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This thesis reports a constraint of the neutrino oscillation parameters $\Delta m^{2}_{32}$, $\sin^2 \theta_{23}$, and $\delta_{CP}$ using the NuMI Off-Axis $\nu$ Appearance (NOvA) experiment's Near Detector (ND) data and Far Detector (FD) fake data set simultaneously. This thesis also reports a constraint on NOvA's systematic uncertainty model solely with its Near Detector data. The Hamiltonian Monte Carlo algorithm is used to estimate Bayesian Credible Intervals for the oscillation and interaction parameters. The $1\sigma$ Credible Intervals for $\sin^2 \theta_{23}$ are $(0.44, 0.512)$ $\cup$ $(0.536, 0.56)$, for $\Delta m^{2}_{32}$ $(2.41 \times 10^{-3}$ eV$^2,\ 2.52 \times 10^{-3}$ eV$^2)$, and for $\delta_{CP}$ $(0.74\pi,\ 1.1\pi)$ $\cup$ $(1.38\pi,\ 1.58\pi)$. The statistical power of the ND data constrains NOvA's interaction parameters, while the FD fake data constrains the oscillation parameters. This is the first analysis within NOvA to constrain the ND and FD prediction sim ultaneously, and to investigate the neutrino interaction modeling in the context of constraining the oscillation parameters. To constrain the ND data requires a sophisticated understanding of the neutrino interaction modeling and its uncertainties. The interested reader is advised to focus on Chapters 4 and 6, which discuss the ND selection, uncertainties, and ND-only fits to data. The reader interested in oscillation parameter constraints will find this in Chapter 7.
NOvA is a long baseline neutrino experiment with an 810 km baseline, using the NuMIbeam at Fermilab, and a functionally identical near and far detector operating at an angle14 mrad off axis from the beam. NOvA jointly measures muon neutrino (and antineutrino)disappearance and electron neutrino (and antineutrino) appearance to make a measurementof sin2θ23, δCP, and ∆m232, including its sign, the mass ordering.This dissertation reports a new measurement from NOvA, using 10 years of data, with a totalexposure of 26.6 ×1020 POT of neutrino beam and 12.5 ×1020 POT of antineutrino beam.This represents 95.6% more neutrino beam exposure since the last NOvA analysis. Aspects ofthe analysis are discussed in detail, including neutrino energy estimation, analysis systematicuncertainties, including the implementation of systematics new to the NOvA analysis, andthe Bayesian fit infrastructure using Markov Chain Monte Carlo (MCMC).The analysis yields the following credible intervals for the oscillation parameters assumingthe normal ordering: δCP = 0.930+0.210−0.290 π ∪0.150+0.150−0.110 π,∆m232 = 2.424+0.035−0.040 × 10−3eV2,and sin2θ23 = 0.55+0.02−0.06, with a 76% preference for normal ordering using a prior for sin2(2θ13)using Daya Bay’s measurement. If the Daya Bay sin2(2θ13) vs ∆m232 constraint is used as aprior instead, an 87% preference for normal ordering emerges.
Here, this paper presents the development and demonstration of massively parallel probabilistic machine learning (ML) and uncertainty quantification (UQ) capabilities within the Multiphysics Object-Oriented Simulation Environment (MOOSE), an open-source computational platform for parallel finite element and finite volume analyses. In addressing the computational expense and uncertainties inherent in complex multiphysics simulations, this paper integrates Gaussian process (GP) variants, active learning, Bayesian inverse UQ, adaptive forward UQ, Bayesian optimization, evolutionary optimization, and Markov chain Monte Carlo (MCMC) within MOOSE. It also elaborates on the interaction among key MOOSE systems — Sampler, MultiApp, Reporter, and Surrogate — in enabling these capabilities. The modularity offered by these systems enables development of a multitude of probabilistic ML and UQ algorithms in MOOSE. Example code demonstrations include parallel active learning and parallel Bayesian inference via active learning. The impact of these developments is illustrated through five applications relevant to computational energy applications: UQ of nuclear fuel fission product release, using parallel active learning Bayesian inference; very rare events analysis in nuclear microreactors using active learning; advanced manufacturing process modeling using multi-output GPs (MOGPs) and dimensionality reduction; fluid flow using deep GPs (DGPs); and tritium transport model parameter optimization for fusion energy, using batch Bayesian optimization. These capabilities are part of the MOOSE framework.
