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At least 73 records · Page 4

Unorthodox parallelization for Bayesian quantum state estimation

Quantum state tomography (QST) allows for the reconstruction of quantum states through measurements and some inference technique under the assumption of repeated state preparations. Bayesian inference provides a promising platform to achieve both efficient QST and accurate uncertainty quantification, yet is generally plagued by the computational limitations associated with long Markov chains. In this work, we present a novel Bayesian QST approach that leverages modern distributed parallel computer architectures to efficiently sample a D-dimensional Hilbert space. Using a parallelized preconditioned Crank–Nicholson Metropolis–Hastings algorithm, we demonstrate our approach on simulated data and experimental results from IBM Quantum systems up to four qubits, showing significant speedups through parallelization. Although highly unorthodox in pooling independent Markov chains, our method proves remarkably practical, with validation ex post facto via diagnostics like the intrachain autocorrelation time. We conclude by discussing scalability to higher-dimensional systems, offering a path toward efficient and accurate Bayesian characterization of large quantum systems.

Bayesian inference

Calibrating Bayesian generative machine learning for Bayesiamplification

Recently, combinations of generative and Bayesian deep learning have been introduced in particle physics for both fast detector simulation and inference tasks. These neural networks aim to quantify the uncertainty on the generated distribution originating from limited training statistics. The interpretation of a distribution-wide uncertainty however remains ill-defined. We show a clear scheme for quantifying the calibration of Bayesian generative machine learning models. For a Continuous Normalizing Flow applied to a low-dimensional toy example, we evaluate the calibration of Bayesian uncertainties from either a mean-field Gaussian weight posterior, or Monte Carlo sampling network weights, to gauge their behaviour on unsteady distribution edges. Well calibrated uncertainties can then be used to roughly estimate the number of uncorrelated truth samples that are equivalent to the generated sample and clearly indicate data amplification for smooth features of the distribution.

97 MATHEMATICS AND COMPUTING

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

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

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

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

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

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

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

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

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

Identifying microbial drivers in biological phenotypes with a Bayesian network regression model

Abstract In Bayesian Network Regression models, networks are considered the predictors of continuous responses. These models have been successfully used in brain research to identify regions in the brain that are associated with specific human traits, yet their potential to elucidate microbial drivers in biological phenotypes for microbiome research remains unknown. In particular, microbial networks are challenging due to their high dimension and high sparsity compared to brain networks. Furthermore, unlike in brain connectome research, in microbiome research, it is usually expected that the presence of microbes has an effect on the response (main effects), not just the interactions. Here, we develop the first thorough investigation of whether Bayesian Network Regression models are suitable for microbial datasets on a variety of synthetic and real data under diverse biological scenarios. We test whether the Bayesian Network Regression model that accounts only for interaction effects (edges in the network) is able to identify key drivers (microbes) in phenotypic variability. We show that this model is indeed able to identify influential nodes and edges in the microbial networks that drive changes in the phenotype for most biological settings, but we also identify scenarios where this method performs poorly which allows us to provide practical advice for domain scientists aiming to apply these tools to their datasets. BNR models provide a framework for microbiome researchers to identify connections between microbes and measured phenotypes. We allow the use of this statistical model by providing an easy‐to‐use implementation which is publicly available Julia package at https://github.com/solislemuslab/BayesianNetworkRegression.jl .

59 BASIC BIOLOGICAL SCIENCES

Enhancing approximate modular Bayesian inference by emulating the conditional posterior

In modular Bayesian analyses, complex models are composed of distinct modules, each representing different aspects of the data or prior information. In this context, fully Bayesian approaches can sometimes lead to undesirable feedback between modules, compromising the integrity of the inference. The “cut-distribution” prevents unwanted influence between modules by “cutting” feedback. The direct sampling (DS) algorithm is standard practice for approximating the cut-distribution, but it can be computationally intensive, especially when the number of imputations required is large. An enhanced method is proposed, the Emulating the Conditional Posterior (ECP) algorithm, which leverages emulation to increase the number of imputations. Through numerical experiment it is demonstrated that the ECP algorithm outperforms the traditional DS approach in terms of accuracy and computational efficiency, particularly when resources are constrained. Here, it is also shown how the DS algorithm can be improved using ideas from design of experiments. Some practical recommendations are given for algorithm choice in modular Bayesian analyses.

97 MATHEMATICS AND COMPUTING

Using Flory–Huggins-informed human-in-the-loop Bayesian optimization to map the phase diagram of polymer blends

Mapping the phase diagram of polymer blends is an essential step in controlling the structure–property relationship of polymer-based materials. However, traditional grid-based approaches are inefficient and rely on subjective judgements for terminating the experimental campaign. Artificial intelligence-guided experimentation offers a compelling alternative, especially when data-driven decision-making is interfaced with established polymer thermodynamics to improve efficiency and interpretability. Here, we introduce a physics-informed Bayesian optimization approach to guide the mapping of the phase diagram of a model blend containing poly(methyl methacrylate) and poly(styrene-ran-acrylonitrile). Physical information is derived from a Flory–Huggins representation of the spinodal curve, which is integrated into the Bayesian optimization process as a structured prior mean that acts as a soft constraint. Implemented as a human-in-the-loop workflow, the approach leverages optical imaging of film cloudiness with iterative Gaussian process surrogate modeling and a parameter selection decision policy to identify the composition-temperature conditions for sequential iterations. Convergence of kernel and Flory–Huggins-based hyperparameters provided a stopping criterion, ensuring an objective and interpretable termination of the experimental campaign. The framework recovered the known lower critical solution temperature (∼160 °C), while increasing material efficiency through targeted sampling. This work establishes a proof-of-concept for the application of Bayesian optimization workflows to study polymer blend miscibility.

