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DOE OSTI2021

Forecasting Multi-Wave Epidemics Through Bayesian Inference

We present a simple, near-real-time Bayesian method to infer and forecast a multiwave outbreak, and demonstrate it on the COVID-19 pandemic. The approach uses timely epidemiological data that has been widely available for COVID-19. It provides short-term forecasts of the outbreak’s evolution, which can then be used for medical resource planning. The method postulates one- and multiwave infection models, which are convolved with the incubation-period distribution to yield competing disease models. The disease models’ parameters are estimated via Markov chain Monte Carlo sampling and information-theoretic criteria are used to select between them for use in forecasting. The method is demonstrated on two- and three-wave COVID-19 outbreaks in California, New Mexico and Florida, as observed during Summer-Winter 2020. We find that the method is robust to noise, provides useful forecasts (along with uncertainty bounds) and that it reliably detected when the initial single-wave COVID-19 outbreaks transformed into successive surges as containment efforts in these states failed by the end of Spring 2020.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

MFNets: Multifidelity data-driven networks for Bayesian learning and prediction

This paper presents a multifidelity uncertainty quantification framework called MFNets. We seek to address three existing challenges that arise when experimental and simulation data from different sources are used to enhance statistical estimation and prediction with quantified uncertainty. Specifically, we demonstrate that MFNets can (1) fuse heterogeneous data sources arising from simulations with different parameterizations, e.g simulation models with different uncertain parameters or data sets collected under different environmental conditions; (2) encode known relationships among data sources to reduce data requirements; and (3) improve the robustness of existing multi-fidelity approaches to corrupted data. MFNets construct a network of latent variables (LVs) to facilitate the fusion of data from an ensemble of sources of varying credibility and cost. These LVs are posited as explanatory variables that provide the source of correlation in the observed data. Furthermore, MFNets provide a way to encode prior physical knowledge to enable efficient estimation of statistics and/or construction of surrogates via conditional independence relations on the LVs. We highlight the utility of our framework with a number of theoretical results which assess the quality of the posterior mean as a frequentist estimator and compare it to standard sampling approaches that use single fidelity, multilevel, and control variate Monte Carlo estimators. We also use the proposed framework to derive the Monte Carlo-based control variate estimator entirely from the use of Bayes rule and linear-Gaussian models -- to our knowledge the first such derivation. Finally, we demonstrate the ability to work with different uncertain parameters across different models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

A quantification of the effectiveness of EPID dosimetry and software-based plan verification systems in detecting incidents in radiotherapy

Purpose: Complex treatments in radiation therapy require robust verification in order to prevent errors that can adversely affect the patient. For this purpose, the authors estimate the effectiveness of detecting errors with a “defense in depth” system composed of electronic portal imaging device (EPID) based dosimetry and a software-based system composed of rules-based and Bayesian network verifications. Methods: The authors analyzed incidents with a high potential severity score, scored as a 3 or 4 on a 4 point scale, recorded in an in-house voluntary incident reporting system, collected from February 2012 to August 2014. The incidents were categorized into different failure modes. The detectability, defined as the number of incidents that are detectable divided total number of incidents, was calculated for each failure mode. Results: In total, 343 incidents were used in this study. Of the incidents 67% were related to photon external beam therapy (EBRT). The majority of the EBRT incidents were related to patient positioning and only a small number of these could be detected by EPID dosimetry when performed prior to treatment (6%). A large fraction could be detected by in vivo dosimetry performed during the first fraction (74%). Rules-based and Bayesian network verifications were found to be complimentary to EPID dosimetry, able to detect errors related to patient prescriptions and documentation, and errors unrelated to photon EBRT. Combining all of the verification steps together, 91% of all EBRT incidents could be detected. Conclusions: This study shows that the defense in depth system is potentially able to detect a large majority of incidents. The most effective EPID-based dosimetry verification is in vivo measurements during the first fraction and is complemented by rules-based and Bayesian network plan checking.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Seismic Event Characterization Using Full Moment Tensors on the Hypersphere

