Robust Inference for Physical Parameters with Bayesian Model Calibration.
Abstract not provided.
Rumsey, Kelin↗
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Inference finds consistency between a neutrino flavor evolution model and Earth-based solar neutrino measurements
We continue examining statistical data assimilation (SDA), an inference methodology, to infer solutions to neutrino flavor evolution, for the first time using real - rather than simulated - data. The model represents neutrinos streaming from the Sun's center and undergoing a Mikheyev-Smirnov-Wolfenstein (MSW) resonance in flavor space, due to the radially-varying electron number density. The model neutrino energies are chosen to correspond to experimental bins in the Sudbury Neutrino Observatory (SNO) and Borexino experiments, which measure electron-flavor survival probability at Earth. In conclusion, the procedure successfully finds consistency between the observed fluxes and the model, if the MSW resonance - that is, flavor evolution due to solar electrons - is included in the dynamical equations representing the model.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Large-scale Gravitational Lens Modeling with Bayesian Neural Networks for Accurate and Precise Inference of the Hubble Constant
We investigate the use of approximate Bayesian neural networks (BNNs) in modeling hundreds of time delay gravitational lenses for Hubble constant (H 0 ) determination. Here, our BNN was trained on synthetic Hubble Space Telescope quality images of strongly lensed active galactic nuclei with lens galaxy light included. The BNN can accurately characterize the posterior probability density functions (PDFs) of model parameters governing the elliptical power-law mass profile in an external shear field. We then propagate the BNN-inferred posterior PDFs into an ensemble H 0 inference, using simulated time delay measurements from a plausible dedicated monitoring campaign. Assuming well-measured time delays and a reasonable set of priors on the environment of the lens, we achieve a median precision of 9.3% per lens in the inferred H 0 . A simple combination of a set of 200 test lenses results in a precision of 0.5 km s –1 Mpc –1 (0.7%), with no detectable bias in this H 0 recovery test. The computation time for the entire pipeline—including the generation of the training set, BNN training and H0 inference—translates to 9 minutes per lens on average for 200 lenses and converges to 6 minutes per lens as the sample size is increased. Being fully automated and efficient, our pipeline is a promising tool for exploring ensemble-level systematics in lens modeling for H 0 inference.
79 ASTRONOMY AND ASTROPHYSICS↗
Combined selection of the dynamic model and modeling error in nonlinear aeroelastic systems using Bayesian Inference
Here, we report a Bayesian framework for concurrent selection of physics-based models and (modeling) error models. We investigate the use of colored noise to capture the mismatch between the predictions of calibrated models and observational data that cannot be explained by measurement error alone within the context of Bayesian estimation for stochastic ordinary differential equations. Proposed models are characterized by the average data-fit, a measure of how well a model fits the measurements, and the model complexity measured using the Kullback–Leibler divergence. The use of a more complex error models increases the average data-fit but also increases the complexity of the combined model, possibly over-fitting the data. Bayesian model selection is used to find the optimal physical model as well as the optimal error model. The optimal model is defined using the evidence, where the average data-fit is balanced by the complexity of the model. The effect of colored noise process is illustrated using a nonlinear aeroelastic oscillator representing a rigid NACA0012 airfoil undergoing limit cycle oscillations due to complex fluid–structure interactions. Several quasi-steady and unsteady aerodynamic models are proposed with colored noise or white noise for the model error. The use of colored noise improves the predictive capabilities of simpler models.
42 ENGINEERING↗
End-to-end deep learning pipeline for real-time Bragg peak segmentation: from training to large-scale deployment
X-ray crystallography reconstruction, which transforms discrete X-ray diffraction patterns into three-dimensional molecular structures, relies critically on accurate Bragg peak finding for structure determination. As X-ray free electron laser (XFEL) facilities advance toward MHz data rates (1 million images per second), traditional peak finding algorithms that require manual parameter tuning or exhaustive grid searches across multiple experiments become increasingly impractical. While deep learning approaches offer promising solutions, their deployment in high-throughput environments presents significant challenges in automated dataset labeling, model scalability, edge deployment efficiency, and distributed inference capabilities. We present an end-to-end deep learning pipeline with three key components: (1) a data engine that combines traditional algorithms with our peak matching algorithm to generate high-quality training data at scale, (2) a modular architecture that scales from a few million to hundreds of million parameters, enabling us to train large expert-level models offline while deploying smaller, distilled models at the edge, and (3) a decoupled producer-consumer architecture that separates specialized data source layer from model inference, enabling flexible deployment across diverse computing environments. Using this integrated approach, our pipeline achieves accuracy comparable to traditional methods tuned by human experts while eliminating the need for experiment-specific parameter tuning. Although current throughput requires optimization for MHz facilities, our system's scalable architecture and demonstrated model compression capabilities provide a foundation for future high-throughput XFEL deployments.
