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DOE OSTI2023

Empirical radius formulas for canonical neutron stars from bidirectionally selecting features of equations of state in extended Bayesian analyses of observational data

Significant advancement in Bayesian inference of nuclear equation of state (EOS) from gravitational wave and x-ray observations of neutron stars (NSs) has been made by the nuclear astrophysics community especially since GW170817. By extending the traditional Bayesian analysis which normally ends at presenting the marginalized posterior probability distribution functions (PDFs) of individual EOS parameters and their correlations (or sometimes only the Pearson correlation coefficients which are only reliably useful when the variables are linearly correlated while they are actually often not), we search for a data-driven and robust empirical formula for the radius 𝑅 1.4 of canonical NSs in terms of the characteristic EOS parameters (features). We also identify the single most important but currently poorly known EOS parameter for determining the 𝑅 1.4 . Using three regression-model-building methodologies: bidirectional stepwise feature selection, least absolute shrinkage selection operator (LASSO) regression, and neural network regression on a large set of posterior EOSs and the corresponding 𝑅 1.4 values inferred from earlier comprehensive Bayesian analyses of NS observational data, we systematically and rigorously develop the most probable 𝑅 1.4 formulas with varying statistical accuracy and technical complexity. Here, the most important EOS parameters for determining 𝑅 1.4 are found consistently in each of the feature selection processes to be (in order of decreasing importance): curvature 𝐾 sym , slope 𝐿, skewness 𝐽 sym of nuclear symmetry energy, skewness 𝐽 0 , incompressibility 𝐾 0 of symmetric nuclear matter, and the magnitude 𝐸 sym ⁡(𝜌 0 ) of symmetry energy at the saturation density 𝜌 0 of nuclear matter.

Bayesian methods↗

DOE OSTI2019

Thermonuclear fusion rates for tritium + deuterium using Bayesian methods

The 3 H(d, n) 4 He reaction has a large low-energy cross section and will likely be utilized in future commercial fusion reactors. This reaction also takes place during Big Bang nucleosynthesis. Studies of both scenarios require accurate and precise fusion rates. To this end, we implement a one-level, two-channel R-matrix approximation into a Bayesian model. Our main goals are to predict reliable astrophysical S-factors and to estimate R-matrix parameters using the Bayesian approach. All relevant parameters are sampled in our study, including the channel radii, boundary condition parameters, and data set normalization factors. In addition, we take uncertainties in both measured bombarding energies and S-factors rigorously into account. Thermonuclear rates and reactivities of the 3 H(d, n) 4 He reaction are derived by numerically integrating the Bayesian S-factor samples. The present reaction rate uncertainties at temperatures between 1.0 MK and 1.0 GK are in the range of 0.2% to 0.6%. Our reaction rates differ from previous results by 2.9% near 1.0 GK.Our reactivities are smaller than previous results, with a maximum deviation of 2.9% near a thermal energy of 4 keV. The present rate or reactivity uncertainties are more reliable compared to previous studies that did not include the channel radii, boundary condition parameters, and data set normalization factors in the fitting. Finally, we investigate previous claims of electron screening effects in the published 3 H(d, n) 4 He data. No such effects are evident and only an upper limit for the electron screening potential can be obtained.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Calibration of RAFM Micromechanical Model for Creep Using Bayesian Optimization for Functional Output