Moment tensor solutions provide insights into the deformation that has occurred in the source region of a seismic event and are therefore of great value in identifying different types of seismic sources, such as when monitoring for underground nuclear tests. Despite this utility, inversion of waveforms recorded by seismometers for their full seismic moment tensor is not yet routine, and development of robust methods to classify events based on this information is in its infancy. Here, we assemble an inventory of 1405 full moment tensor solutions that include explosive, earthquake, and collapse events, and investigate the use of anisotropic probability distribution functions on the 5D hypersphere to discriminate between these sources. Using a Bayesian classifier, we obtain optimal success rates of 98.4% across all events and demonstrate that modification of the prior probabilities provides a natural way to alter the balance between not missing desirable events (such as explosions) versus misclassifying large numbers of undesired events (such as earthquakes). The approach is specifically designed to progress from traditional, bipolar event screening metrics to more generalized event identification across multiple types of seismic sources. Despite current databases containing insufficient numbers of events to definitively demonstrate at present, we also find intriguing evidence of subgroupings within individual source populations on the hypersphere, for example, between chemical and nuclear explosions, raising the potential possibility of discriminating between these event types in the future.

Geosciences↗

DOE OSTI2026

Automated ICRF heating surrogate modeling via machine learning

This work introduces automated machine learning workflows that address critical bottlenecks in surrogate model development for Ion Cyclotron Range of Frequencies (ICRF) heating applications. The automated framework includes data analysis tools that transform raw datasets into actionable insights in seconds, replacing weeks of manual exploratory effort and ensuring consistent, reproducible dataset characterization. By integrating advanced hyperparameter optimization (HPO) methods including Bayesian optimization via BoTorch and Tree-structured Parzen Estimators (TPE), the framework significantly reduces model development time from weeks to hours, decreasing computational cost and required expertise, while enabling high-accuracy surrogate models. Compared to traditional hyperparameter scanning (HPS) techniques such as methodical, randomized, and grid searches, HPO methods achieve superior convergence and predictive performance, even when compared to already well-tuned reference models. On NSTX High Harmonic Fast Wave (HHFW) heating datasets, both Random Forest Regressor (RFR) and neural network surrogates demonstrate improved accuracy, achieving R 2 values beyond 0.97 and 0.98, respectively. The results show that while HPO gains are modest for robust architectures like RFR, they become essential for more sensitive models such as neural networks, highlighting the trade-offs across optimization strategies. Through automated workflows that eliminate manual hyperparameter tuning and require minimal ML expertise, this work enables widespread adoption of high-fidelity surrogate models across the fusion community for real-time plasma control, uncertainty quantification, rapid experimental scenario development, and integrated system optimization.

Sanchez-Villar, Alvaro [Princeton Plasma Physics L↗

DOE OSTI2026

Gaussian processes for inferring parton distributions

The extraction of parton distribution functions (PDFs) from experimental or lattice QCD data is an ill-posed inverse problem, where regularization strongly impacts both systematic uncertainties and the reliability of the results. We study a framework based on Gaussian Process Regression (GPR) to reconstruct PDFs from lattice QCD matrix elements. Within a Bayesian framework, Gaussian processes serve as flexible priors that encode uncertainties, correlations, and constraints without imposing rigid functional forms. We investigate a wide range of kernel choices, mean functions, and hyperparameter treatments. We quantify information gained from the data using the Kullback-Leibler divergence. Synthetic data tests demonstrate the consistency and robustness of the method. Our study establishes GPR as a systematic and non-parametric approach to PDF reconstruction, offering controlled uncertainty estimates and reduced model bias in lattice QCD analyses.