When sampling for Bayesian inference, one popular approach is to use Hamiltonian Monte Carlo (HMC) and the No-U-Turn Sampler (NUTS). However, HMC and NUTS can require numerous numerical gradients of the target density and can prove slow in practice. We propose Hamiltonian neural networks (HNNs) with HMC and NUTS for solving Bayesian inference problems [1, 2]. Once trained, HNNs do not require gradients of the target density while sampling. Moreover, they satisfy important properties such as perfect time reversibility and Hamiltonian conservation, making them well suited for use within HMC and NUTS because stationarity can be shown. We also propose an HNN extension called latent HNNs (L-HNNs), which predict latent variable outputs. Compared to HNNs, L-HNNs offer improved expressivity and a reduction in integration errors. Finally, we propose employing L-HNNs in NUTS with an online error monitoring scheme to prevent degeneracy of the sampling in regions of low probability density. We demonstrate L-HNNs in NUTS with online error monitoring by using several example cases involving complex, heavy-tailed, and high local curvature probability densities. Overall, L-HNNs in NUTS with online error monitoring satisfactorily inferred these probability densities. Compared to traditional NUTS, L-HNNs in NUTS with online error monitoring improved the effective sample size (ESS) per gradient by an order of magnitude.
Agent-based simulation provides a powerful tool for in silico system modeling. However, these simulations do not provide built-in methods for uncertainty quantification (UQ). Within these types of models a typical approach to UQ is to run multiple realizations of the model then compute aggregate statistics. This approach is limited due to the compute time required for a solution. When faced with an emerging biothreat, public health decisions need to be made quickly and solutions for integrating near real-time data with analytic tools are needed. We propose an integrated Bayesian UQ framework for agent-based models based on sequential Monte Carlo sampling. Given streaming or static data about the evolution of an emerging pathogen this Bayesian framework provides a distribution over the parameters governing the spread of a disease through a population. These estimates of the spread of a disease may be provided to public health agencies seeking to abate the spread. By coupling agent-based simulations with Bayesian modeling in a data assimilation, our proposed framework provides a powerful tool for modeling dynamical systems in silico. We propose a method which reduces model error and provides a range of realistic possible outcomes. Moreover, our method addresses two primary limitations of ABMs: the lack of UQ and an inability to assimilate data. Our proposed framework combines the flexibility of an agent-based model with UQ provided by the Bayesian paradigm in a workflow which scales well to HPC systems. We provide algorithmic details and results on a simulated outbreak with both static and streaming data.
The Monte Carlo method delivers an unbiased estimate of the probability of failure. However, the variance of the estimate depends on the number of evaluated samples. This number must be very large for estimations of a low probability of failure. If the evaluation of each sample is computationally expensive, the crude Monte Carlo simulation strategy is impracticable. Therefore, subset simulations are used to reduce the required number of evaluations. Subset simulations require a Markov Chain Monte Carlo sampler, such as the random walk Metropolis-Hastings algorithm. The algorithm, however, struggles with sampling in low-probability regions, especially if they are narrow. As a consequence, advanced Markov Chain Monte Carlo simulations have been developed. In particular, the Hamiltonian Monte Carlo method explores the target distribution rapidly. Driven by the idea of Hamiltonian dynamics, this sampler provides a non-random walk through the target distribution. The incorporation of subset simulation and Hamiltonian Monte Carlo methods has shown promising results for reliability analysis. One downside of the Hamiltonian Monte Carlo method is that gradient evaluations are computationally expensive, especially when dealing with high-dimensional problems and evaluating long trajectories. We show that integrating Hamiltonian neural networks in Hamiltonian Monte Carlo simulations significantly speeds up the sampling task. Furthermore, the enhancement of adaptive trajectory length within the Hamiltonian Monte Carlo results in the efficient proposal of the following states. Based on this recent enhancement, we provide a fast sampling strategy for subset simulations using Hamiltonian neural networks to replace the evaluation of the gradient and significantly speed up the Hamiltonian Monte Carlo simulation.
