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At least 541 records · Page 30

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↗

A Strong Gravitational Lens Is Worth a Thousand Dark Matter Halos: Inference on Small-scale Structure Using Sequential Methods

Strong gravitational lenses are a singular probe of the Universe’s small-scale structure—they are sensitive to the gravitational effects of low-mass (<10 10 M ⊙ ) halos even without a luminous counterpart. Recent strong-lensing analyses of dark matter structure rely on simulation-based inference (SBI). Modern SBI methods, which leverage neural networks as density estimators, have shown promise in extracting the halo-population signal. However, it is unclear whether the constraints from these models are limited by the methodology or the data. In this study, we introduce an accelerator-optimized simulation pipeline that can generate lens images with realistic subhalo populations in milliseconds. Leveraging this simulator, we identify the main limitation of our fiducial SBI analysis: training set size. We then adopt a sequential neural posterior estimation (SNPE) approach, allowing us to refine the training distribution to align with the observed data. Using only one-fifth as many mock Hubble Space Telescope images, SNPE matches the constraints on the low-mass halo population produced by our best nonsequential model. Our experiments suggest that an over 3 order-of-magnitude increase in training set size and GPU hours would be required to achieve an equivalent result without sequential methods. While the full potential of the existing lens sample remains to be explored, the notable improvement in constraining power enabled by our sequential approach highlights that current constraints are limited primarily by methodology and not the data itself. Moreover, our results emphasize the need to treat training set generation and model optimization as interconnected stages of any cosmological analysis using SBI.

79 ASTRONOMY AND ASTROPHYSICS↗

Computer Vision Pipeline for Image Analysis for Freeze‐Fracture Electron Microscopy: Rosette Cellulose Synthase Complexes Case

In materials science, plant biology, agriculture, and environmental research, the automated analysis of high-magnification, complex microscopy images, such as those generated by freeze-fracture electron microscopy (FF-TEM), remains a critical challenge that limits the scalability of data interpretation. We present a deep learning computer vision pipeline for high-throughput detection and morphological characterization analysis of cellulose synthase complexes (CSCs, or rosettes) in FF-TEM images. The pipeline integrates preprocessing, detection, human-in-the-loop verification, and semantic segmentation to quantify features such as rosette diameter and inter-lobe spacing. The approach was trained and tested on a curated dataset of high-resolution FF-TEM micrographs of Physcomitrium patens, expanded via strategic tiling and augmentation to over 650 images. We compare YOLOv8 and YOLOv9 architectures and demonstrate that YOLOv9 achieves superior performance in both localization accuracy (mAP50-95 = 0.854) and inference speed. The resulting distributions revealed biological variability consistent with prior manual studies, validating the approach for high-throughput applications. Our results show that the pipeline achieves human-expert level accuracy while dramatically reducing analysis time, enabling scalable, reproducible structural characterization of intramembrane protein complexes. The pipeline is broadly applicable to other domains requiring precise interpretation of complex microscopy data and establishes a foundation for future artificial intelligence (AI)-assisted workflows in biological imaging.

59 BASIC BIOLOGICAL SCIENCES↗

Infrasonic directivity of monopole, dipole and bipole ground-surface reflected sources

