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At least 307 records · Page 17

PRIME - A Software Toolkit for the Characterization of Partially Observed Epidemics in a Bayesian Framework

PRIME is a modeling framework designed for the “real-time’” characterization and forecasting of partially observed epidemics. Characterization is the estimation of infection spread parameters using daily counts of symptomatic patients. The method is designed to help guide medical resource allocation in the early epoch of the outbreak. The estimation problem is posed as one of Bayesian inference and solved using a Markov Chain Monte Carlo technique. The framework can accommodate multiple epidemic waves and can help identify different disease dynamics at the regional, state, and country levels. We include examples using publicly available COVID-19 data.

97 MATHEMATICS AND COMPUTING↗

Bayesian Attack Model (BAM) User Story

This document presents a user story for the Bayesian Attack Model (BAM) tool designed to aggregate and analyze cyber-attack observables for operational technology (OT) systems. BAM aims to empower cybersecurity analysts by providing a streamlined interface for collecting observable data from various sources, enabling real-time analysis of potential adversary activity. By enhancing the response capabilities of security teams, BAM facilitates risk-informed decision-making and improves organizational security posture. This user story outlines the key functionalities, user interactions, and requirements necessary to successfully integrate BAM with other security information and event management (SIEM) technology and cybersecurity operations centers (CSOCs).

97 MATHEMATICS AND COMPUTING↗

Fermilab Booster loss modelling and rebalancing using Bayesian methods

Fermilab Booster is being upgraded for the PIP-II project to support 20Hz ramp rate at higher intensities. Loss trip limits determine the achievable peak power. To meet PIP-II requirements, losses need to be halved as compared to current levels. Losses primarily occur at injection and transition crossing, with both gradually increasing and threshold-like intensity-dependent behaviors. The existing simulation models are not yet good enough for quantitative loss predictions. In practice, it will be necessary to tune up the Booster using iterative methods and operator intuition. In this paper we present an effort to systematically model Booster losses using active learning (Bayesian exploration) techniques, and subsequently to rebalance them for higher trip limit margins. We first created several sets of spatially and temporally isolated orbit and optics knobs, and trained Gaussian process models for each beam loss monitor as well as beam current. This is a complex task due to safety and timing requirements – we discuss mitigations such as uncertainty constraints and approximate fitting. Once models are stable, we perform large-scale single and multi-objective tuning using scalarized objectives made up of critical beam loss locations. Our results demonstrate significant rebalancing of losses, increasing trip margins, as well as an overall improvement in beam transmission efficiency. We are exploring how to combine existing simulations with experimental data and automate the collection procedure so that more advanced surrogate models can be created over time.

Kuklev, Nikita [Fermilab]↗

Hierarchical Bayesian Modeling for Cosmology: Can NPE reliably replace MCMC?

Hierarchical neural posterior estimation has its place Hierarchical Bayesian Modeling (HBM) combined with MCMC algorithms has been shown to provide more robust and accurate inference for real-world phenomena in which nature takes a nested form. However, MCMC-based inference can be computationally expensive, and its performance often suffers for complex posterior geometries. These costs are especially pertinent for HBM. Studies have recently demonstrated the potential for a flexible, expressive, and amortized hierarchical neural posterior estimator (HNPE) built on Normalizing Flows. These studies have mostly been performed on simple datasets, or they focus on a single parameter from each level of the hierarchy. A systematic study analyzing how both hierarchical methods compare for more complex and realistic datasets is necessary before applying HNPE for scientific measurements. Here, we re-explore the theory behind HNPE and conduct comparative numerical experiments of HNPE and MCMC-based HBM methods on real and synthetic data, including strong gravitational lensing simulations. In particular, we use a suite of diagnostics to show trade-offs in terms of accuracy, precision, time to train or sample, reproducibility, and the need for expert domain knowledge. Especially for higher dimensional and complex posteriors, HNPE is expected to drastically improve on time for inference, accuracy, and precision with an upfront training time cost.

Hur, Rachel [Chicago U.] (ORCID:000900089890445X)↗

Probing Non-Standard Interactions in NOvA with Bayesian MCMC Methods

We present a search for non-standard neutrino interactions (NSI) using NOvA's joint $\nu_e$ appearance and $\nu_\mu$ disappearance samples in both neutrino and antineutrino beam modes. A Bayesian Markov Chain Monte Carlo approach is used to map the posterior distribution over NSI parameters $\varepsilon_{e\mu}$, $\varepsilon_{e\tau}$, and $\varepsilon_{\mu\tau}$, simultaneously with standard oscillation parameters. We investigate the effect of prior choice for the complex NSI parameters and present projected sensitivity to off-diagonal NSI.