A Bayesian optimization procedure is presented for calibrating a multimechanism micromechanical model for creep to experimental data of F82H steel. Reduced activation ferritic martensitic (RAFM) steels based on Fe(8–9)%Cr are the most promising candidates for some fusion reactor structures. Although there are indications that RAFM steel could be viable for fusion applications at temperatures up to 600°C, the maximum operating temperature will be determined by the creep properties of the structural material and the breeder material compatibility with the structural material. Due to the relative paucity of available creep data on F82H steel compared to other alloys such as Grade 91 steel, micromechanical models are sought for simulating creep based on relevant deformation mechanisms. As a point of departure, this work recalibrates a model form that was previously proposed for Grade 91 steel to match creep curves for F82H steel. Due to the large number of parameters (9) and cost of the nonlinear simulations, an automated approach for tuning the parameters is pursued using a recently developed Bayesian optimization for functional output (BOFO) framework (Huang et al., 2021, “Bayesian optimization of functional output in inverse problems,” Optim. Eng., 22, pp. 2553–2574). Incorporating extensions such as batch sequencing and weighted experimental load cases into BOFO, a reasonably small error between experimental and simulated creep curves at two load levels is achieved in a reasonable number of iterations. In conclusion, validation with an additional creep curve provides confidence in the fitted parameters obtained from the automated calibration procedure to describe the creep behavior of F82H steel.

42 ENGINEERING↗

DOE OSTI2025

Hierarchical Bayesian Inverse Problems: A High-Dimensional Statistics Viewpoint

This paper analyzes hierarchical Bayesian inverse problems using techniques from highdimensional statistics. Furthermore, our analysis leverages a property of hierarchical Bayesian regularizers that we call approximate decomposability to obtain non-asymptotic bounds on the reconstruction error attained by maximum a posteriori estimators. The new theory explains how hierarchical Bayesian models that exploit sparsity, group sparsity, and sparse representations of the unknown parameter can achieve accurate reconstructions in high-dimensional settings.

MAP estimation↗

DOE OSTI2020

A Bayesian Approach to Regional Decadal Predictability: Sparse Parameter Estimation in High-Dimensional Linear Inverse Models of High-Latitude Sea Surface Temperature Variability

Stochastic reduced models are an important tool in climate systems whose many spatial and temporal scales cannot be fully discretized or underlying physics may not be fully accounted for. One form of reduced model, the linear inverse model (LIM), has been widely used for regional climate predictability studies—typically focusing more on tropical or midlatitude studies. However, most LIM fitting techniques rely on point estimation techniques deriving from fluctuation–dissipation theory. In this methodological study we explore the use of Bayesian inference techniques for LIM parameter estimation of sea surface temperature (SST), to quantify the skillful decadal predictability of Bayesian LIM models at high latitudes. We show that Bayesian methods, when compared to traditional point estimation methods for LIM-type models, provide better calibrated probabilistic skill, while simultaneously providing better point estimates due to the regularization effect of the prior distribution in high-dimensional problems. We compare the effect of several priors, as well as maximum likelihood estimates, on 1) estimating parameter values on a perfect model experiment and 2) producing calibrated 1-yr SST anomaly forecast distributions using a preindustrial control run of the Community Earth System Model (CESM). Finally, we employ a host of probabilistic skill metrics to determine the extent to which an LIM can forecast SST anomalies at high latitudes. We find that the choice of prior distribution has an appreciable impact on estimation outcomes, and priors that emphasize physically relevant properties enhance the model’s ability to capture variability of SST anomalies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Emulator-Based Bayesian Calibration of the CISNET Colorectal Cancer Models