Infrasound (acoustic waves below 20 Hz) can be used to detect, locate and quantify activity in the atmosphere such as volcanic eruptions and anthropogenic explosions. Attempts to quantify volcanic eruption parameters such as exit velocity, plume height and mass flow rate using infrasound data depend strongly on assumptions of the acoustic source type. Infrasonic sources may produce omnidirectional or directional wavefields, while propagation effects, such as interaction with topography, can induce further wavefield directivity that is measured by field instrumentation. Limited sampling of these wavefields can hinder our ability to infer the underlying source, and thus our understanding of the eruption characteristics. Equivalent sources are often used to represent acoustic source mechanisms and resultant wavefields. In this study, we review equivalent acoustic sources as they pertain to infrasonic scale and wavelengths commonly encountered in very local (⁠<5 km range) geophysical field deployments. We highlight the equivalent infrasonic bipole source that can be induced by ground-reflection of an elevated monopole; we are not aware of any prior infrasound studies that use the bipole source concept. We use analytical and numerical methods to explore source directivity of monopole, dipole and bipole ground-reflected sources at infrasonic frequencies as well as the additional directivity complications introduced by interactions with topography. We illustrate that for typical volcano-infrasound wavelengths, increasing height above the ground as well as increasing source frequency leads to increased wavefield directivity. Numerical modelling using a simple omnidirectional monopole source embedded in topography further illustrates that both horizontal and vertical infrasound directionality can be induced by topography at the distance scales appropriate for local volcano infrasound monitoring. Information summarized in this analytical and numerical exploration of infrasound directivity may be used to help guide future volcano-infrasound field deployments intended to estimate source parameters or quantify wavefield directivity. Analytic solutions for simple whole-space or half-space atmospheres provide useful formulations for planning or initially analysing geophysical field-scale experimental data; however, especially at very local distances from the source (⁠<5 km), 3-D simulations are necessary to account for complex topography commonly encountered in volcano-infrasound applications.

Infrasound↗

Observable optimization for precision theory: machine learning energy correlators

The practice of collider physics typically involves the marginalization of multi-dimensional collider data to uni-dimensional observables relevant for some physics task. In many cases, such as classification or anomaly detection, the observable can be arbitrarily complicated, such as the output of a neural network. However, for precision measurements, the observable must correspond to something computable systematically beyond the level of current simulation tools. In this work, we demonstrate that precision-theory-compatible observable space exploration can be systematized by using neural simulation-based inference techniques from machine learning. We illustrate this approach by exploring the space of marginalizations of the energy 3-point correlator to optimize sensitivity to the top quark mass. We first learn the energy-weighted probability density from simulation, then search in the space of marginalizations for an optimal triangle shape. Although simulations and machine learning are used in the process of observable optimization, the output is an observable definition which can be then computed to high precision and compared directly to data without any memory of the computations which produced it. We find that the optimal marginalization is isosceles triangles on the sphere with a side ratio approximately $1 : 1 : \sqrt{2}$ (i.e. right triangles) within the set of marginalizations we consider.

Jets and Jet Substructure↗

Electron-impact excitation data for W 2+ in support of tungsten spectroscopy and re-deposition measurements for magnetically-confined plasmas

Abstract To better understand plasma wall interactions involving tungsten, accurate atomic structure and electron-impact driven collisional processes for near-neutral ion stages of tungsten are required. Complementing existing work on neutral and singly ionised tungsten, atomic structure and collisional calculations for W 2+ electron-impact excitation have been completed. These excitation calculations are an important component of S/XB coefficients for near-neutral charge states, which may be used to spectroscopically infer re-deposition of tungsten at the plasma-solid boundary of fusion relevant devices. With W 2+ in particular having emission lines that can be observed at ultraviolet (UV) wavelengths, while higher charge states of tungsten are unlikely to have lines possible to observe outside of the vacuum UV range. The atomic structure was generated using the General-purpose Relativistic Atomic Structure Package (GRASP 0 ), implementing the Multi-configuration Dirac Fock approach. This structure was the basis for a subsequent Dirac R -matrix electron-impact excitation calculation to provide Maxwellian averaged rate coefficients. A synthetic spectrum was generated from this data using a collisional-radiative model to predict the strongest W III spectral lines and these lines were compared to emission from the Compact Toroidal Hybrid (CTH) plasma device. Several of the strongest W III lines are observed in CTH and agree well with the modelled line wavelengths and intensities, a table of these lines is provided that could be observed in other devices.