hadronic spectroscopy↗

DOE OSTI2013

STARS DO NOT EAT THEIR YOUNG MIGRATING PLANETS: EMPIRICAL CONSTRAINTS ON PLANET MIGRATION HALTING MECHANISMS

The discovery of ''hot Jupiters'' very close to their parent stars confirmed that Jovian planets migrate inward via several potential mechanisms. We present empirical constraints on planet migration halting mechanisms. We compute model density functions of close-in exoplanets in the orbital semi-major axis-stellar mass plane to represent planet migration that is halted via several mechanisms, including the interior 1:2 resonance with the magnetospheric disk truncation radius, the interior 1:2 resonance with the dust sublimation radius, and several scenarios for tidal halting. The models differ in the predicted power-law dependence of the exoplanet orbital semi-major axis as a function of stellar mass, and thus we also include a power-law model with the exponent as a free parameter. We use a Bayesian analysis to assess the model success in reproducing empirical distributions of confirmed exoplanets and Kepler candidates that orbit interior to 0.1 AU. Our results confirm a correlation of the halting distance with stellar mass. Tidal halting provides the best fit to the empirical distribution of confirmed Jovian exoplanets at a statistically robust level, consistent with the Kozai mechanism and the spin-orbit misalignment of a substantial fraction of hot Jupiters. We can rule out migration halting at the interior 1:2 resonances with the magnetospheric disk truncation radius and the interior 1:2 resonance with the dust disk sublimation radius, a uniform random distribution, and a distribution with no dependence on stellar mass. Note that our results do not rule out Type-II migration, but rather eliminate the role of a circumstellar disk in stopping exoplanet migration. For Kepler candidates, which have a more restricted range in stellar mass compared to confirmed planets, we are unable to discern between the tidal dissipation and magnetospheric disk truncation braking mechanisms at a statistically significant level. The power-law model favors exponents in the range of 0.38-0.9. This is larger than that predicted for tidal halting (0.23-0.33), which suggests that additional physics may be missing in the tidal halting theory.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Calibration of energy density functionals with deformed nuclei

Nuclear density functional theory is the prevalent theoretical framework for accurately describing nuclear properties at the scale of the entire chart of nuclides. Given an energy functional and a many-body scheme (e.g., single- or multireference level), the predictive power of the theory depends strongly on how the parameters of the energy functionals have been calibrated with experimental data. Expanded algorithms and computing power have enabled recent optimization protocols to include data in deformed nuclei in order to optimize the coupling constants of the energy functional. The primary motivation of this work is to test the robustness of such protocols with respect to some of the technical and numerical details of the underlying calculations, especially when the calibration explores a large parameter space. To this end, we quantify the effect of these uncertainties on both the optimization and statistical emulation of composite objective functions. We also emphasize that Bayesian calibration can provide better estimates of the theoretical errors used to define objective functions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Generalized Bayesian MARS: Tools for Stochastic Computer Model Emulation

The multivariate adaptive regression spline (MARS) approach of Friedman and its Bayesian counterpart are effective approaches for the emulation of computer models. The traditional assumption of Gaussian errors limits the usefulness of MARS, and many popular alternatives, when dealing with stochastic computer models. Here, we propose a generalized Bayesian MARS (GBMARS) framework which admits the broad class of generalized hyperbolic distributions as the induced likelihood function. This allows us to develop tools for the emulation of stochastic simulators which are parsimonious, scalable, and interpretable and require minimal tuning, while providing powerful predictive and uncertainty quantification capabilities. GBMARS is capable of robust regression with t distributions, quantile regression with asymmetric Laplace distributions, and a general form of “Normal-Wald” regression in which the shape of the error distribution and the structure of the mean function are learned simultaneously. We demonstrate the effectiveness of GBMARS on various stochastic computer models, and we show that it compares favorably to several popular alternatives.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Multimodal parameter spaces of a complex multi-channel neuron model