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.
The design of criticality experiments is typically an iterative process that employs a Monte Carlo transport code. The goal is to find a design that optimizes some variable, like the sensitivity of a response to a cross section, while simultaneously ensuring criticality. The high fidelity of the Monte Carlo code is a great asset, but it makes exploring the design space computationally expensive. Herein, we present how a constrained Bayesian optimization algorithm can be used to efficiently design a criticality experiment. It uses Gaussian processes as a surrogate model to probe the design space and to reduce the number of code executions that are needed to find the optimum. We demonstrate constrained Bayesian optimization with a Pu-239/polyethylene solution system and a TEX experiment that is designed for criticality safety validation of a nuclear waste model at the Hanford Site. For both systems, a global optimum was found within 75 Monte Carlo simulations.
With increasing simulation and measurement data, machine learning and artificial intelligence have been widely used in computational decision-making of complex engineering systems. The resulting tools, such as uncertainty quantification solvers, reinforcement learning, and physics-informed machine learning, have achieved great success in critical DOE tasks such as material discovery and design, energy system modeling and control, and numerical weather and climate prediction. A core topic in scientific machine learning and artificial intelligence is Bayesian inference: given an observed data set, people want to estimate the posterior distribution of a (possibly large) number of hidden parameters. Due to the flexibility and weak assumptions, Bayesian sampling has been the mainstream Bayesian inference solvers despite the rapid progress of approximate Bayesian inference. Classical Bayesian sampling methods such as Markov-chain Monte Carlo suffer from a low-acceptance rate due to the random walk nature, therefore state-of-the-art techniques use Hamiltonian Monte Carlo and its variants to efficiently draw posterior samples in a high dimension. The key idea of Hamiltonian Monte Carlo and its variants is to simulate the Hamiltonian dynamics of a classical particle with a fixed mass, and their performance significantly degrades when the posterior distribution is highly spiky or has multiple modes. Leveraging the idea of quantum physics, this project has investigated new theory, algorithms and applications of Bayesian inference (especially Bayesian sampling). The main results include: (1) novel quantum-inspired Bayesian sampling methods that can lead to better accuracy for challenging multi-modal or spiky distributions, (2) more scalable machine learning framework leveraging tensor-compressed Bayesian inference, and (3) Bayesian and sampling approaches for verifying the robustness of continuous and binary neural networks.
Here, in this work, we develop a novel Bayesian approach to study the adsorption and desorption of CO onto a Pd(111) surface, a process of great importance in natural sciences. The motivation for this work comes from the recent availability of time-resolved infrared spectroscopy data and the need for model interpretability and uncertainty quantification in chemical processes. The objective is to learn the relevant parameters that characterize the process: coverage with time, rate constants, activation energies, and pre-exponential factors. Our approach consists of three main schemes: (i) a problem design and probabilistic model for the whole system, (ii) a particle Markov chain Monte Carlo sampler to learn the hidden coverages and rate constant parameters, and (iii) two Bayesian formulations to infer the activation energies and pre-exponential factors. The flexibility of the Bayesian framework allows for uncertainty quantification where possible and integration of mathematical constraints in the model to reflect the system physically. We found that our results for the activation energies and pre-exponential factor are in agreement with those reported in the experimental literature, independently, and we provide discussions on the advantages and disadvantages as well as applicability to other systems.