McCann, M. (ORCID:0000000215321240)↗

MOOSE ProbML: Parallelizable Probabilistic Machine Learning and Uncertainty Quantification Capabilities

The Multiphysics Object Oriented Simulation Environment (MOOSE) is a widely used open- source finite element software for performing multiphysics multiscale simulations in a massively parallel fashion. Recently, the computational team at Idaho National Laboratory (INL) has implemented Probabilistic Machine Learning (ProbML) capabilities in MOOSE—in a parallelized fashion—and enable active learning with large-scale computational models for tasks such as surrogate model development, scale bridging, forward/inverse uncertainty quantification (UQ), Bayesian optimization, etc. This presentation summarizes these developments in MOOSE along with demonstrations on several real applications relevant to nuclear energy. At the fundamental level, samplers like Monte Carlo/Latin Hypercube, variance reduction, parallelized Markov Chain Monte Carlo (MCMC) support uncertainty propagation in both forward and inverse settings. These samplers can be integrated with the Gaussian processes (GP) suite in MOOSE, which offer several variants like scalar GPs, multi-output GPs, and deep GPs, to enable active learning. These GPs can be tuned using gradient-based optimization methods like Adam and its variants or gradient-free methods like the elliptical slice sampler (a variant of MCMC adept under Gaussian settings) for more complex covariance kernels or likelihoods whose gradient computations can be cumbersome. A variety of batch acquisition functions permit parallelized evaluation of the computational model and support different learning objectives with high efficiency like Bayesian inference, global surrogate development, optimization, etc. Furthermore, libtorch integration supports training, evaluation, and re-training of neural networks and other complex machine learning models in active learning settings. The impacts of these developments are shown on several real applications: (1) nuclear fuel inverse UQ and model inadequacy assessment using the Kennedy O’Hagan framework; (2) uncertainty aware surrogate modeling for additive manufacturing to predict field quantities; (3) nuclear reactor rare events analysis; and (4) complex fluid flow prediction using a global surrogate with quantified prediction uncertainty. Finally, the outlook of MOOSE ProbML is discussed for both outer-loop and inner-loop computations in the broad view to accelerate fuels and materials qualification, address gaps in knowledge and data, and assess new reactor/fuel systems.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

The SRG/eROSITA All-Sky Survey: Constraints on the structure growth from cluster number counts

Recent advancements in methods used in wide-area surveys have demonstrated the reliability of the number density of galaxy clusters as a viable tool for precision cosmology. Beyond testing the current cosmological paradigm, cluster number counts can also be used to investigate the discrepancies currently affecting cosmological measurements. In particular, cosmological studies based on cosmic shear and other large-scale structure probes routinely find a value for the amplitude of the fluctuations in the universe S​ 8 = σ 8 (Ω m /0.3) 0.5 smaller than the one inferred from the primary cosmic microwave background. In this work, we investigate this tension by measuring structure evolution across cosmic time as probed by the number counts of massive halos with the first SRG/eROSITA All-Sky Survey cluster catalog in the western Galactic hemisphere, complemented with the overlapping Dark Energy Survey Year-3, Kilo-Degree Survey, and Hyper Suprime-Cam data for weak lensing mass calibration, by implementing two different parameterizations and a model-agnostic method. In the first model, we measured the cosmic linear growth index as γ = 1.19 ± 0.21, which is in tension with the standard value of γ = 0.55 but in good statistical agreement with other large-scale structure probes. The second model is a phenomenological scenario in which we rescale the linear matter power spectrum at low redshift to investigate a potential reduction of structure formation, and it provided similar results. Finally, in a third strategy, we considered a standard ΛCDM cosmology, but we separated the cluster catalog into five redshift bins, measuring the cosmological parameters in each and inferring the evolution of the structure formation, finding hints of a reduction. Interestingly, the S ​8 value inferred from the number counts of the cluster eRASS1 when we add a degree of freedom to the matter power spectrum recovers the value inferred by cosmic shear studies. The observed reduction in the growth rate or systematic uncertainties associated with various measurements may account for the discrepancy in the S 8 ​ values suggested between cosmic shear probes and eROSITA cluster number counts and Planck CMB measurements.

cosmological parameters↗

Empirical Comparison of Machine Learning Approaches for Black-Box Modeling of Power Conversion System Dynamics

Inverter-based resources are key components in modern power systems, but accurately modeling their complex behavior can be challenging. Standard, generic converter models often oversimplify inverter dynamics, leading to significant errors in predicting performance. In this work, we compare several data-driven machine learning (ML) approaches for inverter modeling, performing experiments on power conversion systems, systematically varying input conditions, and recording the resulting voltages and currents. The ML models were then trained on this measured data to capture the inverter's dynamic response and to predict the inverter's output current. A performance comparison between the four ML models under study is conducted, laying the foundation for future work on hardware implementation for real-time inference.