Wang, Cong↗
Better practices for inferring ecosystem water use strategy from eddy covariance data
Eddy covariance data are critical for inferring ecosystem water use strategies. Yet, such inferences are sensitive to a range of assumptions applied across studies, hindering our understanding of water use strategies within and across eddy covariance sites. A recent analysis across 151 FLUXNET2015 and AmeriFlux-FLUXNET datasets found that poor model performance was the key driver of non-robust inferences of ecosystem water use strategies. Here, we leverage this previous analysis to (i) identify the specific assumptions that improve inference model performance across most sites, (ii) explain the mechanisms behind the performance improvements, and (iii) check whether better performance improves water use inference. We find that the common practice of fitting a model to canopy conductance (G c ) derived from the evapotranspiration (ET) observations, rather than to observed ET itself, artificially amplifies data errors and degrades the model performance. Next, accounting for vegetation dynamics by applying a growing season filter or incorporating satellite LAI data improves performance, but the former practice may remove soil water stress periods. Lastly, using the leaf-to-air vapor pressure deficit (VPD l ) derived from ET observations as a model input may artificially inflate performance. Based on these results, we recommend selecting observed ET (rather than derived G c ) as the response variable, carefully accounting for vegetation dynamics, and avoiding derived VPD l as a model input; these best practices improve model performance by c. 20% and robustness by c. 80% across all eddy covariance sites. Nevertheless, the performance improvements do not always correspond to more robust inference of water use strategies, as model parameter selection and surface energy budget closure corrections still strongly influence the ecosystem water use parameter estimation in a site-specific manner.
AmeriFlux↗
Assessing and benchmarking the fidelity of posterior inference methods for astrophysics data analysis
In this era of large and complex astronomical survey data, interpreting, validating, and comparing inference techniques becomes increasingly difficult. This is particularly critical for emerging inference methods like Simulation-Based Inference (SBI), which offer significant speedup potential and posterior modeling flexibility, especially when deep learning is incorporated. We present a study to assess and compare the performance and uncertainty prediction capability of Bayesian inference algorithms – from traditional MCMC sampling of analytic functions to deep learning-enabled SBI. We focus on testing the capacity of hierarchical inference modeling in those scenarios. Before we extend this study to cosmology, we first use astrophysical simulation data to ensure interpretability. We demonstrate a probabilistic programming implementation of hierarchical and non-hierarchical Bayesian inference using simulations derived from the DeepBench software library, a benchmarking tool developed by our group that generates simple and controllable astrophysical objects from first principles. This study will enable astronomers and physicists to harness the inference potential of these methods with confidence.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Kinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of β-glucosidase function in Cellvibrio japonicus
Understanding the complex growth and metabolic dynamics in microorganisms requires advanced kinetic models containing both metabolic reactions and enzymatic regulation to predict phenotypic behaviors under different conditions and perturbations. Most current kinetic models lack gene expression dynamics and are separately calibrated to distinct media, which consequently makes them unable to account for genetic perturbations or multiple substrates. This challenge limits our ability to gain a comprehensive understanding of microbial processes towards advanced metabolic optimizations that are desired for many biotechnology applications. Here, we present an integrated computational and experimental approach for the development and optimization of mechanistic kinetic models for microbial growth and metabolic and enzymatic dynamics. Our approach integrates growth dynamics, gene expression, protein secretion, and gene-deletion phenotypes. We applied this methodology to build a dynamic model of the growth kinetics in batch culture of the bacterium Cellvibrio japonicus grown using either cellobiose or glucose media. The model parameters were inferred from an experimental data set using an evolutionary computation method. The resulting model was able to explain the growth dynamics of C. japonicus using either cellobiose or glucose media and was also able to accurately predict the metabolite concentrations in the wild-type strain as well as in β-glucosidase gene deletion mutant strains. We validated the model by correctly predicting the non-diauxic growth and metabolite consumptions of the wild-type strain in a mixed medium containing both cellobiose and glucose, made further predictions of mutant strains growth phenotypes when using cellobiose and glucose media, and demonstrated the utility of the model for designing industrially-useful strains. Importantly, the model is able to explain the role of the different β-glucosidases and their behavior under genetic perturbations. Here, this integrated approach can be extended to other metabolic pathways to produce mechanistic models for the comprehensive understanding of enzymatic functions in multiple substrates.