Purpose To calibrate Cancer Intervention and Surveillance Modeling Network (CISNET)'s SimCRC, MISCAN-Colon, and CRC-SPIN simulation models of the natural history colorectal cancer (CRC) with an emulator-based Bayesian algorithm and internally validate the model-predicted outcomes to calibration targets.Methods We used Latin hypercube sampling to sample up to 50,000 parameter sets for each CISNET-CRC model and generated the corresponding outputs. We trained multilayer perceptron artificial neural networks (ANNs) as emulators using the input and output samples for each CISNET-CRC model. We selected ANN structures with corresponding hyperparameters (i.e., number of hidden layers, nodes, activation functions, epochs, and optimizer) that minimize the predicted mean square error on the validation sample. We implemented the ANN emulators in a probabilistic programming language and calibrated the input parameters with Hamiltonian Monte Carlo-based algorithms to obtain the joint posterior distributions of the CISNET-CRC models' parameters. We internally validated each calibrated emulator by comparing the model-predicted posterior outputs against the calibration targets.Results The optimal ANN for SimCRC had 4 hidden layers and 360 hidden nodes, MISCAN-Colon had 4 hidden layers and 114 hidden nodes, and CRC-SPIN had 1 hidden layer and 140 hidden nodes. The total time for training and calibrating the emulators was 7.3, 4.0, and 0.66 h for SimCRC, MISCAN-Colon, and CRC-SPIN, respectively. The mean of the model-predicted outputs fell within the 95% confidence intervals of the calibration targets in 98 of 110 for SimCRC, 65 of 93 for MISCAN, and 31 of 41 targets for CRC-SPIN.Conclusions Using ANN emulators is a practical solution to reduce the computational burden and complexity for Bayesian calibration of individual-level simulation models used for policy analysis, such as the CISNET CRC models. In this work, we present a step-by-step guide to constructing emulators for calibrating 3 realistic CRC individual-level models using a Bayesian approach.

artificial neural networks↗

DOE OSTI2013

Light-sheet Bayesian microscopy enables deep-cell super-resolution imaging of heterochromatin in live human embryonic stem cells

Heterochromatin in the nucleus of human embryonic cells plays an important role in the epigenetic regulation of gene expression. The architecture of heterochromatin and its dynamic organization remain elusive because of the lack of fast and high-resolution deep-cell imaging tools. We enable this task by advancing instrumental and algorithmic implementation of the localization-based super-resolution technique. We present light-sheet Bayesian super-resolution microscopy (LSBM). We adapt lightsheet illumination for super-resolution imaging by using a novel prism-coupled condenser design to illuminate a thin slice of the nucleus with high signal-to-noise ratio. Coupled with a Bayesian algorithm that resolves overlapping fluorophores from high-density areas, we show, for the first time, nanoscopic features of the heterochromatin structure in both fixed and live human embryonic stem cells. The enhanced temporal resolution allows capturing the dynamic change of heterochromatin with a lateral resolution of 50–60 nm on a time scale of 2.3 s. Light-sheet Bayesian microscopy opens up broad new possibilities of probing nanometer-scale nuclear structures and real-time sub-cellular processes and other previously difficult-to-access intracellular regions of living cells at the single-molecule, and single cell level.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Semi-Analytical Hierarchical Bayesian Inference of Nonlinear Model Structure in Stochastic Dynamics: Applied to Compartmental Models of Infectious Diseases

A Bayesian computational framework for parsimonious inference in stochastic nonlinear dynamical systems is presented. This framework enables the concurrent estimation of system states, time-varying parameters, time-invariant parameters, and the optimal sparsity structure of the model parameters. Because differential equation-based models are often simplified mechanistic or phenomenological representations, robust inference from noisy measurement data requires explicit treatment of model error and uncertainty. Model error and time-varying parameters can be represented as random processes, enabling inference while making minimal assumptions about the underlying sources of discrepancy and variability. Adopting stochastic differential equation representations affords the model significant flexibility, but can also render it susceptible to overfitting during statistical inversion, where the inferred model may track noise rather than the underlying signal. To alleviate the effects of overfitting and to enable the discovery of the optimal sparse representation of the time-invariant parameters, a Bayesian sparse learning algorithm is embedded within the framework. This sparse learning framework adopts an approximate hierarchical Bayesian setting defined by a series of semi-analytical expressions. The model structure inference framework is validated using a stochastic compartmental model for tracking and forecasting active cases of an infectious disease. Compartmental models describe population-level infectious disease dynamics through interactions among population fractions grouped by disease state. Mathematically, such models consist of a system of coupled ordinary differential equations. This example adopts an expressive compartmental model that includes multiple possible interactions between disease states, motivated by early uncertainty surrounding COVID-19 reinfection dynamics and their implications for long-term epidemic forecasting. The sparse learning exercise permits the inference of a priori unknown epidemiological dynamics from simulated public health data, discovering the nested compartmental model that optimizes the trade-off between average data-fit and model complexity. It is shown that inducing sparsity among the model parameters eliminates redundant interactions between compartments, equivalently revealing the optimal coupling structure between differential equations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Bayesian inference of Stochastic reaction networks using Multifidelity Sequential Tempered Markov Chain Monte Carlo

