothness of the driving term of the evolution equations. The implementation is model independent, storage and communication efficient, and straightforward. We demonstrate its efficiency, accuracy, scaling with dimension of the parameter space, and convergence in distribution with two problems: a quasi-one-dimensional bar impact, and a two material notched plate impact. For the bar impact problem, we provide an analytical solution to PDF of the solution fields for method validation. With the notched plate problem, we also demonstrate good parallel efficiency and scaling of the method.

42 ENGINEERING↗
DOE OSTI2025

Demonstration of TOFFEE: A Response Uncertainty Quantification Tool

A key characteristic in neutron transport is nuclear data. Cross-section uncertainty is not used in MCNP6.3 to propagate response uncertainty without external analysis. Here, the TOol For Fast Error Estimation (TOFFEE) is a Python-based code developed to automate the propagation of cross-section uncertainty for MCNP evaluations. TOFFEE implements the sandwich rule to calculate the uncertainty from cross sections with sensitivity coefficients from MCNP6.3 and ENDF/B covariance data. In this paper, TOFFEE has been tested with benchmark experiments, and it has been compared to the uncertainty quantification capabilities of Sampler and TSUNAMI, within SCALE, to verify the application’s capabilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Sequential Learning of Active Subspaces

This study shows that in recent years, active subspace methods (ASMs) have become a popular means of performing subspace sensitivity analysis on black-box functions. Naively applied, however, ASMs require gradient evaluations of the target function. In the event of noisy, expensive, or stochastic simulators, evaluating gradients via finite differencing may be infeasible. In such cases, often a surrogate model is employed, on which finite differencing is performed. When the surrogate model is a Gaussian process (GP), we show that the ASM estimator is available in closed form, rendering the finite-difference approximation unnecessary. We use our closed-form solution to develop acquisition functions focused on sequential learning tailored to sensitivity analysis on top of ASMs. We also show that the traditional ASM estimator may be viewed as a method of moments estimator for a certain class of GPs. We demonstrate how uncertainty on GP hyperparameters may be propagated to uncertainty on the sensitivity analysis, allowing model-based confidence intervals on the active subspace. Our methodological developments are illustrated on several examples.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

maranasgroup/uncFBA

In the repository are example scripts that perform uncertainty injection and propagation to flux balance analysis with outputs for a small sample size (for demonstration purpose only). For proper analysis, user should download the scripts and run for a large sample size (e.g., 10,000 samples). If you use the scripts, please cite the following Metabolic Engineering article: “Quantifying the propagation of parametric uncertainty on flux balance analysis” (https://doi.org/10.1016/j.ymben.2021.10.012) There are two subdirectories: /uncFBA/uncBiom: injection of normally distributed noise to biomass precursor coeffcients and ATP maintenance (growth-associated ATP maintenance (GAM) and non-growth associated ATP maintenance (NGAM)) /uncFBA/uncRHS: departure from steady-state by adding noise drawn from normal distribution to the RHS terms of mass balance constraints

Dinh, Hoang↗
DOE OSTI2021

Processing Aleatory and Epistemic Uncertainties in Experimental Data From Sparse Replicate Tests of Stochastic Systems for Real-Space Model Validation

This paper presents a practical methodology for propagating and processing uncertainties associated with random measurement and estimation errors (that vary from test-to-test) and systematic measurement and estimation errors (uncertain but similar from test-to-test) in inputs and outputs of replicate tests to characterize response variability of stochastically varying test units. Also treated are test condition control variability from test-to-test and sampling uncertainty due to limited numbers of replicate tests. These aleatory variabilities and epistemic uncertainties result in uncertainty on computed statistics of output response quantities. The methodology was developed in the context of processing experimental data for “real-space” (RS) model validation comparisons against model-predicted statistics and uncertainty thereof. The methodology is flexible and sufficient for many types of experimental and data uncertainty, offering the most extensive data uncertainty quantification (UQ) treatment of any model validation method the authors are aware of. It handles both interval and probabilistic uncertainty descriptions and can be performed with relatively little computational cost through use of simple and effective dimension- and order-adaptive polynomial response surfaces in a Monte Carlo (MC) uncertainty propagation approach. A key feature of the progressively upgraded response surfaces is that they enable estimation of propagation error contributed by the surrogate model. Sensitivity analysis of the relative contributions of the various uncertainty sources to the total uncertainty of statistical estimates is also presented. Finally, the methodologies are demonstrated on real experimental validation data involving all the mentioned sources and types of error and uncertainty in five replicate tests of pressure vessels heated and pressurized to failure. Simple spreadsheet procedures are used for all processing operations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

