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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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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Evaluating the limitations of Bayesian metabolic control analysis

AbstractBayesian Metabolic Control Analysis (BMCA) has emerged as a promising framework for inferring metabolic control coefficients in data-limited scenarios by integrating Bayesian inference with linlog rate laws. However, its predictive accuracy and limitations remain underexplored. This study systematically evaluates BMCA’s ability to infer elasticity values, flux control coefficients (FCCs), and concentration control coefficients (CCCs) under varying data availability conditions using three synthetic metabolic network models. Our findings highlight the strengths and weaknesses of BMCA, guiding its application in metabolic engineering and emphasizing the need for methodological refinements.Author summaryUnderstanding how enzymes control metabolic pathways is crucial for optimizing biomanufacturing and synthetic biology applications. Bayesian Metabolic Control Analysis (BMCA) is a promising computational method that integrates Bayesian inference with metabolic control analysis to estimate key control parameters, even in cases with limited experimental data. However, the accuracy and limitations of BMCA remain unclear. In this study, we systematically evaluate BMCA using three synthetic metabolic networks to determine how different types of physiological data impact its predictive performance. We find that BMCA requires flux and enzyme concentration data for accurate predictions, while external metabolite concentrations contribute little. Additionally, BMCA fails to predict elasticity values beyond a magnitude of 1.5 and reliably infer allosteric regulation, even when strong regulatory interactions exist. In addition, BMCA does not accurately rank metabolic control points, which may limit its utility in identifying key enzymes in engineered pathways. Our work provides practical insights into when and how BMCA can be applied, guiding future research in metabolic modeling and control analysis.

Shin, Janis (ORCID:0000000216572455)↗
DOE OSTI2025

Bayesian inference of nuclear-matter density from proton scattering

Background: Proton elastic scattering at intermediate energy is widely employed as a tool for determining the matter radius of atomic nuclei. Here, the sensitivity of the approach relies on high-resolution measurements at small scattering angles and low-momentum transfer. Under these conditions, the Glauber multiple scattering theory accurately describes the proton-nucleus elastic cross section. Purpose: Investigate the sensitivity of the Glauber multiple scattering theory to uncertainties associated with input parameters such as the nuclear-matter density distribution and nucleon-nucleon data. Method: A joint Bayesian inference was performed using 12 angular distributions of elastic scattering at different energies on 58 Ni, 90 Zr, and 208 Pb targets. A Metropolis-Hastings algorithm was implemented to make an uncertainty quantification analysis for the input parameters used in the Glauber multiple scattering theory. Results: The experimental cross sections were fitted simultaneously using a joint Bayesian inference approach. Posterior probability density distributions of 42 input parameters were obtained from the analysis. A moderate correlation between the nuclear density parameters and the nucleon-nucleon cross sections was found. This correlation impacts the extraction of the nuclear-matter radius. Conclusions: The present analysis provided a consistent method for extracting the nuclear-matter density distribution of 58 Ni, 90 Zr, and 208 Pb from data across different incident energies. Due to the correlation of the nucleon-nucleon cross sections with the other input parameters, a constrained Bayesian inference using free nucleon-nucleon cross section data was performed. The nuclear-matter radii obtained from the analysis are in good agreement with multiple results reported in the literature.

190 ≤ A ≤ 219↗
DOE OSTI2024

New metric improving Bayesian calibration of a multistage approach studying hadron and inclusive jet suppression

We study parton energy-momentum exchange with the quark gluon plasma (QGP) within a multistage approach composed of in-medium Dokshitzer-Gribov-Lipatov-Altarelli-Parisi evolution at high virtuality, and (linearized) Boltzmann transport formalism at lower virtuality. This multistage simulation is then calibrated in comparison with high- p T charged hadrons, D mesons, and the inclusive jet nuclear modification factors, using Bayesian model-to-data comparison, to extract the virtuality-dependent transverse momentum broadening transport coefficient q ̂ . To facilitate this undertaking, we develop a quantitative metric for validating the Bayesian workflow, which is used to analyze the sensitivity of various model parameters to individual observables. The usefulness of this new metric in improving Bayesian model emulation is shown to be highly beneficial for future such analyses. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Bayesian second law of thermodynamics