Stochastic reaction network models are often used to explain and predict the dynamics of gene regulation in single cells.These models usually involve several parameters, such as the kinetic rates of chemical reactions, that are not directly measurable and must be inferred from experimental data. Bayesian inference provides a rigorous probabilistic frame-work for identifying these parameters by finding a posterior parameter distribution that captures their uncertainty.Traditional computational methods for solving inference problems such as Markov Chain Monte Carlo methods based on classical Metropolis-Hastings algorithm involve numerous serial evaluations of the likelihood function, which in turn requires expensive forward solutions of the chemical master equation (CME). We propose an alternate approach based on a multifidelity extension of the Sequential Tempered Markov Chain Monte Carlo (ST-MCMC) sampler. This algorithm is built upon Sequential Monte Carlo and solves the Bayesian inference problem by decomposing it into a sequence of efficiently solved subproblems that gradually increase both model fidelity and the influence of the observed data. We reformulate the finite state projection (FSP) algorithm, a well-known method for solving the CME, to produce a hierarchy of surrogate master equations to be used in this multifidelity scheme. To determine the appropriate fidelity, we introduce a novel information-theoretic criteria that seeks to extract the most information about the ultimate Bayesian posterior from each model in the hierarchy without inducing significant bias. This novel sampling scheme is tested with high performance computing resources using biologically relevant problems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Technical Report for Bayesian Optimization and Reinforcement Learning for Beam Polarization Increase in the BNL Hadron Injectors

This project developed and evaluated physics-informed Bayesian learning and machine learning (ML)-based optimization methods for improving beam polarization preservation in the BNL hadron injector chain. The work focused on uncertainty-aware digital twin modeling, Bayesian calibration of accelerator simulations using beam measurements, and data-efficient optimization strategies including Bayesian optimization and reinforcement learning. These methods were applied to injector tuning and RF control problems in realistic accelerator settings to support improved operational robustness and readiness for RHIC operations and future Electron–Ion Collider facilities. No subject inventions were disclosed under this award.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Materials Design using an Active Subspace-based Batch Bayesian Optimization Approach

Integrated computational materials engineering (ICME) calls for integrating simulation tools and/or experiments to develop new materials and materials systems. However, implementation of ICME approaches is challenging mainly due to the considerable computational expense of such frameworks and large dimensionality of the design space. Addressing these challenges is thus critical to the success of ICME initiatives. We present here a specific Bayesian optimization framework designed to address these two challenges. In particular, we propose an active subspace batch Bayesian optimization framework. The framework makes use of dimension reduction via the active subspace method and makes use of the ability to query in parallel via the batch Bayesian optimization approach. Here, the integration of these techniques leads to significant efficiency improvements while maintaining accuracy.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Lowering the computational barrier: Partially Bayesian neural networks for transparency in medical imaging AI

Deep Neural Networks (DNNs) can provide clinicians with fast and accurate predictions that are highly valuable for high-stakes medical decision-making, such as in brain tumor segmentation and treatment planning. However, these models largely lack transparency about the uncertainty in their predictions, potentially giving clinicians a false sense of reliability that may lead to grave consequences in patient care. Growing calls for Transparent and Responsible AI have promoted Uncertainty Quantification (UQ) to capture and communicate uncertainty in a systematic and principled manner. However, traditional Bayesian UQ methods remain prohibitively costly for large, million-dimensional tumor segmentation DNNs such as the U-Net. In this work, we discuss a computationally-efficient UQ approach via the partially Bayesian neural networks (pBNN). In pBNN, only a single layer, strategically selected based on gradient-based sensitivity analysis, is targeted for Bayesian inference. We illustrate the effectiveness of pBNN in capturing the full uncertainty for a 7.8-million parameter U-Net. We also demonstrate how practitioners and model developers can use the pBNN's predictions to better understand the model's capabilities and behavior.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Bayesian Optimization of Non-Invariant Systems with Constraints Developed for Application to the ECR Ion Source VENUS