The role of collisional energy transfer in the thermal and prompt dissociation of 1-methyl allyl

Collisional energy transfer plays a pivotal role in a-priori calculations of the pressure-dependent rate constants obtained from a master equation. However, accurate determinations of collisional energy transfer parameters are rare and so most kinetic studies rely on best-fits of these parameters to experimental measurements (if available) or estimates guided from literature studies. In this work, we have quantified the effect of the uncertainty in energy transfer parameters on the thermal and prompt dissociation kinetics of a resonance stabilized radical, 1-methyl allyl (1MA), of relevance to the combustion of 1- and 2-butene isomers. Simulations using literature kinetics models were performed to assess the impact of these uncertainties on flame propagation and speciation data in laminar flames of 1- and 2-butene. Analyses of the uncertainty propagated by the energy transfer parameters for 1MA dissociation to the flame simulations, in particular the laminar flame speed, indicate an intricate coupling between the kinetics of 1MA dissociation (chain propagation) and its reaction with H-atoms (chain-termination). Ab-initio based theoretical calculations were also performed to obtain pressure-dependent kinetics for the reaction of 1MA with H-atoms. Lastly, theoretically calculated energy transfer parameters were used to best characterize the kinetics and branching between the chain propagating 1MA dissociation and the chain-terminating reaction 1MA + H.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A Tutorial on Bayesian analysis of linear shock compression data

Gas gun and other shock compression experiments often produce shock wave velocity measurements that are linearly associated with particle velocity. Traditionally, this empirical relationship is quantified with a single Hugoniot curve that is estimated using least squares regression. However, for downstream modeling and simulation tasks, it is often more useful to have multiple Hugoniot curves in the pressure–volume plane that are consistent with the data. We employ Bayesian uncertainty quantification methods as a framework for propagating measurement uncertainty through to model parameters and predictions. Specifically, this Tutorial shows how to sample multiple Hugoniot curves in the pressure–volume plane that are consistent with the shock wave-particle velocity measurements in a two-step Bayesian approach. First, we obtain an analytical expression for the posterior distribution of the linear model parameters using Bayesian linear regression. Second, we propagate samples from the posterior distribution through the Rankine–Hugoniot equations to yield Hugoniot curves in the pressure–volume plane. The procedure is demonstrated with publicly available data on argon, copper, and nickel, and compared against bootstrapping and linear regression. The Bayesian procedure is shown to be interpretable, computationally inexpensive, and less sensitive than an alternative bootstrapping approach to the removal of the point in the copper dataset that has the largest particle velocity. As a Tutorial on Bayesian methodology for the shock compression community, we provide several derivations and explanations that make this paper self-contained, and make all code and data available at github.com/llnl/BALSCD.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Driving mode analysis—How uncertain functional inputs propagate to an output

Abstract Driving mode analysis elucidates how correlated features of uncertain functional inputs jointly propagate to produce uncertainty in the output of a computation. Uncertain input functions are decomposed into three terms: the mean functions, a zero‐mean driving mode, and zero‐mean residual. The random driving mode varies along a single direction, having fixed functional shape and random scale. It is uncorrelated with the residual, and under linear error propagation, it produces an output variance equal to that of the full input uncertainty. Finally, the driving mode best represents how input uncertainties propagate to the output because it minimizes expected squared Mahalanobis distance amongst competitors. These characteristics recommend interpretation of the driving mode as the single‐degree‐of‐freedom component of input uncertainty that drives output uncertainty. We derive the functional driving mode, show its superiority to other seemingly sensible definitions, and demonstrate the utility of driving mode analysis in an application. The application is the simulation of neutron transport in criticality experiments. The uncertain input functions are nuclear data that describe how Pu reacts to bombardment by neutrons. Visualization of the driving mode helps scientists understand what aspects of correlated functional uncertainty have effects that either reinforce or cancel one another in propagating to the output of the simulation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Opinion: The importance of historical and paleoclimate aerosol radiative effects