30 DIRECT ENERGY CONVERSION↗

Impact of Limited Degree of Freedom Drag Coefficients on a Floating Offshore Wind Turbine Simulation

The worldwide effort to design and commission floating offshore wind turbines (FOWT) is motivating the need for reliable numerical models that adequately represent their physical behavior under realistic sea states. However, properly representing the hydrodynamic quadratic damping for FOWT remains uncertain, because of its dependency on the choice of drag coefficients (dimensionless or not). It is hypothesized that the limited degree of freedom (DoF) drag coefficient formulation that uses only translational drag coefficients causes mischaracterization of the rotational DoF drag, leading to underestimation of FOWT global loads, such as tower base fore-aft shear. To address these hydrodynamic modeling uncertainties, different quadratic drag models implemented in the open-source mid-fidelity simulation tool, OpenFAST, were investigated and compared with the experimental data from the Offshore Code Comparison Collaboration, Continued, with Correlation (OC5) project. The tower base fore-aft shear and up-wave mooring line tension were compared under an irregular wave loading condition to demonstrate the effects of the different damping models. Two types of hydrodynamic quadratic drag formulations were considered: (1) member-based dimensionless drag coefficients applied only at the translational DoF (namely limited-DoF drag model) and (2) quadratic drag matrix model (in dimensional form). Based on the results, the former consistently underestimated the 95th percentile peak loads and spectral responses when compared to the OC5 experimental data. In contrast, the drag matrix models reduced errors in estimates of the tower base shear peak load by 7–10% compared to the limited-DoF drag model. The underestimation in the tower base fore-aft shear was thus inferred be related to mischaracterization of the rotational pitch drag and the heave motion/drag by the limited-DoF model.

17 WIND ENERGY↗

A resolution independent neural operator

The Deep operator network (DeepONet) is a powerful yet simple neural operator architecture that utilizes two deep neural networks to learn mappings between infinite-dimensional function spaces. This architecture is highly flexible, allowing the evaluation of the solution field at any location within the desired domain. However, it imposes a strict constraint on the input space, requiring all input functions to be discretized at the same locations; this limits its practical applications. Here, in this work, we introduce a general framework for operator learning from input–output data with arbitrary number and locations of sensors. This begins by introducing a resolution-independent DeepONet (RI-DeepONet), enabling it to handle input functions that are arbitrarily, but sufficiently finely, discretized. To this end, we propose two dictionary learning algorithms to adaptively learn a set of appropriate continuous basis functions, parameterized as implicit neural representations (INRs), from correlated signals defined on arbitrary point cloud data. These basis functions are then used to project arbitrary input function data as a point cloud onto an embedding space (i.e., a vector space of finite dimensions) with dimensionality equal to the dictionary size, which can be directly used by DeepONet without any architectural changes. In particular, we utilize sinusoidal representation networks (SIRENs) as trainable INR basis functions. The introduced dictionary learning algorithms are then used in a similar way to learn an appropriate dictionary of basis functions for the output function data, which defines a new neural operator architecture referred to as the R esolution I ndependent N eural O perator (RINO). In the RINO, the operator learning task simplifies to learning a mapping from the coefficients of input basis functions to the coefficients of output basis functions. We demonstrate the robustness and applicability of RINO in handling arbitrarily (but sufficiently richly) sampled input and output functions during both training and inference through several numerical examples.