In this work, we consider the optimization of non-invariant systems with both safety and control constraints. We present a new approach based on Bayesian optimization for the dynamic, safe and controlled optimization of such systems. Although there are other possible use cases, we focus on the application to the electron cyclotron resonance ion source VENUS. From experimental data, we have observed that VENUS behaves to first order as a non-invariant dynamic system with moving areas of instability. Our novel approach aims at providing a tool that can maintain system optimization in a safe way. This is accomplished by making sure the objective function, the beam current in the case of VENUS, does not fall under an operational minimum, while simultaneously requiring the optimization to avoid areas where VENUS is unstable. We compare the result of our approach on synthetic data modeled to mimic the behavior of VENUS with two methods from the literature, a standard Bayesian optimizer and a safe Bayesian optimizer, both adapted to deal with dynamic systems. A cross Student T-test is conducted to show the significance of the improvement given by the new method we introduce here, regarding the two preexisting methods we compared to. The results of the tests conducted on synthetic data show that the proposed method succeeds at maintaining the system optimized and obeys the predefined constraints better than the literature methods explored.

Bayesian optimization↗

DOE OSTI2021

Contaminant Source Identification from Finite Sensor Data: Perron–Frobenius Operator and Bayesian Inference

Sensors in the built environment ensure safety and comfort by tracking contaminants in the occupied space. In the event of contaminant release, it is important to use the limited sensor data to rapidly and accurately identify the release location of the contaminant. Identification of the release location will enable subsequent remediation as well as evacuation decision-making. In previous work, we used an operator theoretic approach—based on the Perron–Frobenius (PF) operator—to estimate the contaminant concentration distribution in the domain given a finite amount of streaming sensor data. In the current work, the approach is extended to identify the most probable contaminant release location. The release location identification is framed as a Bayesian inference problem. The Bayesian inference approach requires considering multiple release location scenarios, which is done efficiently using the discrete PF operator. The discrete PF operator provides a fast, effective and accurate model for contaminant transport modeling. The utility of our PF-based Bayesian inference methodology is illustrated using single-point release scenarios in both two and three-dimensional cases. The method provides a fast, accurate, and efficient framework for real-time identification of contaminant source location.

42 ENGINEERING↗

DOE OSTI2023

Integrating Survival Analysis with Bayesian Statistics to Forecast the Remaining Useful Life of a Centrifugal Pump Conditional to Multiple Fault Types

To improve the viability of nuclear power plants, there is a need to reduce their operational costs. Operational costs account for a significant portion of a plant’s yearly budget, due to their scheduled-based maintenance approach. In order to reduce these costs, proactive methods are required that estimate and forecast the state of a machine in real time to optimize maintenance schedules. In this research, we use Bayesian networks to develop a framework that can forecast the remaining useful life of a centrifugal pump. To do so, we integrate survival analysis with Bayesian statistics to forecast the health of the pump conditional to its current state. We complete our research by successfully using the Bayesian network on a case study. This solution provides an informed probabilistic viewpoint of the pumping system for the purpose of predictive maintenance.

