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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Mads.jl

Mads.jl (Model analysis and decision support in Julia) is a code that streamlines the process of using data and models for analysis and decision support. It is based on another open-source code developed at LANL and written in C/C++ (MADS; http://mads.lanl.gov; LA-CC-11- 035). Mads.jl can work with external models of arbitrary complexity as well as built-in models of flow and transport in porous media. It enables a number of data- and model-based analyses including model calibration, sensitivity analysis, uncertainty quantification, and decision analysis. The code also can use a series of alternative adaptive computational techniques for Bayesian sampling, Monte Carlo, and Bayesian Information-Gap Decision Theory. The code is implemented in the Julia programming language, and has high-performance (parallel) and memory management capabilities. The code uses a series of third party modules developed by others. The code development will also include contributions to the existing third party modules written in Julia; this contributions will be important for the efficient implementation of the algorithm used by Mads.jl. The code also uses a series of LANL developed modules that are developed by Dan O'Malley; these modules will be also a part of the Mads.jl release. Mads.jl will be released under GPL V3 license. The code will be distributed as a Git repo at gitlab.com and github.com. Mads.jl manual and documentation will be posted at madsjulia.lanl.gov.

Vesselinov, Velimir↗
DOE OSTI2016

BAYESIAN SEMI-BLIND COMPONENT SEPARATION FOR FOREGROUND REMOVAL IN INTERFEROMETRIC 21 cm OBSERVATIONS

In this paper, we present a new Bayesian semi-blind approach for foreground removal in observations of the 21 cm signal measured by interferometers. The technique, which we call H i Expectation–Maximization Independent Component Analysis (HIEMICA), is an extension of the Independent Component Analysis technique developed for two-dimensional (2D) cosmic microwave background maps to three-dimensional (3D) 21 cm cosmological signals measured by interferometers. This technique provides a fully Bayesian inference of power spectra and maps and separates the foregrounds from the signal based on the diversity of their power spectra. Relying only on the statistical independence of the components, this approach can jointly estimate the 3D power spectrum of the 21 cm signal, as well as the 2D angular power spectrum and the frequency dependence of each foreground component, without any prior assumptions about the foregrounds. This approach has been tested extensively by applying it to mock data from interferometric 21 cm intensity mapping observations under idealized assumptions of instrumental effects. We also discuss the impact when the noise properties are not known completely. As a first step toward solving the 21 cm power spectrum analysis problem, we compare the semi-blind HIEMICA technique to the commonly used Principal Component Analysis. Under the same idealized circumstances, the proposed technique provides significantly improved recovery of the power spectrum. This technique can be applied in a straightforward manner to all 21 cm interferometric observations, including epoch of reionization measurements, and can be extended to single-dish observations as well.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

The impact of response measurement error on the analysis of designed experiments

This study considers the analysis of designed experiments when there is measurement error in the true response or so-called response measurement error. We consider both additive and multiplicative response measurement errors. Through a simulation study, we investigate the impact of ignoring the response measurement error in the analysis, that is, by using a standard analysis based on t-tests. In addition, we examine the role of repeat measurements in improving the quality of estimation and prediction in the presence of response measurement error. We also study a Bayesian approach that accounts for the response measurement error directly through the specification of the model, and allows including additional information about variability in the analysis. We consider the impact on power, prediction, and optimization. Copyright © 2015 John Wiley & Sons, Ltd.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Evolutionary Dynamics of West Nile Virus in the United States, 1999–2011: Phylogeny, Selection Pressure and Evolutionary Time-Scale Analysis