Huang, Xiaoyan [Mississippi U.]↗

Contextual modeling and Bayesian Optimization for Improved Injection at the Fermilab Booster

The Fermilab accelerator complex delivers high-intensity proton beams to serve the lab’s neutrino, muon, and fixed-target programs. A normal-conducting Linac accelerates H− beam to 400 MeV and injects into the Booster rapid cycling synchrotron via charge exchange, which accelerates protons to 8 GeV. Injection from the Linac into the Booster is a critical area for high-power performance of the Fermilab proton complex. The Booster is a high-intensity proton ring with extreme space-charge forces which necessitates precise control over the beam losses through the acceleration cycle. The main challenge for the reliability of Booster performance is compensating for drifting conditions in the beam from the Linac, which can drift daily in energy by up to O(1) MeV w.r.t. design. Drifts in Linac orbit and energy must be corrected to match the Booster, while simultaneously accommodating interdependent drifts in transverse and longitudinal beam quality. Operationally, compensation for these changes is addressed by manual tuning of the Linac output energy and/or Booster acceptance, which can be inefficient and time-consuming. This works describes contextual Bayesian Optimization for injection tuning that takes into account the state of Linac beam via information from instrumentation in the injection line (Beam position monitors (BPMs), beam loss monitors (BLMs), wire scanners for transverse profiles (WSs)), as well as RF cavity setting parameters from the Linac.

Sharankova, R. [Fermilab] (ORCID:000000027014593X)↗

Bayesian Exploration and Surrogate Emulation of Nonlinear Beam-Response Geometry in the LBNF Beamline

Next-generation long-baseline neutrino experiments aim to achieve multi-MW proton beam power while reducing accelerator-induced systematic uncertainties. At Fermilab, the LBNF beamline is designed for 1.2 MW operation with PIP-II and is upgradeable to 2.4 MW. DUNE will probe the three-flavor neutrino paradigm and search for CP violation, requiring precise neutrino-flux normalization and improved control of accelerator-related uncertainties. Within the LBNF beamline, the System for On-Axis Neutrino Detection (SAND) will constrain flux uncertainties using precision near-detector measurements, while the Muon Monitor System (MuMS) will provide beamline diagnostics sensitive to the proton beam, target, and horn configuration. However, the pion phase space relevant for DUNE depends simultaneously on many correlated parameters, including beam centroid, beam width, horn current and alignment, target position, optics shifts, and radiation-induced changes. Consequently, MuMS observables exhibit nonlinear and coupled responses that are difficult to characterize using traditional one-parameter scans. To address this challenge, we are developing a Bayesian Exploration framework coupled to physics-informed surrogate emulators trained on Geant4 beamline simulations. Gaussian-process emulators provide both fast predictions and uncertainty estimates, enabling adaptive selection of new simulation points in beam-parameter space. As an initial demonstration, we construct surrogate emulators for MuMS response observables using a verified simulation campaign spanning proton-beam steering conditions. The emulators reproduce the simulated dependence of MuMS centroid and gradient observables while providing predictive uncertainties, and serve as the foundation for future multidimensional exploration including beam width, horn current, and additional beamline parameters. This work establishes a framework for uncertainty-aware beam monitoring, adaptive simulation campaigns, and rapid beam-response inference for future DUNE operations.

Ganguly, Sudeshna [Fermilab] (ORCID:00000003163482↗

Synergistic Integration of Multiple Wave Energy Converters with Adaptive Resonance and Offshore Floating Wind Turbines through Bayesian Optimization

We developed a synergistic ocean renewable system where an array of Wave Energy Converters (WEC) with adaptive resonance was collocated with a Floating Offshore Wind Turbine (FOWT) such that the WECs, capturing wave energy through the resonance adapting to varying irregular waves, consequently reduced FOWFT loads and turbine motions. Combining Surface-Riding WECs (SR-WEC) individually designed to feasibly relocate their natural frequency at the peak of the wave excitation spectrum for each sea state, and to obtain the highest capture width ratio at one of the frequent sea states for annual average power in a tens of kilowatts scale with a 15 MW FOWT based on a semi-submersible, Bayesian Optimization is implemented to determine the arrangement of WECs that minimize the annual representation of FOWT’s wave excitation spectra. The time-domain simulation of the system in the optimized arrangement is performed, including two sets of interactions: one set is the wind turbine dynamics, mooring lines, and floating body dynamics for FOWT, and the other set is the nonlinear power-take-off dynamics, linear mooring, and individual WECs’ floating body dynamics. Those two sets of interactions are further coupled through the hydrodynamics of diffraction and radiation. For sea states comprising Annual Energy Production, we investigate the capture width ratio of WECs, wave excitation on FOWT, and nacelle acceleration of the turbine compared to their single unit operations. We find that the optimally arranged SR-WECs reduce the wave excitation spectral area of FOWT by up to 60% and lower the turbine’s peak nacelle acceleration by nearly 44% in highly occurring sea states, while multiple WECs often produce more than the single operation, achieving adaptive resonance with a larger wave excitation spectra for those sea states. The synergistic system improves the total Annual Energy Production (AEP) by 1440 MWh, and we address which costs of Levelized Cost Of Energy (LCOE) can be reduced by the collocation.