Here, we derive a generalization of the second law of thermodynamics that uses Bayesian updates to explicitly incorporate the effects of a measurement of a system at some point in its evolution. By allowing an experimenter's knowledge to be updated by the measurement process, this formulation resolves a tension between the fact that the entropy of a statistical system can sometimes fluctuate downward and the information-theoretic idea that knowledge of a stochastically evolving system degrades over time. The Bayesian second law can be written as Δ H ( ρ m , ρ ) + 〈 Q 〉 F | m ≥ 0 , where Δ H ( ρ m , ρ ) is the change in the cross entropy between the original phase-space probability distribution ρ and the measurement-updated distribution ρ m and 〈 Q 〉 F | m is the expectation value of a generalized heat flow out of the system. Furthermore, we derive refined versions of the second law that bound the entropy increase from below by a non-negative number, as well as Bayesian versions of integral fluctuation theorems. We demonstrate the formalism using simple analytical and numerical examples.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Identifying Adversarial Cyber-Activity in Operational Technology Environments Using Bayesian Networks

Critical infrastructure and other operational technology (OT) environments face increasing cybersecurity risks from adversarial behavior. This paper describes the development of a risk model using a Bayesian network to enhance the comprehension of observable cyber events caused by malicious activity in OT environments. The core of the Bayesian network is a process model that describes the stages of adversary behavior. The remainder of the model is based on the MITRE ATT&CK® for Industrial Control Systems (ICS) taxonomy, which includes tactics and techniques that may be used by the adversary. The observables provide evidence for adversary behavior through the intermediary technique and tactic nodes. One challenge in constructing this model is a lack of open-source data from cyber-attacks on OT systems. This paper discusses learning from limited data, the elicitation of expert opinion to construct the conditional probability tables when data is scarce, and the refinement of the most difficult conditional probabilities tables using several forms of sensitivity analyses. Finally, the Bayesian network is demonstrated using two historical case studies: the DarkSide ransomware attack on the Colonial Pipeline and the destructive cyberattack targeting the ThyssenKrupp blast furnace. Index Terms—Cybersecurity, industrial control systems, operational technology

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Stochastic Gradient-Based Distributed Bayesian Estimation in Cooperative Sensor Networks

Distributed Bayesian inference provides a full quantification of uncertainty offering numerous advantages over point estimates that autonomous sensor networks are able to exploit. However, fully-decentralized Bayesian inference often requires large communication overheads and low network latency, resources that are not typically available in practical applications. In this paper, we propose a decentralized Bayesian inference approach based on stochastic gradient Langevin dynamics, which produces full posterior distributions at each of the nodes with significantly lower communication overhead. We provide analytical results on convergence of the proposed distributed algorithm to the centralized posterior, under typical network constraints. Finally, we also provide extensive simulation results to demonstrate the validity of the proposed approach.

42 ENGINEERING↗
DOE OSTI2025

eDNAjoint: An R package for interpreting paired or semi‐paired environmental DNA and traditional survey data in a Bayesian framework