West Nile virus (WNV), an arbovirus maintained in a bird-mosquito enzootic cycle, can infect other vertebrates including humans. WNV was first reported in the US in 1999 where, to date, three genotypes belonging to WNV lineage I have been described (NY99, WN02, SW/WN03). We report here the WNV sequences obtained from two birds, one mosquito, and 29 selected human samples acquired during the US epidemics from 2006–2011 and our examination of the evolutionary dynamics in the open-reading frame of WNV isolates reported from 1999–2011. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses and selection pressure analyses were conducted with the HyPhy package. Phylogenetic analysis identified human WNV isolates within the main WNV genotypes that have circulated in the US. Within genotype SW/WN03, we have identified a cluster with strains derived from blood donors and birds from Idaho and North Dakota collected during 2006–2007, termed here MW/WN06. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. The mean nucleotide substitution rate for WNV isolates obtained from humans was calculated to be 5.0661024 substitutions/site/year (s/s/y). The Bayesian skyline plot shows that after a period of high genetic variability following the introduction of WNV into the US, the WNV population appears to have reached genetic stability. The establishment of WNV in the US represents a unique opportunity to understand how an arbovirus adapts and evolves in a naive environment. We describe a novel, well-supported cluster of WNV formed by strains collected from humans and birds from Idaho and North Dakota. Adequate genetic surveillance is essential to public health since new mutants could potentially affect viral pathogenesis, decrease performance of diagnostic assays, and negatively impact the efficacy of vaccines and the development of specific therapies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Astrophysical data analysis with information field theory

Non-parametric imaging and data analysis in astrophysics and cosmology can be addressed by information field theory (IFT), a means of Bayesian, data based inference on spatially distributed signal fields. IFT is a statistical field theory, which permits the construction of optimal signal recovery algorithms. It exploits spatial correlations of the signal fields even for nonlinear and non-Gaussian signal inference problems. The alleviation of a perception threshold for recovering signals of unknown correlation structure by using IFT will be discussed in particular as well as a novel improvement on instrumental self-calibration schemes. IFT can be applied to many areas. Here, applications in in cosmology (cosmic microwave background, large-scale structure) and astrophysics (galactic magnetism, radio interferometry) are presented.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Combining Astrometry and Elemental Abundances: The Case of the Candidate Pre-Gaia Halo Moving Groups G03-37, G18-39, and G21-22

While most moving groups are young and nearby, a small number have been identified in the Galactic halo. Understanding the origin and evolution of these groups is an important piece of reconstructing the formation history of the halo. Here we report on our analysis of three putative halo moving groups: G03-37, G18-39, and G21-22. Based on Gaia EDR3 data, the stars associated with each group show some scatter in velocity (e.g., Toomre diagram) and integrals of motion (energy, angular momentum) spaces, counter to expectations of moving-group stars. We choose the best candidate of the three groups, G21-22, for follow-up chemical analysis based on high-resolution spectroscopy of six presumptive members. Using a new Python code that uses a Bayesian method to self-consistently propagate uncertainties from stellar atmosphere solutions in calculating individual abundances and spectral synthesis, we derive the abundances of α- (Mg, Si, Ca, Ti), Fe-peak (Cr, Sc, Mn, Fe, Ni), odd-Z (Na, Al, V), and neutron-capture (Ba, Eu) elements for each star. We find that the G21-22 stars are not chemically homogeneous. Based on the kinematic analysis for all three groups and the chemical analysis for G21-22, we conclude the three are not genuine moving groups. The case for G21-22 demonstrates the benefit of combining kinematic and chemical information in identifying conatal populations when either alone may be insufficient. Comparing the integrals of motion and velocities of the six G21-22 stars with those of known structures in the halo, we tentatively associate them with the Gaia-Enceladus accretion event.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

pygwb: A Python-based Library for Gravitational-wave Background Searches

The collection of gravitational waves (GWs) that are either too weak or too numerous to be individually resolved is commonly referred to as the gravitational-wave background (GWB). A confident detection and model-driven characterization of such a signal will provide invaluable information about the evolution of the universe and the population of GW sources within it. We present a new, user-friendly, Python-based package for GW data analysis to search for an isotropic GWB in ground-based interferometer data. We employ cross-correlation spectra of GW detector pairs to construct an optimal estimator of the Gaussian and isotropic GWB, and Bayesian parameter estimation to constrain GWB models. The modularity and clarity of the code allow for both a shallow learning curve and flexibility in adjusting the analysis to one’s own needs. We describe the individual modules that make up pygwb, following the traditional steps of stochastic analyses carried out within the LIGO, Virgo, and KAGRA Collaboration. We then describe the built-in pipeline that combines the different modules and validate it with both mock data and real GW data from the O3 Advanced LIGO and Virgo observing run. We successfully recover all mock data injections and reproduce published results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