42 ENGINEERING↗

NASA NTRS2019

Bayesian Inference and the Effects of Varying Uncertainty Models in Charring Ablator Calibration and Uncertainty Quantification Problems

The Mars Science Laboratory (MSL) vehicle utilized a heat shield constructed from NASA’s Phenolic-Impregnated Carbon Ablator (PICA) material to protect the main structure from the high enthalpy environment encountered during hypersonic atmospheric entry. During the vehicle’s descent through Martian atmosphere, multiple thermocouples embedded within the heat shield captured in-depth material temperature data that allow for studies to be conducted on current material response reconstruction tools. In the present work, material temperature data obtained from thermocouples within the MISP-4 plug (MEDLI (Mars Science Laboratory Entry, Descent, and Landing Instrument) Integrated Sensor Plug) are utilized in the calibration of Theoretical Ablative Composite for Open Testing (TACOT) model parameters in conjunction with NASA’s Porous material Analysis Toolbox (PATO) through Bayesian inference where uncertainty due to parametric, modeling, and experimental sources is simultaneously quantified. Prior to the study, a sensitivity analysis is performed through computation of the robust Sobol indices in an effort to study the relationship between input space and model response and to reduce the dimensionality of the statistical inverse problem. The Bayesian inference methodology necessitates an a-priori choice to be made for the uncertainty model for which numerous possibilities are available. Across most works, however, only basic additive or multiplicative models are utilized with pre-defined magnitudes of uncertainty based on a-priori knowledge or to-be-calibrated multipliers of static covariance matrix structures. The present effort explores the effects of informed uncertainty models, ones with temporal dependence that are simultaneously calibrated through Bayesian inference, on calibrated results for parameters that make up the uncertain input space.

Sensitivity Analysis↗

NASA NTRSDate not supplied

Enhancing Fault Isolation for Health Monitoring of Electric Aircraft Propulsion by Embedding Failure Mode and Effect Analysis into Bayesian Networks

This paper describes a fault isolation approach for electric powertrains of unmanned aerial vehicles. The approach leverages the combination of failure mode and effect analysis (FMEA) and Bayesian networks, thus introducing depend-ability structures into a diagnostic framework. Faults and failure events from the FMEA are mapped within a Bayesian network, where network edges replicate the links embedded within FMEAs. This framework helps the fault isolation process by identifying the probability of occurrence of specific faults or root causes given evidence observed through sensor signals. The framework is applied to an electric power-train system of a small, rotary-wing unmanned aerial vehicle, demonstrating how a Bayesian network enhanced by FMEA helps disambiguate between root causes of incipient failures, which would otherwise be considered as equally probable.

Fault Isolation↗

NASA NTRSDate not supplied

Systems Health Monitoring: Integrating FMEA into Bayesian Networks

The foreseeable high traffic density suggests that a large number of electric propulsion systems will enter the airspace, and that they will also operate at high frequency, e.g., large number of take offs and landings per unit time. The reliability of such critical systems is therefore key to ensure high safety standards in the low-altitude airspace. Diagnostic systems, which aim at identifying incipient faults, can mitigate unexpected failures or lower-than-expected reliability by performing early fault detection by monitoring the systems. A key element of fault diagnosis is fault detection and isolation (FDI), which complexity increases with the complexity of the system itself, namely the number of subsystems and components, interactions among sub-systems, and the number of sensors available. The proposed approach leverages combination of failure mode and effect analysis (FMEA) integrated with Bayesian networks, thus introducing dependability structures into a diagnostic framework to aid FDI. Faults and failure events from the FMEA are mapped within a Bayesian network, where network edges replicate the links embedded within FMEAs. The integrated framework enables the fault isolation process by identifying the probability of occurrence of specific faults or root causes given evidence observed through sensor signals. In this work, sub systems of Urban Air Mobility (UAM) type vehicle like avionics, structures, power-train etc. are taken into account to show the approach at the system level. This work integrates early design phase in the development of UAM type vehicles with diagnostic tools, which are often developed later in the product life-cycle, or retrofitted at a later time on systems. Failure mode and effect analysis (FMEA) derived for the system in the design phase is embedded within a Bayesian network (BN).

UAM↗