Sequential Monte Carlo (SMC) samplers are powerful tools for Bayesian inference but suffer from high computational costs due to their reliance on large particle ensembles for accurate estimates. We introduce persistent sampling (PS), an extension of SMC that systematically retains and reuses particles from all prior iterations to construct a growing, weighted ensemble. By leveraging multiple importance sampling and resampling from a mixture of historical distributions, PS mitigates the need for excessively large particle counts, directly addressing key limitations of SMC such as particle impoverishment and mode collapse. Crucially, PS achieves this without additional likelihood evaluations-weights for persistent particles are computed using cached likelihood values. This framework not only yields more accurate posterior approximations but also produces marginal likelihood estimates with significantly lower variance, enhancing reliability in model comparison. Furthermore, the persistent ensemble enables efficient adaptation of transition kernels by leveraging a larger, decorrelated particle pool. Experiments on high-dimensional Gaussian mixtures, hierarchical models, and non-convex targets demonstrate that PS consistently outperforms standard SMC and related variants, including recycled and waste-free SMC, achieving substantial reductions in mean squared error for posterior expectations and evidence estimates, all at reduced computational cost. PS thus establishes itself as a robust, scalable, and efficient alternative for complex Bayesian inference tasks.
The design of criticality experiments is typically an iterative process that employs a Monte Carlo transport code. The goal is to find a design that optimizes some variable, like the sensitivity of a response to a cross section, while simultaneously ensuring criticality. The high fidelity of the Monte Carlo code is a great asset, but it makes exploring the design space computationally expensive. Herein, we present how a constrained Bayesian optimization algorithm can be used to efficiently design a criticality experiment. It uses Gaussian processes as a surrogate model to probe the design space and to reduce the number of code executions that are needed to find the optimum. Furthermore, we demonstrate constrained Bayesian optimization with a Pu-239/polyethylene solution system and a TEX experiment that is designed for criticality safety validation of a nuclear waste model at the Hanford Site. For both systems, a global optimum was found within 75 Monte Carlo simulations.
The design of criticality experiments is typically an iterative process that employs a Monte Carlo transport code. The goal is to find a design that optimizes some variable, like the sensitivity of a response to a cross section, while simultaneously ensuring criticality. The high fidelity of the Monte Carlo code is a great asset, but it makes exploring the design space computationally expensive. Herein, we present how a constrained Bayesian optimization algorithm can be used to efficiently design a criticality experiment. It uses Gaussian processes as a surrogate model to probe the design space and to reduce the number of code executions that are needed to find the optimum. We demonstrate constrained Bayesian optimization with a Pu-239/polyethylene solution system and a TEX experiment that is designed for critical ity safety validation of a nuclear waste model at the Hanford Site. For both systems, a global optimum was found within 75 Monte Carlo simulations.
When sampling for Bayesian inference, one popular approach in the computational field is to use Hamiltonian Monte Carlo (HMC) and specifically the No-U-Turn Sampler (NUTS), which automatically decides the end time of the Hamiltonian trajectory. However, HMC and NUTS can require numerous numerical gradients of the target density and can prove slow in practice when relying on computationally expensive forward models. We propose Latent Hamiltonian neural networks (L-HNNs) with HMC and NUTS for solving Bayesian inference problems. Once trained, L-HNNs do not require numerical gradients of the target density during sampling, and hence numerous evaluations of the forward computational model. Moreover, L-HNNs satisfy important properties such as perfect time reversibility and Hamiltonian conservation, making them well-suited for use within HMC and NUTS because stationarity can be shown. We also propose the integration of L-HNNs in an online error monitoring scheme, in which numerical gradients of the target density are used for a few samples whenever the L-HNNs prediction errors are large. This online error monitor scheme prevents sample degeneracy in regions of low probability density and ensures robust uncertainty quantification. We demonstrate L-HNNs in NUTS with online error monitoring on several analytical examples involving complex, heavy-tailed, and high-local-curvature probability densities. We then demonstrate the applicability of L-HNNs in NUTS to two computational case studies, namely the Allen-Cahn stochastic partial differential equation and an elliptic partial differential equation with 25 and 50 inference parameters, respectively. Overall, the L-HNNs in NUTS with online error monitoring satisfactorily inferred these probability densities. In conclusion, compared to traditional NUTS, L-HNNs in NUTS with online error monitoring required 1–2 orders of magnitude fewer numerical gradients of the target density and improved the effective sample size (ESS) per gradient (which is a measure of both the sampling quality and the computational expense) by an order of magnitude.