One of the most common types of models that helps us to understand neuron behavior is based on the Hodgkin–Huxley ion channel formulation (HH model). A major challenge with inferring parameters in HH models is non-uniqueness: many different sets of ion channel parameter values produce similar outputs for the same input stimulus. Such phenomena result in an objective function that exhibits multiple modes (i.e., multiple local minima). This non-uniqueness of local optimality poses challenges for parameter estimation with many algorithmic optimization techniques. HH models additionally have severe non-linearities resulting in further challenges for inferring parameters in an algorithmic fashion. To address these challenges with a tractable method in high-dimensional parameter spaces, we propose using a particular Markov chain Monte Carlo (MCMC) algorithm, which has the advantage of inferring parameters in a Bayesian framework. The Bayesian approach is designed to be suitable for multimodal solutions to inverse problems. We introduce and demonstrate the method using a three-channel HH model. We then focus on the inference of nine parameters in an eight-channel HH model, which we analyze in detail. We explore how the MCMC algorithm can uncover complex relationships between inferred parameters using five injected current levels. The MCMC method provides as a result a nine-dimensional posterior distribution, which we analyze visually with solution maps or landscapes of the possible parameter sets. The visualized solution maps show new complex structures of the multimodal posteriors, and they allow for selection of locally and globally optimal value sets, and they visually expose parameter sensitivities and regions of higher model robustness. We envision these solution maps as enabling experimentalists to improve the design of future experiments, increase scientific productivity and improve on model structure and ideation when the MCMC algorithm is applied to experimental data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

SPT clusters with DES and HST weak lensing. I. Cluster lensing and Bayesian population modeling of multiwavelength cluster datasets

We present a Bayesian population modeling method to analyze the abundance of galaxy clusters identified by the South Pole Telescope (SPT) with a simultaneous mass calibration using weak gravitational lensing data from the Dark Energy Survey (DES) and the Hubble Space Telescope (HST). We discuss and validate the modeling choices with a particular focus on a robust, weak-lensing-based mass calibration using DES data. For the DES Year 3 data, we report a systematic uncertainty in weak-lensing mass calibration that increases from 1% at z = 0.25 to 10% at z = 0.95 , to which we add 2% in quadrature to account for uncertainties in the impact of baryonic effects. We implement an analysis pipeline that joins the cluster abundance likelihood with a multiobservable likelihood for the Sunyaev-Zel’dovich effect, optical richness, and weak-lensing measurements for each individual cluster. We validate that our analysis pipeline can recover unbiased cosmological constraints by analyzing mocks that closely resemble the cluster sample extracted from the SPT-SZ, SPTpol ECS, and SPTpol 500d surveys and the DES Year 3 and HST-39 weak-lensing datasets. This work represents a crucial prerequisite for the subsequent cosmological analysis of the real dataset.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Efficient high-dimensional variational data assimilation with machine-learned reduced-order models

Abstract. Data assimilation (DA) in geophysical sciences remains the cornerstone of robust forecasts from numerical models. Indeed, DA plays a crucial role in the quality of numerical weather prediction and is a crucial building block that has allowed dramatic improvements in weather forecasting over the past few decades. DA is commonly framed in a variational setting, where one solves an optimization problem within a Bayesian formulation using raw model forecasts as a prior and observations as likelihood. This leads to a DA objective function that needs to be minimized, where the decision variables are the initial conditions specified to the model. In traditional DA, the forward model is numerically and computationally expensive. Here we replace the forward model with a low-dimensional, data-driven, and differentiable emulator. Consequently, gradients of our DA objective function with respect to the decision variables are obtained rapidly via automatic differentiation. We demonstrate our approach by performing an emulator-assisted DA forecast of geopotential height. Our results indicate that emulator-assisted DA is faster than traditional equation-based DA forecasts by 4 orders of magnitude, allowing computations to be performed on a workstation rather than a dedicated high-performance computer. In addition, we describe accuracy benefits of emulator-assisted DA when compared to simply using the emulator for forecasting (i.e., without DA). Our overall formulation is denoted AIEADA (Artificial Intelligence Emulator-Assisted Data Assimilation).