Deep operator network (DeepONet)↗

PaleoSTeHM v1.0: a modern, scalable spatiotemporal hierarchical modeling framework for paleo-environmental data

Abstract. Geological records of past environmental change provide crucial insights into long-term climate variability, trends, non-stationarity, and nonlinear feedback mechanisms. However, reconstructing spatiotemporal fields from these records is statistically challenging due to their sparse, indirect, and noisy nature. Here, we present PaleoSTeHM, a scalable and modern framework for spatiotemporal hierarchical modeling of paleo-environmental data. This framework enables the implementation of flexible statistical models that rigorously quantify spatial and temporal variability from geological data while clearly distinguishing measurement and inferential uncertainty from process variability. We illustrate its application by reconstructing temporal and spatiotemporal paleo-sea-level changes across multiple locations. Using various modeling and analysis choices, PaleoSTeHM demonstrates the impact of different methods on inference results and computational efficiency. Our results highlight the critical role of model selection in addressing specific paleo-environmental questions, showcasing the PaleoSTeHM framework's potential to enhance the robustness and transparency of paleo-environmental reconstructions.

58 GEOSCIENCES↗

Exploring Resonance Structures in the Partial-Wave Analysis of ¿p0 Photoproduction at GlueX

This thesis studies what happens when a photon (¿) collides with a proton (p) and produces a neutral omega (¿) and pion (p0) pair, with a recoiling proton (p'), expressed as ¿p ¿ ¿p0p'. We study this and other reactions to better understand the strong nuclear force; one of the four fundamental forces that govern all the physics of the universe. This force is specifically responsible for the binding and decay of subatomic particles, such as the ones here. While we understand the ¿ and p0, what we are actually interested in is a short-lived unknown particle X that decays via X ¿ ¿p0. There are a multitude of possible particles X can be, and so our focus in this work is to find out what X is by determining its properties from the particles we measure. We do this via an intricate analysis procedure known as “partial-wave analysis”. By analogy, one can think of our particle detector as a buoy, and the particles we want to analyze (X) as pebbles hitting a pond. The waves created by the pebble will move our buoy, giving us information about the pebble that produced the wave. However, when multiple pebbles hit our pond, the waves overlap and interfere with each other. Our buoy only can measure the complicated interfering result of all the waves. To disentangle this, our partial-wave analysis works by modeling this interference pattern so that we may infer the properties of the pebbles (particles) we produced. In this thesis, we review the relevant experimental history in photoproduction and related production mechanisms, as well as the theoretical foundations that motivate our measurement. We describe the methods used to collect our data at the GlueX experiment stationed at the Jefferson Lab accelerator facility in Newport News, Virginia. We then detail the selections we apply to ensure our events are almost exclusively ¿p ¿ ¿p0p'. We cover the intensity model, how we verify its capabilities, and finally present our results together with systematic studies. Our primary result is the detection of a b1(1235) meson interfering with a wide JPC = 1-- vector state, measured via a mass-independent partial-wave analysis. It provides precise experimental results that can be used as input for theoretical models of the reaction, yielding conclusions about the procedures responsible for how our universe behaves at its most basic level.

Scheuer, Kevin [College of William and Mary, Willi↗

Applying simulation-based inference to spectral and spatial information from the Galactic Center gamma-ray excess

Abstract The two most favored explanations of theFermiGalactic Center gamma-ray excess (GCE) are millisecond pulsars and self annihilation of the smooth dark matter halo of the galaxy. In order to distinguish between these possibilities, we would like to optimally use all information in the available data, including photon direction and energy information.To date, analyses of the GCE have generally treated directional and energy information separately, or have ignored one or the other completely.Here, we develop a method for analyzing the GCE that relies on simulation-basedinference with neural posterior models to jointly analyze photon directional and spectral information while correctly accounting for the spatial and energy resolution of the telescope, here assumed to be theFermiLarge Area Telescope (LAT).Our results also have implications for analyses of the diffuse gamma-ray background, which we discuss.