The background index (BI) is an important quantity to project and calculate the half-life sensitivity of neutrinoless double-𝛽 decay (0𝜈𝛽𝛽) experiments. An analysis framework is presented to calculate the BI using the specific activities, masses, and simulated efficiencies of an experiments components as distributions. This Bayesian framework includes a unified approach to combine specific activities from assay. Monte Carlo uncertainty propagation is used to build a BI distribution from the specific activity, mass, and efficiency distributions. This method is applied to the M AJORANA D EMONSTRATOR , which deployed arrays of high-purity Ge detectors enriched in 76 Ge to search for 0𝜈𝛽𝛽. The original assay-based projection is requantified in the new framework, using the as-built geometry of the Demonstrator and additional assay information. While 47% higher than the original projection, the resulting BI of [8.95±0.36]×10 −4 cts/(keVkgyr) from the 232 Th and 238 U decay chains does not account for the higher-than-expected BI observed by the D EMONSTRATOR . Finally, this method enables us to demonstrate the statistical incompatibility between the D EMONSTRATOR 's observed background and the assay results.
Distribution-based analyses, such as the distribution of relaxation times (DRT) and the distribution of diffusion times (DDT), present model-free alternatives to equivalent circuit modeling for analysis of electrochemical impedance spectroscopy (EIS) data. However, reconstructing such distributions from noisy impedance data is an ill-posed problem that must be solved with specialized inversion algorithms, requiring careful control and tuning. Furthermore, most inversion algorithms developed to date can only solve problems of limited complexity. Herein, we present a new hierarchical Bayesian method for EIS inversion, leveraging efficient algorithms for optimization and Hamiltonian Monte Carlo (HMC) sampling to solve models of arbitrary complexity. We overcome the challenge of ad-hoc parameter tuning by encoding intrinsic characteristics of the DRT and DDT into flexible prior distributions and “pre-calibrating” the model to simulated data. This approach is versatile, highly robust to noise, and provides quantitative estimates of both the error structure of the data and the uncertainty in the recovered distributions. The model is validated with simulated data to demonstrate accurate recovery of the DRT and the DDT. The method also shows promise for simultaneous recovery of multiple distributions, raising the intriguing possibility of semi-autonomous EIS analysis and ad-hoc model construction. Finally, the practical utility of the method is illustrated with experimental data. Throughout, we draw comparisons to several recently published EIS inversion methodologies.
Deep learning has been successfully applied to the segmentation of 3D Computed Tomography (CT) scans. Establishing the credibility of these segmentations requires uncertainty quantification (UQ) to identify untrustworthy predictions. Recent UQ architectures include Monte Carlo dropout networks (MCDNs), which approximate deep Gaussian processes, and Bayesian neural networks (BNNs), which learn the distribution of the weight space. BNNs are advantageous over MCDNs for UQ but are thought to be computationally infeasible in high dimension, and neither architecture has produced interpretable geometric uncertainty maps. We propose a novel 3D Bayesian convolutional neural network (BCNN), the first deep learning method which generates statistically credible geometric uncertainty maps and scales for application to 3D data. We present experimental results on CT scans of graphite electrodes and laser-welded metals and show that our BCNN outperforms an MCDN in recent uncertainty metrics. The geometric uncertainty maps generated by our BCNN capture distributions of sigmoid values that are interpretable as confidence intervals, critical for applications that rely on deep learning for high-consequence decisions.