Abstract Environmental DNA (eDNA) sampling is increasingly used in surveys of species distribution as a potentially sensitive and efficient monitoring method. Yet access to modelling tools designed specifically for interpreting this new data type lags behind its ubiquity. While occupancy modelling software has dominated the analytical landscape for eDNA data analysis of single species, this type of model may not always be the most appropriate. The rate of eDNA detection often corresponds to species density, rather than just occupancy, and researchers often have access to observations from non‐genetic sampling methods at the same sites. To provide users access to a modelling framework designed to maximize the use of all available data, we developed an R package, eDNAjoint . The package provides an easy‐to‐use interface for fitting a ‘joint’ model that integrates data from paired or semi‐paired eDNA and traditional surveys in a Bayesian framework. The model can be used to estimate parameters like the probability of a false positive eDNA detection and mean catch rate at a site, and the package allows access to multiple model variations and Bayesian prior customization. Additional functionality can be used for model selection, summarising posteriors and comparing the relative sensitivities of the two survey methods. We demonstrate the use of eDNAjoint by fitting a variation of the model with site‐level covariates that scale the sensitivity of eDNA sampling relative to traditional sampling. The example workflow uses binary eDNA and seine count data for the endangered tidewater goby ( Eucyclogobius newberryi ) from a study by Schmelzle and Kinziger (2016). This use case includes a prior sensitivity analysis and an evaluation of the relationship between detection rates and environmental variables. eDNAjoint has the potential to greatly increase the range of users who will be able to rigorously analyse eDNA and traditional survey data in a Bayesian framework, understand if and how eDNA can improve monitoring practices, and gain confidence in the interpretability of eDNA data.

Keller, Abigail G. [Department of Environment Scie↗
DOE OSTI2022

Bayesian optimized collection strategies for fatigue strength testing

Abstract A statistical framework is presented enabling optimal sampling and analysis of constant life fatigue data. Protocols using Bayesian maximum entropy sampling are built based on conventional staircase and stress step methods, reducing the requirement of prior knowledge for data collection. The Bayesian Staircase method shows improved parameter estimation efficiency, and the Bayesian Stress Step method shows equal accuracy to the standard method at larger step size allowing experimentalists to lessen concerns of loading history. Statistical methods for determining model suitability are shown, highlighting the influence of protocol. Experimental validation is performed, showing the applicability of the methods in laboratory testing.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Optimal Experimental Design Using a Consistent Bayesian Approach

We consider the utilization of a computational model to guide the optimal acquisition of experimental data to inform the stochastic description of model input parameters. Our formulation is based on the recently developed consistent Bayesian approach for solving stochastic inverse problems, which seeks a posterior probability density that is consistent with the model and the data in the sense that the push-forward of the posterior (through the computational model) matches the observed density on the observations almost everywhere. Given a set of potential observations, our optimal experimental design (OED) seeks the observation, or set of observations, that maximizes the expected information gain from the prior probability density on the model parameters. We discuss the characterization of the space of observed densities and a computationally efficient approach for rescaling observed densities to satisfy the fundamental assumptions of the consistent Bayesian approach. Finally, numerical results are presented to compare our approach with existing OED methodologies using the classical/statistical Bayesian approach and to demonstrate our OED on a set of representative partial differential equations (PDE)-based models.

42 ENGINEERING↗
DOE OSTI2020

sMF-BO-2CoGP: A sequential multi-fidelity constrained Bayesian optimization framework for design applications

Bayesian optimization (BO) is an effective surrogate-based method that has been widely used to optimize simulation-based applications. While the traditional Bayesian optimization approach only applies to single-fidelity models, many realistic applications provide multiple levels of fidelity with various levels of computational complexity and predictive capability. In this work, we propose a multi-fidelity Bayesian optimization method for design applications with both known and unknown constraints. The proposed framework, called sMF-BO-2CoGP, is built on a multi-level CoKriging method to predict the objective function. An external binary classifier, which we approximate using a separate CoKriging model, is used to distinguish between feasible and infeasible regions. Finally, the sMF-BO-2CoGP method is demonstrated using a series of analytical examples and a flip-chip application for design optimization to minimize the deformation due to warping under thermal loading conditions.