A Bayesian method to estimate the neutron response matrix of a single crystal CVD diamond detector

Detectors made from artificial chemical vapor deposition (CVD) single crystal diamond are very promising candidates for applications where high resolution neutron spectrometry in very high neutron fluxes is required, for example in fusion research. We propose a Bayesian method to estimate the neutron response function of the detector for a continuous range of neutron energies (in our case, 10 MeV ≤ E{sub n} ≤ 16 MeV) based on a few measurements with quasi-monoenergetic neutrons. This method is needed because a complete set of measurements is not available and the alternative approach of using responses based on Monte Carlo calculations is not feasible. Our approach uses Bayesian signal-background separation techniques and radial basis function interpolation methods. We present the analysis of data measured at the PTB accelerator facility PIAF. The method is quite general and it can be applied to other particle detectors with similar characteristics.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Probability of committed warming exceeding 1.5 ∘ C and 2.0 ∘ C Paris targets

Abstract The feasibility of achieving the Paris 1.5 ∘ C target continues to be a complex and hotly debated question. To help resolve this question we calculate probability distributions of the committed warming that would ensue if all anthropogenic emissions were stopped immediately, or at successive future times. We use a simple Earth system model together with a Bayesian approach that incorporates multiple lines of evidence and accounts for known model biases. This analysis reveals a wide range of possible outcomes, including no further warming, but also a 15% chance of overshooting the 1.5 ∘ C target, and 1%–2% chance for 2 ∘ C, even if all emissions had stopped in 2020. If emissions merely stabilize in 2020 and stop in 2040, these probabilities increase to 90% and 17%. The uncertainty arises mainly from that of present forcing by aerosols. Rather than there being a fixed date by which emissions must stop, the probability of reaching either target—which is already below 100%—gradually diminishes with delays in eliminating emissions, by 3%–4% per year for 1.5 ∘ C.

Sherwood, Steven C. (ORCID:0000000174208216)↗
DOE OSTI2025

Advancements in Constitutive Model Calibration: Leveraging the Power of Full‐Field DIC Measurements and In Situ Load Path Selection for Reliable Parameter Inference

Accurate material characterization and model calibration are essential for computationally supported high-consequence engineering decisions. Historically, characterization and calibration methods (1) use simplified test specimen geometries and global data, (2) cannot guarantee that sufficient characterization data are collected for a specific model of interest, (3) use deterministic methods that provide best-fit parameter values with no uncertainty quantification, and (4) are sequential, inflexible, and time-consuming. This work brings together several recent advancements into an improved workflow called interlaced characterization and calibration (ICC) that advances the state-of-the-art in constitutive model calibration. The ICC paradigm (1) employs tools to efficiently use full-field data to calibrate high-fidelity material models, (2) aligns the data needed with the data collected by adopting an optimal experimental design protocol, (3) quantifies parameter uncertainty through Bayesian inference and (4) incorporates these advancements into a quasi real-time feedback loop. The ICC framework is demonstrated here on the calibration of a material model using simulated full-field data for an aluminium cruciform specimen being deformed biaxially. The cruciform is actively driven through the myopically preferred load path using Bayesian optimal experimental design, which selects load steps that yield the maximum expected information gain (EIG). Principal component analysis (PCA) is performed on the model predictions of full-field displacements, and fast surrogate models are built to approximate the input-output relationships of the expensive finite element model. Furthermore, the tools developed and demonstrated here show that high-fidelity constitutive models can be efficiently and reliably calibrated with quantified uncertainty, thus supporting credible decision-making and potentially increasing the agility of solid mechanics modelling by enabling utilization of computational simulations at earlier stages of the design cycle.