58 GEOSCIENCES↗

DOE OSTI2022

Towards automating structural discovery in scanning transmission electron microscopy *

Abstract Scanning transmission electron microscopy is now the primary tool for exploring functional materials on the atomic level. Often, features of interest are highly localized in specific regions in the material, such as ferroelectric domain walls, extended defects, or second phase inclusions. Selecting regions to image for structural and chemical discovery via atomically resolved imaging has traditionally proceeded via human operators making semi-informed judgements on sampling locations and parameters. Recent efforts at automation for structural and physical discovery have pointed towards the use of ‘active learning’ methods that utilize Bayesian optimization with surrogate models to quickly find relevant regions of interest. Yet despite the potential importance of this direction, there is a general lack of certainty in selecting relevant control algorithms and how to balance a priori knowledge of the material system with knowledge derived during experimentation. Here we address this gap by developing the automated experiment workflows with several combinations to both illustrate the effects of these choices and demonstrate the tradeoffs associated with each in terms of accuracy, robustness, and susceptibility to hyperparameters for structural discovery. We discuss possible methods to build descriptors using the raw image data and deep learning based semantic segmentation, as well as the implementation of variational autoencoder based representation. Furthermore, each workflow is applied to a range of feature sizes including NiO pillars within a La:SrMnO 3 matrix, ferroelectric domains in BiFeO 3 , and topological defects in graphene. The code developed in this manuscript is open sourced and will be released at github.com/nccreang/AE_Workflows .

47 OTHER INSTRUMENTATION↗

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 OSTI2026

Hierarchical Gaussian Random Field Sampling for Multilevel Markov Chain Monte Carlo: Coupling Stochastic Partial Differential Equation and the Karhunen–Loève Decomposition

This work introduces structure preserving hierarchical decompositions for sampling Gaussian random fields (GRFs) within the context of multilevel Bayesian inference in high-dimensional space. Existing scalable hierarchical sampling methods, such as those based on stochastic partial differential equations (SPDEs), often reduce the dimensionality of the sample space at the cost of accuracy of inference. Other approaches, such that those based on Karhunen-Loève (KL) expansions, offer sample space dimensionality reduction but sacrifice GRF representation accuracy and ergodicity of the Markov chain Monte Carlo (MCMC) sampler and are computationally expensive for high-dimensional problems. The proposed method integrates the dimensionality reduction capabilities of KL expansions with the scalability of SPDE-based sampling, thereby providing a robust, unified framework for high-dimensional uncertainty quantification (UQ) that is scalable and accurate, preserves ergodicity, and offers dimensionality reduction of the sample space. The hierarchy in our multilevel algorithm is derived from the geometric multigrid hierarchy. By constructing a hierarchical decomposition that maintains the covariance structure across the levels in the hierarchy, the approach enables efficient coarse-to-fine sampling while ensuring that all samples are drawn from the desired distribution. The effectiveness of the proposed method is demonstrated on a benchmark subsurface flow problem, demonstrating its effectiveness in improving computational efficiency and statistical accuracy. Furthermore, our proposed technique is more efficient and accurate and displays better convergence properties than existing methods for high-dimensional Bayesian inference problems.

Gaussian random fields↗

DOE OSTI2022

GIGA-Lens: Fast Bayesian Inference for Strong Gravitational Lens Modeling

We present GIGA-Lens: a gradient-informed, GPU-accelerated Bayesian framework for modeling strong gravitational lensing systems, implemented in TensorFlow and JAX. The three components, optimization using multistart gradient descent, posterior covariance estimation with variational inference, and sampling via Hamiltonian Monte Carlo, all take advantage of gradient information through automatic differentiation and massive parallelization on graphics processing units (GPUs). We test our pipeline on a large set of simulated systems and demonstrate in detail its high level of performance. The average time to model a single system on four Nvidia A100 GPUs is 105 s. The robustness, speed, and scalability offered by this framework make it possible to model the large number of strong lenses found in current surveys and present a very promising prospect for the modeling of ${ \mathcal O }({10}^{5})$ lensing systems expected to be discovered in the era of the Vera C. Rubin Observatory, Euclid, and the Nancy Grace Roman Space Telescope.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