59 BASIC BIOLOGICAL SCIENCES↗
Kernel learning backward SDE filter for data assimilation
In this paper, we develop a kernel learning backward SDE filter method to estimate the state of a stochastic dynamical system based on its partial noisy observations. A system of forward backward stochastic differential equations is used to propagate the state of the target dynamical model, and Bayesian inference is applied to incorporate the observational information. Further, to characterize the dynamical model in the entire state space, we introduce a kernel learning method to learn a continuous global approximation for the conditional probability density function of the target state by using discrete approximated density values as training data. Numerical experiments demonstrate that the kernel learning backward SDE is highly effective.
97 MATHEMATICS AND COMPUTING↗
Estimating redshift distributions using hierarchical logistic Gaussian processes
ABSTRACT This work uses hierarchical logistic Gaussian processes to infer true redshift distributions of samples of galaxies, through their cross-correlations with spatially overlapping spectroscopic samples. We demonstrate that this method can accurately estimate these redshift distributions in a fully Bayesian manner jointly with galaxy-dark matter bias models. We forecast how systematic biases in the redshift-dependent galaxy-dark matter bias model affect redshift inference. Using published galaxy-dark matter bias measurements from the Illustris simulation, we compare these systematic biases with the statistical error budget from a forecasted weak gravitational lensing measurement. If the redshift-dependent galaxy-dark matter bias model is mis-specified, redshift inference can be biased. This can propagate into relative biases in the weak lensing convergence power spectrum on the 10–30 per cent level. We, therefore, showcase a methodology to detect these sources of error using Bayesian model selection techniques. Furthermore, we discuss the improvements that can be gained from incorporating prior information from Bayesian template fitting into the model, both in redshift prediction accuracy and in the detection of systematic modelling biases.
79 ASTRONOMY AND ASTROPHYSICS↗
A hierarchical Bayesian model for background variation in radiation source localization
In this paper, we apply a new model to account for varying background radiation in radiological source localization. We present a hierarchical Bayesian model that simultaneously infers background and source location parameters without requiring separate estimation of the background radiation at each detector location. We employ a simplified photon transport model to reduce the computational expense of Bayesian model calibration. Furthermore, we demonstrate the model accuracy by localizing a cesium-137 source in a simulated city block, and we analyze experimental field measurements with varying background. In both cases, the model provides sufficient fidelity that we can locate the source while simultaneously estimating background radiation.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
An information-matching approach to optimal experimental design and active learning
The efficacy of mathematical models heavily depends on the quality of the training data, yet collecting sufficient data is often expensive and challenging. Many modeling applications require inferring parameters only as a means to predict other quantities of interest (QoI). Because models often contain many unidentifiable (sloppy) parameters, QoIs often depend on a relatively small number of parameter combinations. Therefore, we introduce an information-matching criterion based on the Fisher information matrix to select the most informative training data from a candidate pool. This method ensures that the selected data contain sufficient information to learn only those parameters that are needed to constrain downstream QoIs. It is formulated as a convex optimization problem, making it scalable to large models and datasets. Here, we demonstrate the effectiveness of this approach across various modeling problems in diverse scientific fields, including power systems and underwater acoustics. Finally, we use information-matching as a query function within an active learning (AL) loop for materials science applications. In all these applications, we find that a relatively small set of optimal training data can provide the necessary information for achieving precise predictions. These results are encouraging for diverse future applications, particularly AL in large machine-learning models.
Materials science↗
FPGA Architectures for Distributed ML Systems for Real-time Beam Loss De-blending
The Accelerator Real-time Edge AI for Distributed Systems (READS) project’s goal is to create a Artificial Intelligence (AI) system for real-time beam loss de-blending within the accelerator enclosure, which houses two accelerators: the Main Injector (MI) and the Recycler Ring (RR). In periods of joint operation, when both machines contain high intensity beam, radioactive beam losses from MI and RR overlap on the enclosure’s beam loss monitoring Beam Loss Monitor (BLM) system, making it difficult to attribute those losses to a single machine. Incorrect diagnoses result in unnecessary downtime that incurs both financialand experimental cost. The ML system will automatically disentangle each machine’s contributions to those measured losses, while not disrupting the existing operations-critical functions of the BLM system. This paper will focus on the evolution of the architectures, which provided the high-frequency, low-latency collection of synchronized data streams to make real-time inferences. The ML models, used for learning both local and global machine signatures and producing high quality inferences based on raw BLM loss measurements, will only be discussed at a high-level.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Joint estimation of biogeochemical model parameters from multiple experiments: A bayesian approach applied to mercury methylation
Here, to characterize complex biogeochemical systems, results from multiple experiments, where each targets a specific subprocess, are commonly combined. The resulting datasets are interpreted through the calibration of biogeochemical models for process inference and predictions. Commonly used calibration approaches of fitting datasets from individual experiments to subprocess models one at a time is prone to missing information shared between datasets and incomplete uncertainty propagation. We propose a Bayesian joint-fitting scheme addressing the above-mentioned concerns by jointly fitting all the available datasets, thus calibrating the entire biogeochemical model in one go using Markov Chain Monte Carlo (MCMC). The identification of null spaces in the parameter distributions from MCMC guided the simplification of certain subprocess models. For example, fast kinetic sorption was replaced by equilibrium sorption, and Monod demethylation was replaced by first-order demethylation. Joint fitting of datasets resulted in complete uncertainty propagation with parameter estimates informed by all available data.