Engineering↗

Union through UNITY: Cosmology with 2000 SNe Using a Unified Bayesian Framework

Type Ia supernovae (SNe Ia) were instrumental in establishing the acceleration of the Universe’s expansion. By virtue of their combination of distance reach, precision, and prevalence, they continue to provide key cosmological constraints, complementing other cosmological probes. Individual SN surveys cover only over about a factor of 2 in redshift, so compilations of multiple SN data sets are strongly beneficial. We assemble an up-to-date “Union” compilation of 2087 cosmologically useful SNe Ia from 24 data sets (“Union3”). We take care to put all SNe on the same distance scale and update the light-curve fitting with SALT3 to use the full rest-frame optical. Over the next few years, the number of cosmologically useful SNe Ia will increase by more than a factor of 10, and keeping systematic uncertainties subdominant will be more challenging than ever. We discuss the importance of treating outliers, selection effects, light-curve shape/color populations/standardization relations, unexplained dispersion, and heterogeneous observations simultaneously. We present an updated Bayesian framework, called UNITY1.5 (Unified Nonlinear Inference for Type-Ia cosmologY), that incorporates significant improvements in our ability to model selection effects, standardization, and systematic uncertainties compared to earlier analyses. As an analysis byproduct, we also recover the posterior of the SN-only peculiar-velocity field, although we do not interpret it in this work. We compute updated cosmological constraints with Union3 and UNITY1.5, finding weak 1.7σ–2.6σ tension with flat cold dark matter and possible evidence for thawing dark energy (w0 > − 1, wa < 0). We release our SN distances, light-curve fits, and UNITY1.5 framework to the community.

Rubin, David↗

Bayesian Inference of Hybrid Star Properties from Future High-precision Measurements of Their Radii

Future high-precision X-ray and gravitational-wave observations of neutron stars (NSs) are expected to constrain NS radii with uncertainties as small as σ ≃ 0.1 km. Such unprecedented precision offers a unique opportunity to extract new information about the nature and equation of state (EOS) of supradense matter in NS cores. Using mock radius data with uncertainties ranging from σ = 1.0 to 0.1 km, together with a flexible meta-model NS EOS that allows for a first-order hadron–quark phase transition, we perform a Bayesian statistical analysis to assess the impact of radius measurements on EOS constraints. We find that high-precision radius measurements, particularly for massive NSs, significantly tighten constraints on the hadron–quark transition density ρ t , the quark matter mass fraction in NS cores, and several parameters characterizing the EOS of supranuclear hadronic matter, although the degree of improvement depends on the assumed prior range of ρ t . In contrast, even with the highest precision considered, NS radii—including those of massive stars—remain largely insensitive to the stiffness of quark matter, independent of the measurement accuracy or the prior range adopted for ρ t .

Neutron stars↗

Bayesian Component Separation for DESI LAE Automated Spectroscopic Redshifts and Photometric Targeting

Lyα emitters (LAEs) are valuable high-redshift cosmological probes traditionally identified using specialized narrowband photometric surveys. In ground-based spectroscopy, it can be difficult to distinguish the sharp LAE peak from residual sky emission lines using automated methods, leading to misclassified redshifts. We present a Bayesian spectral component separation technique to automatically determine spectroscopic redshifts for LAEs while marginalizing over sky residuals. We use visually inspected spectra of LAEs obtained using the Dark Energy Spectroscopic Instrument (DESI) to create a data-driven prior and can determine redshift by jointly inferring sky residual, LAE, and residual components for each individual spectrum. We demonstrate this method on 881 spectroscopically observed z = 2–4 DESI LAE candidate spectra and determine their redshifts with >90% accuracy when validated against visually inspected redshifts. Using the Δχ$^{2}$ value from our pipeline as a proxy for detection confidence, we then explore potential survey design choices and implications for targeting LAEs with medium-band photometry. This method allows for scalability and accuracy in determining redshifts from DESI spectra, and the results provide recommendations for LAE targeting in anticipation of future high-redshift spectroscopic surveys.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Optimizing Optical Searches for Supermassive Black Hole Binaries in Active Galactic Nuclei Light Curves: Fourier versus Bayesian Periodicity Detection

