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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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DOE OSTI2017

Inference of Transmission Network Structure from HIV Phylogenetic Trees

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic. Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Calibration verification for stochastic agent-based disease spread models

Accurate disease spread modeling is crucial for identifying the severity of outbreaks and planning effective mitigation efforts. To be reliable when applied to new outbreaks, model calibration techniques must be robust. However, current methods frequently forgo calibration verification (a stand-alone process evaluating the calibration procedure) and instead use overall model validation (a process comparing calibrated model results to data) to check calibration processes, which may conceal errors in calibration. In this work, we develop a stochastic agent-based disease spread model to act as a testing environment as we test two calibration methods using simulation-based calibration, which is a synthetic data calibration verification method. The first calibration method is a Bayesian inference approach using an empirically-constructed likelihood and Markov chain Monte Carlo (MCMC) sampling, while the second method is a likelihood-free approach using approximate Bayesian computation (ABC). Simulation-based calibration suggests that there are challenges with the empirical likelihood calculation used in the first calibration method in this context. These issues are alleviated in the ABC approach. Despite these challenges, we note that the first calibration method performs well in a synthetic data model validation test similar to those common in disease spread modeling literature. We conclude that stand-alone calibration verification using synthetic data may benefit epidemiological researchers in identifying model calibration challenges that may be difficult to identify with other commonly used model validation techniques.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Overview of Algorithms for Using Particle Morphology in Pre-Detonation Nuclear Forensics

A major goal in pre-detonation nuclear forensics is to infer the processing conditions and/or facility type that produced radiological material. This review paper focuses on analyses of particle size, shape, texture (“morphology”) signatures that could provide information on the provenance of interdicted materials. For example, uranium ore concentrates (UOC or yellowcake) include ammonium diuranate (ADU), ammonium uranyl carbonate (AUC), sodium diuranate (SDU), magnesium diuranate (MDU), and others, each prepared using different salts to precipitate U from solution. Once precipitated, UOCs are often dried and calcined to remove adsorbed water. The products can be allowed to react further, forming uranium oxides UO3, U3O8, or UO2 powders, whose surface morphology can be indicative of precipitation and/or calcination conditions used in their production. This review paper describes statistical issues and approaches in using quantitative analyses of measurements such as particle size and shape to infer production conditions. Statistical topics include multivariate t tests (Hotelling’s T 2 ), design of experiments, and several machine learning (ML) options including decision trees, learning vector quantization neural networks, mixture discriminant analysis, and approximate Bayesian computation (ABC). ABC is emphasized as an attractive option to include the effects of model uncertainty in the selected and fitted forward model used for inferring processing conditions.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2021

Quantification of Type I Interferon Inhibition by Viral Proteins: Ebola Virus as a Case Study

Type I interferons (IFNs) are cytokines with both antiviral properties and protective roles in innate immune responses to viral infection. They induce an antiviral cellular state and link innate and adaptive immune responses. Yet, viruses have evolved different strategies to inhibit such host responses. One of them is the existence of viral proteins which subvert type I IFN responses to allow quick and successful viral replication, thus, sustaining the infection within a host. We propose mathematical models to characterise the intra-cellular mechanisms involved in viral protein antagonism of type I IFN responses, and compare three different molecular inhibition strategies. We study the Ebola viral protein, VP35, with this mathematical approach. Approximate Bayesian computation sequential Monte Carlo, together with experimental data and the mathematical models proposed, are used to perform model calibration, as well as model selection of the different hypotheses considered. Finally, we assess if model parameters are identifiable and discuss how such identifiability can be improved with new experimental data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