42 ENGINEERING↗
DOE OSTI2022

Descriptor Aided Bayesian Optimization for Many-Level Qualitative Variables With Materials Design Applications

Abstract Engineering design often involves qualitative and quantitative design variables, which requires systematic methods for the exploration of these mixed-variable design spaces. Expensive simulation techniques, such as those required to evaluate optimization objectives in materials design applications, constitute the main portion of the cost of the design process and underline the need for efficient search strategies—Bayesian optimization (BO) being one of the most widely adopted. Although recent developments in mixed-variable Bayesian optimization have shown promise, the effects of dimensionality of qualitative variables have not been well studied. High-dimensional qualitative variables, i.e., with many levels, impose a large design cost as they typically require a larger dataset to quantify the effect of each level on the optimization objective. We address this challenge by leveraging domain knowledge about underlying physical descriptors, which embody the physics of the underlying physical phenomena, to infer the effect of unobserved levels that have not been sampled yet. We show that physical descriptors can be intuitively embedded into the latent variable Gaussian process approach—a mixed-variable GP modeling technique—and used to selectively explore levels of qualitative variables in the Bayesian optimization framework. This physics-informed approach is particularly useful when one or more qualitative variables are high dimensional (many-level) and the modeling dataset is small, containing observations for only a subset of levels. Through a combination of mathematical test functions and materials design applications, our method is shown to be robust to certain types of incomplete domain knowledge and significantly reduces the design cost for problems with high-dimensional qualitative variables.

Engineering↗
DOE OSTI2025

Improving Trustworthiness of Data-Driven Power Grid Contingency Analysis With Bayesian Residual Graph Neural Networks

The evolving energy landscape requires novel tools to efficiently perform contingency analysis and reliability assessment of power grids, potentially in real-time. The high computational cost of traditional power flow solvers limits their applicability in practice. Machine learning (ML) surrogates such as deep neural networks (NNs) accelerate power flow solvers computations, enabling high-order contingency analysis and real-time decision-making by learning highly nonlinear functions and integrating grid topology via graph architectures. However, (graph) NNs lack predictive power away from training data and do not provide predictive confidence estimates. Here, we present a Bayesian residual graph NN that integrates knowledge from low-fidelity data via residual training and embeds granular quantification of uncertainties, improving trustworthiness critical for high-consequence decision-making. Applying Bayesian concepts to NNs is challenging due to the high-dimensionality of both the parameter space, complicating derivation of a meaningful prior, and the output space in large grid systems, requiring enhanced techniques to assess the predicted high-dimensional uncertainties. Our contributions include: (1) Deriving a prior for fully connected and graph NNs that leverages low-fidelity data to guide mean predictions and appropriately control prior predictive uncertainty. (2) Integrating this prior within an ensembling with anchoring scheme for efficient approximate posterior inference. (3) Deriving enhanced metrics to assess accuracy of both the mean and uncertainty predictions in high dimensions, appropriately accounting for correlations propagated through graph layers. The resulting Bayesian residual graph NN is tested on a contingency analysis task for 14-bus and 118-bus grids.

24 - POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2013

A full-spectral Bayesian reconstruction approach based on the material decomposition model applied in dual-energy computed tomography