$\mathrm{SageNet}$: Fast Neural Network Emulation of the Stiff-amplified Gravitational Waves from Inflation

Accurate modeling of the inflationary gravitational waves (GWs) requires time-consuming, iterative numerical integrations of differential equations to take into account their backreaction on the expansion history. To improve computational efficiency while preserving accuracy, we present the Stiff-amplified Gravitational-wave Emulator Network (SageNet), a deep learning framework designed to replace conventional numerical solvers (code available at https://github.com/YifangLuo/SageNet). SageNet employs a long short-term memory architecture to emulate the present-day energy density spectrum of the inflationary GWs with possible stiff amplification, Ω GW (f). Trained on a data set of 25,689 numerically generated solutions, SageNet allows accurate reconstructions of Ω GW (f) and generalizes well to a wide range of cosmological parameters; 90.9% of the test emulations with randomly distributed parameters exhibit errors of under 4%. In addition, SageNet demonstrates its ability to learn and reproduce the artificial, adaptive sampling patterns in numerical calculations, which implement denser sampling of frequencies around changes in spectral indices in Ω GW (f). The dual capability of learning both physical and artificial features of the numerical GW spectra establishes SageNet as a robust alternative to exact numerical methods. Finally, our benchmark tests show that SageNet reduces the computation time from tens of seconds to milliseconds, achieving a speedup of ∼10 4 times over standard CPU-based numerical solvers with the potential for further acceleration on GPU hardware. These capabilities make SageNet a powerful tool for accelerating Bayesian inference procedures for extended cosmological models. In a broad sense, the SageNet framework offers a fast, accurate, and generalizable solution to modeling cosmological observables whose theoretical predictions demand costly differential equation solvers.

Astronomy data modeling↗

DOE OSTI2017

Robust Estimation of Electron Density From Anatomic Magnetic Resonance Imaging of the Brain Using a Unifying Multi-Atlas Approach

Purpose: To develop a reliable method to estimate electron density based on anatomic magnetic resonance imaging (MRI) of the brain. Methods and Materials: We proposed a unifying multi-atlas approach for electron density estimation based on standard T1- and T2-weighted MRI. First, a composite atlas was constructed through a voxelwise matching process using multiple atlases, with the goal of mitigating effects of inherent anatomic variations between patients. Next we computed for each voxel 2 kinds of conditional probabilities: (1) electron density given its image intensity on T1- and T2-weighted MR images; and (2) electron density given its spatial location in a reference anatomy, obtained by deformable image registration. These were combined into a unifying posterior probability density function using the Bayesian formalism, which provided the optimal estimates for electron density. We evaluated the method on 10 patients using leave-one-patient-out cross-validation. Receiver operating characteristic analyses for detecting different tissue types were performed. Results: The proposed method significantly reduced the errors in electron density estimation, with a mean absolute Hounsfield unit error of 119, compared with 140 and 144 (P<.0001) using conventional T1-weighted intensity and geometry-based approaches, respectively. For detection of bony anatomy, the proposed method achieved an 89% area under the curve, 86% sensitivity, 88% specificity, and 90% accuracy, which improved upon intensity and geometry-based approaches (area under the curve: 79% and 80%, respectively). Conclusion: The proposed multi-atlas approach provides robust electron density estimation and bone detection based on anatomic MRI. If validated on a larger population, our work could enable the use of MRI as a primary modality for radiation treatment planning.

62 RADIOLOGY AND NUCLEAR MEDICINE↗