The chemical homogeneity of open clusters

Determining the level of chemical homogeneity in open clusters is of fundamental importance in the study of the evolution of star-forming clouds and that of the Galactic disk. Yet limiting the initial abundance spread in clusters has been hampered by difficulties in obtaining consistent spectroscopic abundances for different stellar types. Without reference to any specific model of stellar photospheres, a model for a homogeneous cluster is that it forms a one-dimensional sequence, with any differences between members due to variations in stellar mass and observational uncertainties. I present a novel method for investigating the abundance spread in open clusters that tests this one-dimensional hypothesis at the level of observed stellar spectra, rather than constraining homogeneity using derived abundances as is traditionally done. Using high-resolution APOGEE spectra for 49 giants in M67, NGC 6819, and NGC 2420 I demonstrate that these spectra form one-dimensional sequences for each cluster. With detailed forward modeling of the spectra and Approximate Bayesian Computation, I derive strong limits on the initial abundance spread of 15 elements: <0.01 (0.02) dex for C and Fe, ≲0.015 (0.03) dex for N, O, Mg, Si, and Ni, ≲0.02 (0.03) dex for Al, Ca, and Mn, and ≲0.03 (0.05) dex for Na, S, K, Ti, and V (at 68% and 95% confidence, respectively). The strong limits on C and O imply that no pollution by massive core-collapse supernovae occurred during star formation in open clusters, which, thus, need to form within ≲6 Myr. Further development of this and related techniques will bring the power of differential abundances to stars other than solar twins in large spectroscopic surveys and will help unravel the history of star formation and chemical enrichment in the Milky Way through chemical tagging.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

A New Method to Measure the Post-reionization Ionizing Background from the Joint Distribution of Ly α and Ly β Forest Transmission

The amplitude of the ionizing background that pervades the intergalactic medium (IGM) at the end of the epoch of reionization provides a valuable constraint on the emissivity of the sources that reionized the universe. While measurements of the ionizing background at lower redshifts rely on a simulation-calibrated mapping between the photoionization rate and the mean transmission of the Lyα forest, at z ≳ 6 the IGM becomes increasingly opaque and transmission arises solely in narrow spikes separated by saturated Gunn–Peterson troughs. In this regime, the traditional approach of measuring the average transmission over large ~50 Mpc/h regions is less sensitive and suboptimal. In addition, the five times smaller oscillator strength of the Lyβ transition implies that the Lyβ forest is considerably more transparent at z ≳ 6, even in the presence of contamination by foreground z ~ 5 Lyα forest absorption. We present a novel statistical approach to analyze the joint distribution of transmission spikes in the cospatial z ~ 6 Lyα and Lyβ forests. Our method relies on approximate Bayesian computation (ABC), which circumvents the necessity of computing the intractable likelihood function describing the highly correlated Lyα and Lyβ transmission. We apply ABC to mock data generated from a large-volume hydrodynamical simulation combined with a state-of-the-art model of ionizing background fluctuations in the post-reionization IGM and show that it is sensitive to higher IGM neutral hydrogen fractions than previous techniques. As a proof of concept, we apply this methodology to a real spectrum of a z = 6.54 quasar and measure the ionizing background from 5.4 ≤ z ≤ 6.4 along this sightline with ~0.2 dex statistical uncertainties.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Monte Carlo Control Loops for Cosmic Shear Cosmology with DES Year 1