Astronomy & Astrophysics↗

Visible core spectroscopy at Wendelstein 7-X

This paper presents an overview of recent hardware extensions and data analysis developments to the Wendelstein 7-X visible core spectroscopy systems. These include upgrades to prepare the in-vessel components for long-pulse operation, nine additional spectrometers, a new line of sight array for passive spectroscopy, and a coherence imaging charge exchange spectroscopy diagnostic. Progress in data analysis includes ion temperatures and densities from multiple impurity species, a statistical comparison with x-ray crystal spectrometer measurements, neutral density measurements from thermal passive Balmer-alpha emission, and a Bayesian analysis of active hydrogen emission, which is able to infer electron density and main ion temperature profiles.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Nonparametric extensions of nuclear equations of state: Probing the breakdown scale of relativistic mean-field theory

Phenomenological calculations of the properties of dense matter, such as relativistic mean-field theories, represent a pathway to predicting the microscopic and macroscopic properties of neutron stars. However, such theories do not generically have well-controlled uncertainties and may break down within neutron stars. To faithfully represent the uncertainty in this breakdown scale, we develop a hybrid representation of the dense-matter equation of state, which assumes the form of a relativistic mean-field theory at low densities, while remaining agnostic to any nuclear theory at high densities. To achieve this, we use a nonparametric equation of state model to incorporate the correlations of the underlying relativistic mean-field theory equation of state at low pressures and transition to more flexible correlations above some chosen pressure scale. We perform astrophysical inference under various choices of the transition pressure between the theory-informed and theory-agnostic models. Here, we further study whether the chosen relativistic mean-field theory breaks down above some particular pressure and find no such evidence. Using simulated data for future astrophysical observations at about two-to-three times the precision of current constraints, we show that our method can identify the breakdown pressure associated with a potential strong phase transition.

Equations of state of nuclear matter↗

CHMMPY: A python package for constrained Hidden Markov Models

SAND2025-11909O chmmpy software analyzes multivariate timeseries data to detect patterns. It uses a Hidden Markov Model (HMM) and application-specific constraints that reflect known relationships among hidden states to accomplish this. The chmmpy software provides a generic framework for expressing application-specific constraints and supporting constrained HMM inference using optimization solvers. chmmpy is available on GitHub. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Hart, William↗

An integrated integral projection model ( IPM 2 ) to disentangle size‐structured harvest and natural mortality

Abstract Body size is one of the most important traits governing individual‐level demographic rates and modulating population‐level processes. Multiple size‐dependent demographic rates can simultaneously change population structure, so distinguishing their individual contributions to overall population dynamics remains a challenge. Disentangling size‐dependent harvest rates from other demographic rates is critical for assessing the impact of removal on populations of invasive species. Inference about invasive populations can be difficult, however, as observations are often collected opportunistically as part of removal programs, rather than experimentally designed. Yet accurate inference is essential for understanding the feasibility of population suppression and optimising management decisions. We develop an integrated integral projection model (IPM 2 ) that leverages the strengths of the integrated population model and integral projection model to enable inference about complex, size‐structured demographic rates from imperfect observations. We apply the IPM 2 in the context of invasive European green crab ( Carcinus maenas ), a species for which individual body size strongly regulates both the observation‐generating process and latent, population dynamics. The IPM 2 facilitates the distinct estimation of green crab size‐structured harvest and natural mortality rates, parameters for which no explicit data is collected and that are unidentifiable in component datasets of the integrated population model. The model represents how the green crab population changes over time, providing the first estimates of size‐structured abundance of this high‐priority species. By forecasting the stable size distribution and equilibrium population size under varying removal efforts, we demonstrate that extremely high levels of removal effort can reduce the equilibrium green crab population size. Yet these high mortality rates also shift the stable size distribution and increase the equilibrium abundance of smaller crabs, since size‐selective removal alters intraspecific interactions. The ecological outcome of this shift in size structure will be variable, as green crab size modulates only some of its interactions with other species. These results highlight the value of the IPM 2 framework for inferring complex population dynamics with information needs that outpace information in individual observational datasets, providing a path forward for accurate assessment of conservation programs.

Keller, Abigail G. [Department of Environment Scie↗