36 MATERIALS SCIENCE

Evaluating the limitations of Bayesian metabolic control analysis

AbstractBayesian Metabolic Control Analysis (BMCA) has emerged as a promising framework for inferring metabolic control coefficients in data-limited scenarios by integrating Bayesian inference with linlog rate laws. However, its predictive accuracy and limitations remain underexplored. This study systematically evaluates BMCA’s ability to infer elasticity values, flux control coefficients (FCCs), and concentration control coefficients (CCCs) under varying data availability conditions using three synthetic metabolic network models. Our findings highlight the strengths and weaknesses of BMCA, guiding its application in metabolic engineering and emphasizing the need for methodological refinements.Author summaryUnderstanding how enzymes control metabolic pathways is crucial for optimizing biomanufacturing and synthetic biology applications. Bayesian Metabolic Control Analysis (BMCA) is a promising computational method that integrates Bayesian inference with metabolic control analysis to estimate key control parameters, even in cases with limited experimental data. However, the accuracy and limitations of BMCA remain unclear. In this study, we systematically evaluate BMCA using three synthetic metabolic networks to determine how different types of physiological data impact its predictive performance. We find that BMCA requires flux and enzyme concentration data for accurate predictions, while external metabolite concentrations contribute little. Additionally, BMCA fails to predict elasticity values beyond a magnitude of 1.5 and reliably infer allosteric regulation, even when strong regulatory interactions exist. In addition, BMCA does not accurately rank metabolic control points, which may limit its utility in identifying key enzymes in engineered pathways. Our work provides practical insights into when and how BMCA can be applied, guiding future research in metabolic modeling and control analysis.

Shin, Janis (ORCID:0000000216572455)

Bayesian inference of nuclear-matter density from proton scattering

Background: Proton elastic scattering at intermediate energy is widely employed as a tool for determining the matter radius of atomic nuclei. Here, the sensitivity of the approach relies on high-resolution measurements at small scattering angles and low-momentum transfer. Under these conditions, the Glauber multiple scattering theory accurately describes the proton-nucleus elastic cross section. Purpose: Investigate the sensitivity of the Glauber multiple scattering theory to uncertainties associated with input parameters such as the nuclear-matter density distribution and nucleon-nucleon data. Method: A joint Bayesian inference was performed using 12 angular distributions of elastic scattering at different energies on 58 Ni, 90 Zr, and 208 Pb targets. A Metropolis-Hastings algorithm was implemented to make an uncertainty quantification analysis for the input parameters used in the Glauber multiple scattering theory. Results: The experimental cross sections were fitted simultaneously using a joint Bayesian inference approach. Posterior probability density distributions of 42 input parameters were obtained from the analysis. A moderate correlation between the nuclear density parameters and the nucleon-nucleon cross sections was found. This correlation impacts the extraction of the nuclear-matter radius. Conclusions: The present analysis provided a consistent method for extracting the nuclear-matter density distribution of 58 Ni, 90 Zr, and 208 Pb from data across different incident energies. Due to the correlation of the nucleon-nucleon cross sections with the other input parameters, a constrained Bayesian inference using free nucleon-nucleon cross section data was performed. The nuclear-matter radii obtained from the analysis are in good agreement with multiple results reported in the literature.

190 ≤ A ≤ 219

New metric improving Bayesian calibration of a multistage approach studying hadron and inclusive jet suppression

We study parton energy-momentum exchange with the quark gluon plasma (QGP) within a multistage approach composed of in-medium Dokshitzer-Gribov-Lipatov-Altarelli-Parisi evolution at high virtuality, and (linearized) Boltzmann transport formalism at lower virtuality. This multistage simulation is then calibrated in comparison with high- p T charged hadrons, D mesons, and the inclusive jet nuclear modification factors, using Bayesian model-to-data comparison, to extract the virtuality-dependent transverse momentum broadening transport coefficient q ̂ . To facilitate this undertaking, we develop a quantitative metric for validating the Bayesian workflow, which is used to analyze the sensitivity of various model parameters to individual observables. The usefulness of this new metric in improving Bayesian model emulation is shown to be highly beneficial for future such analyses. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Identifying Adversarial Cyber-Activity in Operational Technology Environments Using Bayesian Networks

Critical infrastructure and other operational technology (OT) environments face increasing cybersecurity risks from adversarial behavior. This paper describes the development of a risk model using a Bayesian network to enhance the comprehension of observable cyber events caused by malicious activity in OT environments. The core of the Bayesian network is a process model that describes the stages of adversary behavior. The remainder of the model is based on the MITRE ATT&CK® for Industrial Control Systems (ICS) taxonomy, which includes tactics and techniques that may be used by the adversary. The observables provide evidence for adversary behavior through the intermediary technique and tactic nodes. One challenge in constructing this model is a lack of open-source data from cyber-attacks on OT systems. This paper discusses learning from limited data, the elicitation of expert opinion to construct the conditional probability tables when data is scarce, and the refinement of the most difficult conditional probabilities tables using several forms of sensitivity analyses. Finally, the Bayesian network is demonstrated using two historical case studies: the DarkSide ransomware attack on the Colonial Pipeline and the destructive cyberattack targeting the ThyssenKrupp blast furnace. Index Terms—Cybersecurity, industrial control systems, operational technology

97 - MATHEMATICS AND COMPUTING