Weak lensing by large-scale structure is a powerful probe of cosmology and of the dark universe. This cosmic shear technique relies on the accurate measurement of the shapes and redshifts of background galaxies and requires precise control of systematic errors. The Monte Carlo Control Loops (MCCL) is a forward modelling method designed to tackle this problem. It relies on the Ultra Fast Image Generator (UFig) to produce simulated images tuned to match the target data statistically, followed by calibrations and tolerance loops. We present the first end-to-end application of this method, on the Dark Energy Survey (DES) Year 1 wide field imaging data. We simultaneously measure the shear power spectrum $C_{\ell}$ and the redshift distribution $n(z)$ of the background galaxy sample. The method includes maps of the systematic sources, Point Spread Function (PSF), an Approximate Bayesian Computation (ABC) inference of the simulation model parameters, a shear calibration scheme, and the fast estimation of the covariance matrix. We find a close statistical agreement between the simulations and the DES Y1 data using an array of diagnostics. In a non-tomographic setting, we derive a set of $C_\ell$ and $n(z)$ curves that encode the cosmic shear measurement, as well as the systematic uncertainty. Following a blinding scheme, we measure the combination of $\Omega_m$, $\sigma_8$, and intrinsic alignment amplitude $A_{\rm{IA}}$, defined as $S_8D_{\rm{IA}} = \sigma_8(\Omega_m/0.3)^{0.5}D_{\rm{IA}}$, where $D_{\rm{IA}}=1-0.11(A_{\rm{IA}}-1)$. We find $S_8D_{\rm{IA}}=0.895^{+0.054}_{-0.039}$, where systematics are at the level of roughly 60\% of the statistical errors. We discuss these results in the context of earlier cosmic shear analyses of the DES Y1 data. Our findings indicate that this method and its fast runtime offer good prospects for cosmic shear measurements with future wide-field surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Improved uncertainty quantification in nondestructive assay for nonproliferation

This paper illustrates methods to improve uncertainty quantification (UQ) for non-destructive assay (NDA) measurements used in nuclear nonproliferation. First, it is shown that current bottom-up UQ applied to calibration data is not always adequate, for three main reasons: (1) Because there are errors in both the predictors and the response, calibration involves a ratio of random quantities, and calibration data sets in NDA usually consist of only a modest number of samples (3–10); therefore, asymptotic approximations involving quantities needed for UQ such as means and variances are often not sufficiently accurate; (2) Common practice overlooks that calibration implies a partitioning of total error into random and systematic error, and (3) In many NDA applications, test items exhibit non-negligible departures in physical properties from calibration items, so model-based adjustments are used, but item-specific bias remains in some data. Therefore, improved bottom-up UQ using calibration data should predict the typical magnitude of item-specific bias, and the suggestion is to do so by including sources of item-specific bias in synthetic calibration data that is generated using a combination of modeling and real calibration data. Second, for measurements of the same nuclear material item by both the facility operator and international inspectors, current empirical (top-down) UQ is described for estimating operator and inspector systematic and random error variance components. A Bayesian alternative is introduced that easily accommodates constraints on variance components, and is more robust than current top-down methods to the underlying measurement error distributions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Exploring Data Set Bias and Decision Support with Predictive Uncertainty Through Bayesian Approximations and Convolutional Neural Networks

Individual seismic catalogs can contain multiscale observations from fault level to global scales and associated waveforms from discrete events reflect crustal structure across many different scales and locations. Seismic network aperture, geographic location, and observation distance may not provide informative guidance or intuition on how different catalogs will behave across models trained under different conditions. We rely on uncertainty to provide guardrails for when to trust model decisions, but understanding when our uncertainty is trustworthy is an open challenge. Here, in this work, we explore Bayesian approximation methods for assigning predictive uncertainty in seismic event classification problems. We find that computationally expensive Bayesian approximations do not outperform simple ensemble methods. We also find that when exploiting multiple seismic event catalogs, joint training with data from all the catalogs combined with Bayesian approximations and supervised training for classification can obscure bias and result in less robust uncertainty while also not providing substantial performance benefits compared to training individual models for each catalog.

58 GEOSCIENCES↗
DOE OSTI2023

Developing an Evolutionary Baseline Model for Humans: Jointly Inferring Purifying Selection with Population History

Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics—including quantifying the relative contributions of adaptive versus nonadaptive processes—but also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (e.g., positive or balancing selection). Here, a baseline model was developed for a human population of West African ancestry, the Yoruba, comprising processes constantly operating on the genome (i.e., purifying and background selection, population size changes, recombination rate heterogeneity, and gene conversion). Specifically, to perform joint inference of selective effects with demography, an approximate Bayesian approach was employed that utilizes the decay of background selection effects around functional elements, taking into account genomic architecture. This approach inferred a recent 6-fold population growth together with a distribution of fitness effects that is skewed towards effectively neutral mutations. Importantly, these results further suggest that, although strong and/or frequent recurrent positive selection is inconsistent with observed data, weak to moderate positive selection is consistent but unidentifiable if rare.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Posterior Covariance Matrix Approximations