Abstract. Estimating past aerosol radiative effects and their uncertainties is an important topic in climate science. Aerosol radiative effects propagate into large uncertainties in estimates of how present and future climate evolves with changing greenhouse gas emissions. A deeper understanding of how aerosols affected the atmospheric energy budget under past climates is hindered in part by a lack of relevant paleo-observations and in part because less attention has been paid to the problem. Because of the lack of information we do not seek here to determine the change in the radiative forcing due to aerosol changes but rather to estimate the uncertainties in those changes. Here we argue that current uncertainties from emission uncertainties (90 % confidence interval range spanning 2.8 W m−2) are just as large as model spread uncertainties (2.8 W m−2) in calculating preindustrial to present-day aerosol radiative effects. There are no estimates of radiative forcing for important aerosols such as wildfire and dust aerosols in most paleoclimate time periods. However, qualitative analysis of paleoclimate proxies suggests that changes in aerosols between different past climates are similar in magnitude to changes in aerosols between the preindustrial and present day; plus, there is the added uncertainty from the variability in aerosols and fires in the preindustrial. From the limited literature we crudely estimate a paleoclimate aerosol uncertainty for the Last Glacial Maximum relative to preindustrial of 4.8 W m−2, and we estimate the uncertainty in the aerosol feedback in the natural Earth system over the paleoclimate (Last Glacial Maximum to preindustrial) to be about 3.2 W m−2 K−1. In order to more accurately assess the uncertainty in historical aerosol radiative effects, we propose a new model intercomparison project, which would include multiple plausible emission scenarios tested across a range of state-of-the-art climate models over the historical period. These emission scenarios would then be compared to the available independent aerosol observations to constrain which are most probable. In addition, future efforts should work to characterize and constrain paleo-aerosol forcings and uncertainties. Careful propagation of aerosol uncertainties in the literature is required to ensure an accurate quantification of uncertainties in projections of future climate changes.

Environmental Sciences & Ecology↗
DOE OSTI2021

Linear systematics mitigation in galaxy clustering in the Dark Energy Survey Year 1 Data

ABSTRACT We implement a linear model for mitigating the effect of observing conditions and other sources of contamination in galaxy clustering analyses. Our treatment improves upon the fiducial systematics treatment of the Dark Energy Survey (DES) Year 1 (Y1) cosmology analysis in four crucial ways. Specifically, our treatment (1) does not require decisions as to which observable systematics are significant and which are not, allowing for the possibility of multiple maps adding coherently to give rise to significant bias even if no single map leads to a significant bias by itself, (2) characterizes both the statistical and systematic uncertainty in our mitigation procedure, allowing us to propagate said uncertainties into the reported cosmological constraints, (3) explicitly exploits the full spatial structure of the galaxy density field to differentiate between cosmology-sourced and systematics-sourced fluctuations within the galaxy density field, and (4) is fully automated, and can therefore be trivially applied to any data set. The updated correlation function for the DES Y1 redMaGiC catalogue minimally impacts the cosmological posteriors from that analysis. Encouragingly, our analysis does improve the goodness-of-fit statistic of the DES Y1 3 × 2pt data set (Δχ2 = −6.5 with no additional parameters). This improvement is due in nearly equal parts to both the change in the correlation function and the added statistical and systematic uncertainties associated with our method. We expect the difference in mitigation techniques to become more important in future work as the size of cosmological data sets grows.

79 ASTRONOMY AND ASTROPHYSICS↗