54 ENVIRONMENTAL SCIENCES↗
Sequential Inference of Hospitalization Electronic Health Records Using Probabilistic Models
In the dynamic hospital setting, decision support can be a valuable tool for improving patient outcomes. Data-driven inference of future outcomes is challenging in this dynamic setting, where long sequences such as laboratory tests and medications are updated frequently. This is due in part to heterogeneity of data types and mixed-sequence types contained in variable length sequences. In this work we design a probabilistic unsupervised model for multiple arbitrary-length sequences contained in hospitalization Electronic Health Record (EHR) data. The model uses a latent variable structure and captures complex relationships between medications, diagnoses, laboratory tests, neurological assessments, and medications. It can be trained on original data, without requiring any lossy transformations or time binning. Inference algorithms are derived that use partial data to infer properties of the complete sequences, including their length and presence of specific values. We train this model on data from subjects receiving medical care in the Kaiser Permanente Northern California integrated healthcare delivery system. The results are evaluated against held-out data for predicting the length of sequences and presence of Intensive Care Unit (ICU) in hospitalization bed sequences. Our method outperforms a baseline approach, showing that in these experiments the trained model captures information in the sequences that is informative of their future values.
97 MATHEMATICS AND COMPUTING↗
Advancing Diagnostic Model Evaluation to Better Understand Water Shortage Mechanisms in Institutionally Complex River Basins
Abstract Water resources systems models enable valuable inferences on consequential system stressors by representing both the geophysical processes determining the movement of water and the human elements distributing it to its various competing uses. This study contributes a diagnostic evaluation framework that pairs exploratory modeling with global sensitivity analysis to enhance our ability to make inferences on water scarcity vulnerabilities in institutionally complex river basins. Diagnostic evaluation of models representing institutionally complex river basins with many stakeholders poses significant challenges. First, it needs to exploit a large and diverse suite of simulations to capture important human‐natural system interactions as well as institutionally aware behavioral mechanisms. Second, it needs to have performance metrics that are consequential and draw on decision‐relevant model outputs that adequately capture the multisector concerns that emerge from diverse basin stakeholders. We demonstrate the proposed model diagnostic framework by evaluating how potential interactions between changing hydrologic conditions and human demands influence the frequencies and durations of water shortages of varying magnitudes experienced by hundreds of users in a subbasin of the Colorado River. We show that the dominant factors shaping these effects vary both across users and, for an individual user, across percentiles of shortage magnitude. These differences hold even for users sharing diversion locations, demand levels or water right seniority. Our findings underline the importance of detailed institutional representation for such basins, as institutions strongly shape how dominant factors of stakeholder vulnerabilities propagate through the complex network of users.
Hadjimichael, Antonia↗
Embedded Model Error Representation for Bayesian Model Calibration
Model error estimation remains one of the key challenges in uncertainty quantification and predictive science. For computational models of complex physical systems, model error, also known as structural error or model inadequacy,is often the largest contributor to the overall predictive uncertainty. This work builds on a recently developed framework of embedded, internal model correction, in order to represent and quantify structural errors, together with model parameters, within a Bayesian inference context. We focus specifically on a Polynomial Chaos representation with additive modification of existing model parameters, enabling a non-intrusive procedure for efficient approximate likelihood construction, model error estimation, and disambiguation of model and data errors' contributions to predictive uncertainty. As a result, the framework is demonstrated on several synthetic examples, as well as on a chemical ignition problem
97 MATHEMATICS AND COMPUTING↗
Embedded Model Error Representation for Bayesian Model Calibration
Model error estimation remains one of the key challenges in uncertainty quantification and predictive science. For computational models of complex physical systems, model error, also known as structural error or model inadequacy, is often the largest contributor to the overall predictive uncertainty. This work builds on a recently developed framework of embedded, internal model correction, in order to represent and quantify structural errors, together with model parameters,within a Bayesian inference context. We focus specifically on a Polynomial Chaos representation with additive modification of existing model parameters, enabling a non-intrusive procedure for efficient approximate likelihood construction, model error estimation, and disambiguation of model and data errors’ contributions to predictive uncertainty. The framework is demonstrated on several synthetic examples, as well as on a chemical ignition problem.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