Here, the Davis equation of state (EOS) is commonly used to model thermodynamic relationships for high explosive (HE) reactants. Typically, the parameters in the EOS are calibrated, with uncertainty, using a Bayesian framework and Markov Chain Monte Carlo (MCMC) methods. However, MCMC methods are computationally expensive, especially for complex models with many parameters. This paper provides a comparison between MCMC and less computationally expensive Variational methods (Variational Bayesian and Hessian Variational Bayesian) for computing the posterior distribution and approximating the posterior covariance matrix based on heterogeneous experimental data. All three methods recover similar posterior distributions and posterior covariance matrices. This study demonstrates that for this EOS parameter calibration application, the assumptions made in the two Variational methods significantly reduce the computational cost but do not substantially change the results compared to MCMC.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

An efficient Bayesian data-worth analysis using a multilevel Monte Carlo method

Improving the understanding of subsurface systems and thus reducing prediction uncertainty requires collection of data. As the collection of subsurface data is costly, it is important that the data collection scheme is cost-effective. Design of a cost-effective data collection scheme, i.e., data-worth analysis, requires quantifying model parameter, prediction, and both current and potential data uncertainties. Assessment of these uncertainties in large-scale stochastic subsurface hydrological model simulations using standard Monte Carlo (MC) sampling or surrogate modeling is extremely computationally intensive, sometimes even infeasible. In this paper, we propose an efficient Bayesian data-worth analysis using a multilevel Monte Carlo (MLMC) method. Compared to the standard MC that requires a significantly large number of high-fidelity model executions to achieve a prescribed accuracy in estimating expectations, the MLMC can substantially reduce computational costs using multifidelity approximations. Since the Bayesian data-worth analysis involves a great deal of expectation estimation, the cost saving of the MLMC in the assessment can be outstanding. While the proposed MLMC-based data-worth analysis is broadly applicable, we use it for a highly heterogeneous two-phase subsurface flow simulation to select an optimal candidate data set that gives the largest uncertainty reduction in predicting mass flow rates at four production wells. Finally, the choices made by the MLMC estimation are validated by the actual measurements of the potential data, and consistent with the standard MC estimation. But compared to the standard MC, the MLMC greatly reduces the computational costs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

A continuation multilevel Monte Carlo algorithm

Here, we propose a novel Continuation Multi Level Monte Carlo (CMLMC) algorithm for weak approximation of stochastic models. The CMLMC algorithm solves the given approximation problem for a sequence of decreasing tolerances, ending when the required error tolerance is satisfied. CMLMC assumes discretization hierarchies that are defined a priori for each level and are geometrically refined across levels. Moreover, the actual choice of computational work across levels is based on parametric models for the average cost per sample and the corresponding variance and weak error. These parameters are calibrated using Bayesian estimation, taking particular notice of the deepest levels of the discretization hierarchy, where only few realizations are available to produce the estimates. The resulting CMLMC estimator exhibits a non-trivial splitting between bias and statistical contributions. We also show the asymptotic normality of the statistical error in the MLMC estimator and justify in this way our error estimate that allows prescribing both required accuracy and confidence in the final result. Our numerical results substantiate the above results and illustrate the corresponding computational savings in examples that are described in terms of differential equations either driven by random measures or with random coefficients.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Scale Mixtures of Frechet Distributions as Asymptotic Approximations of Extreme Precipitation