Bayesian optimal experimental design↗
DOE OSTI2021

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C . geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C . geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C . geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C . geophilum , we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

EcoBOT: an AI/ML enabled automated phenotyping capability for model plants

Introduction: Advances in automation and AI/ML offer new opportunities for plant science, including design, modeling, and analysis. This study aimed to develop an automated platform for researching small model plants under axenic conditions and integrate it with AI/ML tools. Methods: The EcoBOT platform was developed, which consists of sterile containers (EcoFABs) for growing plants and imaging for monitoring plant growth and health. Brachypodium distachyon was grown on the EcoBOT, and its response to nutrient limitation and copper stress was evaluated. Results: The results showed that Brachypodium distachyon grown in the EcoBOT maintained sterility and responded to nutrient limitation and copper stress. Analysis of over 6,500 root and shoot images revealed varying sensitivity and response rates to copper. Bayesian Optimization was used to improve model accuracies relating copper concentrations to plant biomass via sequential experiments, resulting in a >30% improvement. Discussion: The findings of this study demonstrate the potential of the EcoBOT platform for researching plant responses to environmental factors. Future experiments could focus on relating other chemical stresses and microbial interactions to create generalized models of plant responses.

AI image analysis↗
DOE OSTI2015

Nuclear Forensics Analysis with Missing and Uncertain Data

We have applied a new imputation-based method for analyzing incomplete data, called Monte Carlo Bayesian Database Generation (MCBDG), to the Spent Fuel Isotopic Composition (SFCOMPO) database. About 60% of the entries are absent for SFCOMPO. The method estimates missing values of a property from a probability distribution created from the existing data for the property, and then generates multiple instances of the completed database for training a machine learning algorithm. Uncertainty in the data is represented by an empirical or an assumed error distribution. The method makes few assumptions about the underlying data, and compares favorably against results obtained by replacing missing information with constant values.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Pervaporative Dehydration of 2,3-Butanediol by Dense Poly(vinylidene fluoride) Hollow Fiber Membranes: Parameter Estimation, Process Design, and Technoeconomic Evaluation under Uncertainty

Pervaporation, combined with other separation processes, can effectively remove water from fermentation product streams, making it highly suitable for purifying alcohols like 2,3-butanediol (BDO). In this study, a dense poly(vinylidene fluoride) (PVDF) hollow fiber membrane module prototype was fabricated for BDO dehydration, achieving >0.2 LMH total flux and >95% BDO rejection. With a Markov chain Monte Carlo (MCMC) approach, Bayesian inference was used to quantify the uncertainty of the permeance parameters. A membrane cascade model was developed to scale up a process that purifies a preconcentrated BDO feed (70 wt %) to high purity (90 wt %). Through propagation of the uncertainty of the parameters and sensitivity analyses of the process variables, a cascade design was recommended. Despite data and model limitations, the framework enabled a reliable system analysis and economic evaluation, validated through tight confidence intervals in key process metrics, establishing the foundation for future applications of Bayesian methods in membrane-based processes.

Animal feed↗
DOE OSTI2019

Cosmological Evidence Modelling: a new simulation-based approach to constrain cosmology on non-linear scales

Extracting accurate cosmological information from galaxy–galaxy and galaxy–matter correlation functions on non-linear scales (${\lesssim } 10 \, h^{-1}{\rm {Mpc}}$) requires cosmological simulations. Additionally, one has to marginalize over several nuisance parameters of the galaxy–halo connection. However, the computational cost of such simulations prohibits naive implementations of stochastic posterior sampling methods like Markov chain Monte Carlo (MCMC) that would require of order $\mathcal {O}(10^6)$ samples in cosmological parameter space. Several groups have proposed surrogate models as a solution: a so-called emulator is trained to reproduce observables for a limited number of realizations in parameter space. Afterwards, this emulator is used as a surrogate model in an MCMC analysis. In this work, we demonstrate a different method called Cosmological Evidence Modelling (CEM). First, for each simulation, we calculate the Bayesian evidence marginalized over the galaxy–halo connection by repeatedly populating the simulation with galaxies. We show that this Bayesian evidence is directly related to the posterior probability of cosmological parameters. Finally, we build a physically motivated model for how the evidence depends on cosmological parameters as sampled by the simulations. We demonstrate the feasibility of CEM by using simulations from the Aemulus simulation suite and forecasting cosmological constraints from BOSS CMASS measurements of redshift-space distortions. Our analysis includes exploration of how galaxy assembly bias affects cosmological inference. Overall, CEM has several potential advantages over the more common approach of emulating summary statistics, including the ability to easily marginalize over highly complex models of the galaxy–halo connection and greater accuracy, thereby reducing the number of simulations required.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Quantifying and reducing model-form uncertainties in Reynolds-averaged Navier–Stokes simulations: A data-driven, physics-informed Bayesian approach