Simulations predict that supermassive black hole binaries (SMBHBs) will exhibit periodic brightness variations that may exceed the stochastic variability intrinsic to active galactic nuclei (AGN). In this paper, we simulate SMBHBs with damped random walk (DRW) AGN variability and an added sinusoidal signal from the orbital motion, and test three methods—a generalized Lomb–Scargle periodogram (GLSP), a nested Bayesian sampler (NBS), and a weighted wavelet z-transform (or WWZ)—to determine which is best at recovering the periodicity. Our simulated light curves follow the properties of the Catalina Real-Time Transient Survey (or CRTS), Legacy Survey of Space and Time (LSST), and Zwicky Transient Facility (ZTF) to best inform current and future SMBHB searches. We map a broad range of parameter space and identify which DRW-only light curves best mimic periodicity and pass each method’s model selection. The NBS performs best at detecting periodicity and filtering out DRW-only light curves. Combined candidate selection with both the NBS and GLSP significantly reduces false-positive rates (FPRs) with marginal impact on true-positive rates (TPRs). With this joint model selection pipeline, we find the lowest FPRs in ZTF-like simulations and the highest detection rates in LSST-like simulations. Using a modified computation of the false-alarm probability with GLSP, we efficiently triage LSST AGN light curves (∼10 7 light curves in ∼10–30 hr) and achieve TPRs and FPRs of ∼40% and ∼0.5%, respectively.

Banaszak, Sebastian M. [Vanderbilt Univ., Nashvill↗

Bayesian chain graph models to characterize microbe-environment dynamics

Microbiome data require statistical models that can simultaneously decode microbes' reaction to the environment and interactions among microbes. While a multiresponse linear regression model seems like a straight-forward solution, we argue that treating it as a graphical model is problematic given that the regression coefficient matrix does not encode the conditional dependence structure between response and predictor nodes. This observation is especially important in biological settings when we have prior knowledge on the edges from specific experimental interventions that can only be properly encoded under a conditional dependence model. Here, we propose a chain graph model with two sets of nodes (predictors and responses) whose solution yields a graph with edges that indeed represent conditional dependence, thus agreeing with the experimenter's intuition on the average behavior of nodes under treatment. The solution to our model is sparse via the Bayesian linear regression (LASSO). In addition, we propose an adaptive extension so that different shrinkages can be applied to different edges to incorporate edge-specific prior knowledge. Our model is computationally inexpensive through an efficient Gibbs sampling algorithm and can account for binary, counting, and compositional responses via an appropriate hierarchical structure. We test the performance of our model in a variety of simulated datasets, thereby showing superior performance to state-of-the-art approaches. We further apply our model to human gut and soil microbial compositional datasets, and we highlight that CG-LASSO can estimate biologically meaningful network structures in the data.

compositional data↗

Data and code from: Multivariate bayesian regression model for predicting disposed ash composition at U.S. coal fired power stations

This dataset contains the code and data files needed for implementation of a Multivariate Bayesian Regression model, described in Jin et al. (2025), for the historical prediction of the chemical composition of disposed coal ash at U.S. coal fired power plants as a function of annualized coal purchase data. The integrated coal supply data file (CoalSupplyDataset.csv) represents a compilation of monthly fuel purchase records for the period 1973-2022 at major U.S. power stations. These records were obtained from the U.S. Energy Information Administration. The CSV file also contains, for each coal purchase record, the coal region of the mine as defined by the U.S. Geological Survey. Data entry errors and data gaps in the EIA records were corrected as described in Jin et al. This CSV file represents the integrated coal supply data after corrections were made. The model structure and fitting parameters are encoded in pickle file format (Bayesian.pkl). The model was developed with the coal supply data and coal ash composition data, apportioned according to the Stratified Shuffle Split for training and testing subsets. The model was built using Python and the PyMC library. Reference Publication: Jin, Z.; Huang, J.; Hower, J.C.; Hsu-Kim, H.(2025). Predictive Assessment of the Chemical Composition of Coal Ash in Reserve at U.S. Disposal Sites. Environmental Science & Technology.

Coal ash composition↗