This paper is a further development of the results of [20] where, based on the negative binomial model for the duration of wet periods measured in days [16], an asymptotic approximation was proposed for the distribution of the maximum daily precipitation volume within a wet period. This approximation has the form of a scale mixture of the Fr´echet distribution with the gamma mixing distribution and coincides with the distribution of a positive power of a random variable having the Snedecor–Fisher distribution. Here we extend this result to the mth extremes, m ∈ ℕ, and sample quantiles. The proof of this result is based on the representation of the negative binomial distribution as a mixed geometric (and hence, mixed Poisson) distribution [17] and limit theorems for extreme order statistics in samples with random sizes having mixed Poisson distributions [10]. Some analytic properties of the obtained limit distribution are described. In particular, it is demonstrated that under certain conditions the limit distribution of the maximum precipitation is mixed exponential and hence, is infinitely divisible. It is shown that under the same conditions this limit distribution can be represented as a scale mixture of stable or Weibull or Pareto or folded normal laws. The corresponding product representations for the limit random variable can be used for its computer simulation. The results of fitting this distribution to real data are presented illustrating high adequacy of the proposed model. It is also shown that the limit distribution of sample quantiles is the well-known Student distribution. Several methods are proposed for the estimation of the parameters of the asymptotic distributions. The obtained mixture representations for the limit laws and the corresponding asymptotic approximations provide better insight into the nature of mixed probability (“Bayesian”) models.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Scalable Bayesian optimization with randomized prior networks

Several fundamental problems in science and engineering consist of global optimization tasks involving unknown high-dimensional (black-box) functions that map a set of controllable variables to the outcomes of an expensive experiment. Bayesian Optimization (BO) techniques are known to be effective in tackling global optimization problems using a relatively small number objective function evaluations, but their performance suffers when dealing with high-dimensional outputs. To overcome the major challenge of dimensionality, here we propose a deep learning framework for BO and sequential decision making based on bootstrapped ensembles of neural architectures with randomized priors. Using appropriate architecture choices, we show that the proposed framework can approximate functional relationships between design variables and quantities of interest, even in cases where the latter take values in high-dimensional vector spaces or even infinite-dimensional function spaces. In the context of BO, we augmented the proposed probabilistic surrogates with re-parameterized Monte Carlo approximations of multiple-point (parallel) acquisition functions, as well as methodological extensions for accommodating black-box constraints and multi-fidelity information sources. We test the proposed framework against state-of-the-art methods for BO and demonstrate superior performance across several challenging tasks with high-dimensional outputs, including a constrained multi-fidelity optimization task involving shape optimization of rotor blades in turbo-machinery.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Soil moisture estimation using tomographic ground penetrating radar in a MCMC–Bayesian framework

In this paper, we focus on a hydrogeological inverse problem specifically targeting monitoring soil moisture variations using tomographic ground penetrating radar (GPR) travel time data. Technical challenges exist in the inversion of GPR tomographic data for handling non-uniqueness, nonlinearity and high-dimensionality of unknowns. We have developed a new method for estimating soil moisture fields from crosshole GPR data. It uses a pilot-point method to provide a low-dimensional representation of the relative dielectric permittivity field of the soil, which is the primary object of inference: the field can be converted to soil moisture using a petrophysical model. We integrate a multi-chain Markov chain Monte Carlo (MCMC)–Bayesian inversion framework with the pilot point concept, a curved-ray GPR travel time model, and a sequential Gaussian simulation algorithm, for estimating the dielectric permittivity at pilot point locations distributed within the tomogram, as well as the corresponding geostatistical parameters (i.e., spatial correlation range). We infer the dielectric permittivity as a probability density function, thus capturing the uncertainty in the inference. The multi-chain MCMC enables addressing high-dimensional inverse problems as required in the inversion setup. The method is scalable in terms of number of chains and processors, and is useful for computationally demanding Bayesian model calibration in scientific and engineering problems. The proposed inversion approach can successfully approximate the posterior density distributions of the pilot points, and capture the true values. The computational efficiency, accuracy, and convergence behaviors of the inversion approach were also systematically evaluated, by comparing the inversion results obtained with different levels of noises in the observations, increased observational data, as well as increased number of pilot points.

54 ENVIRONMENTAL SCIENCES↗