Despite their well-known limitations, Reynolds-Averaged Navier–Stokes (RANS) models are still the workhorse tools for turbulent flow simulations in today's engineering analysis, design and optimization. While the predictive capability of RANS models depends on many factors, for many practical flows the turbulence models are by far the largest source of uncertainty. As RANS models are used in the design and safety evaluation of many mission-critical systems such as airplanes and nuclear power plants, quantifying their model-form uncertainties has significant implications in enabling risk-informed decision-making. In this work we develop a data-driven, physics-informed Bayesian framework for quantifying model-form uncertainties in RANS simulations. Uncertainties are introduced directly to the Reynolds stresses and are represented with compact parameterization accounting for empirical prior knowledge and physical constraints (e.g., realizability, smoothness, and symmetry). An iterative ensemble Kalman method is used to assimilate the prior knowledge and observation data in a Bayesian framework, and to propagate them to posterior distributions of velocities and other Quantities of Interest (QoIs). We use two representative cases, the flow over periodic hills and the flow in a square duct, to evaluate the performance of the proposed framework. Both cases are challenging for standard RANS turbulence models. Simulation results suggest that, even with very sparse observations, the obtained posterior mean velocities and other QoIs have significantly better agreement with the benchmark data compared to the baseline results. At most locations the posterior distribution adequately captures the true model error within the developed model form uncertainty bounds. The framework is a major improvement over existing black-box, physics-neutral methods for model-form uncertainty quantification, where prior knowledge and details of the models are not exploited. This approach has potential implications in many fields in which the governing equations are well understood but the model uncertainty comes from unresolved physical processes. - Highlights: • Proposed a physics–informed framework to quantify uncertainty in RANS simulations. • Framework incorporates physical prior knowledge and observation data. • Based on a rigorous Bayesian framework yet fully utilizes physical model. • Applicable for many complex physical systems beyond turbulent flows.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Constraining Data Mining with Physical Models: Voltage- and Oxygen Pressure-Dependent Transport in Multiferroic Nanostructures

Development of new generation electronic devices requires understanding and controlling the electronic transport in ferroic, magnetic, and optical materials, which is hampered by two factors. First, the complications of working at the nanoscale, where interfaces, grain boundaries, defects, and so forth, dictate the macroscopic characteristics. Second, the convolution of the response signals stemming from the fact that several physical processes may be activated simultaneously. Here, we present a method of solving these challenges via a combination of atomic force microscopy and data mining analysis techniques. Rational selection of the latter allows application of physical constraints and enables direct interpretation of the statistically significant behaviors in the framework of the chosen physical model, thus distilling physical meaning out of raw data. We demonstrate our approach with an example of deconvolution of complex transport behavior in a bismuth ferrite–cobalt ferrite nanocomposite in ambient and ultrahigh vacuum environments. Measured signal is apportioned into four electronic transport patterns, showing different dependence on partial oxygen and water vapor pressure. These patterns are described in terms of Ohmic conductance and Schottky emission models in the light of surface electrochemistry. Finally and furthermore, deep data analysis allows extraction of local dopant concentrations and barrier heights empowering our understanding of the underlying dynamic mechanisms of resistive switching.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Hierarchical Bayesian estimation for adsorption isotherm parameter determination

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

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