Purpose: Dual-energy computed tomography (DECT) makes it possible to get two fractions of basis materials without segmentation. One is the soft-tissue equivalent water fraction and the other is the hard-matter equivalent bone fraction. Practical DECT measurements are usually obtained with polychromatic x-ray beams. Existing reconstruction approaches based on linear forward models without counting the beam polychromaticity fail to estimate the correct decomposition fractions and result in beam-hardening artifacts (BHA). The existing BHA correction approaches either need to refer to calibration measurements or suffer from the noise amplification caused by the negative-log preprocessing and the ill-conditioned water and bone separation problem. To overcome these problems, statistical DECT reconstruction approaches based on nonlinear forward models counting the beam polychromaticity show great potential for giving accurate fraction images.Methods: This work proposes a full-spectral Bayesian reconstruction approach which allows the reconstruction of high quality fraction images from ordinary polychromatic measurements. This approach is based on a Gaussian noise model with unknown variance assigned directly to the projections without taking negative-log. Referring to Bayesian inferences, the decomposition fractions and observation variance are estimated by using the joint maximum a posteriori (MAP) estimation method. Subject to an adaptive prior model assigned to the variance, the joint estimation problem is then simplified into a single estimation problem. It transforms the joint MAP estimation problem into a minimization problem with a nonquadratic cost function. To solve it, the use of a monotone conjugate gradient algorithm with suboptimal descent steps is proposed.Results: The performance of the proposed approach is analyzed with both simulated and experimental data. The results show that the proposed Bayesian approach is robust to noise and materials. It is also necessary to have the accurate spectrum information about the source-detector system. When dealing with experimental data, the spectrum can be predicted by a Monte Carlo simulator. For the materials between water and bone, less than 5% separation errors are observed on the estimated decomposition fractions.Conclusions: The proposed approach is a statistical reconstruction approach based on a nonlinear forward model counting the full beam polychromaticity and applied directly to the projections without taking negative-log. Compared to the approaches based on linear forward models and the BHA correction approaches, it has advantages in noise robustness and reconstruction accuracy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

SU-E-T-51: Bayesian Network Models for Radiotherapy Error Detection

Purpose: To develop a probabilistic model of radiotherapy plans using Bayesian networks that will detect potential errors in radiation delivery. Methods: Semi-structured interviews with medical physicists and other domain experts were employed to generate a set of layered nodes and arcs forming a Bayesian Network (BN) which encapsulates relevant radiotherapy concepts and their associated interdependencies. Concepts in the final network were limited to those whose parameters are represented in the institutional database at a level significant enough to develop mathematical distributions. The concept-relation knowledge base was constructed using the Web Ontology Language (OWL) and translated into Hugin Expert Bayes Network files via the the RHugin package in the R statistical programming language. A subset of de-identified data derived from a Mosaiq relational database representing 1937 unique prescription cases was processed and pre-screened for errors and then used by the Hugin implementation of the Estimation-Maximization (EM) algorithm for machine learning all parameter distributions. Individual networks were generated for each of several commonly treated anatomic regions identified by ICD-9 neoplasm categories including lung, brain, lymphoma, and female breast. Results: The resulting Bayesian networks represent a large part of the probabilistic knowledge inherent in treatment planning. By populating the networks entirely with data captured from a clinical oncology information management system over the course of several years of normal practice, we were able to create accurate probability tables with no additional time spent by experts or clinicians. These probabilistic descriptions of the treatment planning allow one to check if a treatment plan is within the normal scope of practice, given some initial set of clinical evidence and thereby detect for potential outliers to be flagged for further investigation. Conclusion: The networks developed here support the use of probabilistic models into clinical chart checking for improved detection of potential errors in RT plans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Robust Optimal Experimental Design of Infinite-Dimensional Bayesian Nonlinear Inverse Problems

Abstract. We consider robust optimal experimental design (ROED) for nonlinear Bayesian inverse problems governed by partial differential equations (PDEs). An optimal design is one that maximizes some utility quantifying the quality of the solution of an inverse problem. However, the optimal design is dependent on elements of the inverse problem such as the simulation model, the prior, or the measurement error model. ROED aims to produce an optimal design that is aware of the additional uncertainties encoded in the inverse problem and remains optimal even after variations in them. We follow a worst-case scenario approach to develop a new framework for robust optimal design of nonlinear Bayesian inverse problems. The proposed framework (a) is scalable and designed for infinite-dimensional Bayesian nonlinear inverse problems constrained by PDEs; (b) develops efficient approximations of the utility, namely the expected information gain; (c) employs eigenvalue sensitivity techniques to develop analytical forms and efficient evaluation methods of the gradient of the utility with respect to the uncertainties against which we wish to be robust; and (d) employs a probabilistic optimization paradigm that properly defines and efficiently solves the resulting combinatorial max-min optimization problem. The effectiveness of the proposed approach is illustrated for optimal sensor placement problem in an inverse problem governed by an elliptic PDE.

Chowdhary, Abhijit↗
DOE OSTI2023

Extending the predictive power of perturbative QCD using the principle of maximum conformality and the Bayesian analysis

In addition to the evaluation of high-order loop contributions, the precision and predictive power of perturbative QCD (pQCD) predictions depends on two important issues: (1) how to achieve a reliable, convergent fixed-order series, and (2) how to reliably estimate the contributions of unknown higher-order terms. The recursive use of renormalization group equation, together with the Principle of Maximum Conformality (PMC), eliminates the renormalization scheme-and-scale ambiguities of the conventional pQCD series. The result is a conformal, scale-invariant series of finite order which also satisfies all of the principles of the renormalization group. In this paper we propose a novel Bayesian-based approach to estimate the size of the unknown higher order contributions based on an optimized analysis of probability distributions. We show that by using the PMC conformal series, in combination with the Bayesian analysis, one can consistently achieve high degree of reliability estimates for the unknown high order terms. Thus the predictive power of pQCD can be greatly improved. We illustrate this procedure for two pQCD observables: R e+e– and R τ , which are each known up to four loops in pQCD. Numerical analyses confirm that by using the scale-independent and more convergent PMC conformal series, one can achieve reliable Bayesian probability estimates for the unknown higher-order contributions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Streamflow simulation in data-scarce basins using Bayesian and physics-informed machine learning models

Hydrologic predictions at rural watersheds are important but also challenging due to data shortage. Long short-term memory (LSTM) networks are a promising machine learning approach and have demonstrated good performance in streamflow predictions. However, due to its data-hungry nature, most LSTM applications focus on well-monitored catchments with abundant and high-quality observations. In this work, we investigate predictive capabilities of LSTM in poorly monitored watersheds with short observation records. To address three main challenges of LSTM applications in data-scarce locations, i.e., overfitting, uncertainty quantification (UQ), and out-of-distribution prediction, we evaluate different regularization techniques to prevent overfitting, apply a Bayesian LSTM for UQ, and introduce a physics-informed hybrid LSTM to enhance out-of-distribution prediction. Through case studies in two diverse sets of catchments with and without snow influence, we demonstrate that 1) when hydrologic variability in the prediction period is similar to the calibration period, LSTM models can reasonably predict daily streamflow with Nash–Sutcliffe efficiency above 0.8, even with only 2 years of calibration data; 2) when the hydrologic variability in the prediction and calibration periods is dramatically different, LSTM alone does not predict well, but the hybrid model can improve the out-of-distribution prediction with acceptable generalization accuracy; 3) L2 norm penalty and dropout can mitigate overfitting, and Bayesian and hybrid LSTM have no overfitting; and 4) Bayesian LSTM provides useful uncertainty information to improve prediction understanding and credibility. In conclusion, these insights have vital implications for streamflow simulation in watersheds where data quality and availability are a critical issue.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2012

A Bayesian Model for Pooling Gene Expression Studies That Incorporates Co-Regulation Information

Current Bayesian microarray models that pool multiple studies assume gene expression is independent of other genes. However, in prokaryotic organisms, genes are arranged in units that are co-regulated (called operons). Here, we introduce a new Bayesian model for pooling gene expression studies that incorporates operon information into the model. Our Bayesian model borrows information from other genes within the same operon to improve estimation of gene expression. The model produces the gene-specific posterior probability of differential expression, which is the basis for inference. We found in simulations and in biological studies that incorporating co-regulation information improves upon the independence model. We assume that each study contains two experimental conditions: a treatment and control. We note that there exist environmental conditions for which genes that are supposed to be transcribed together lose their operon structure, and that our model is best carried out for known operon structures.

59 BASIC BIOLOGICAL SCIENCES↗