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A robust approach to Gaussian process implementation

Abstract. Gaussian process (GP) regression is a flexible modeling technique used to predict outputs and to capture uncertainty in the predictions. However, the GP regression process becomes computationally intensive when the training spatial dataset has a large number of observations. To address this challenge, we introduce a scalable GP algorithm, termed MuyGPs, which incorporates nearest-neighbor and leave-one-out cross-validation during training. This approach enables the evaluation of large spatial datasets with state-of-the-art accuracy and speed in certain spatial problems. Despite these advantages, conventional quadratic loss functions used in the MuyGPs optimization, such as root mean squared error (RMSE), are highly influenced by outliers. We explore the behavior of MuyGPs in cases involving outlying observations and, subsequently, develop a robust approach to handle and mitigate their impact. Specifically, we introduce a novel leave-one-out loss function based on the pseudo-Huber function (LOOPH) that effectively accounts for outliers in large spatial datasets within the MuyGPs framework. Our simulation study shows that the LOOPH loss method maintains accuracy despite outlying observations, establishing MuyGPs as a powerful tool for mitigating unusual observation impacts in the large data regime. In the analysis of US ozone data, MuyGPs provides accurate predictions and uncertainty quantification, demonstrating its utility in managing data anomalies. Through these efforts, we advance the understanding of GP regression in spatial contexts.

Mukangango, Juliette↗

Poisson Log-Normal Process for Count Data Prediction

Modeling count data is important in physics and other scientific disciplines, where measurements often involve discrete, non-negative quantities such as photon or neutrino detection events. Traditional parametric approaches can be trained to generate integer-count predictions but may struggle with capturing complex, non-linear dependencies often observed in the data. Gaussian process (GP) regression provides a robust non-parametric alternative to modeling continuous data; however, it cannot generate integer outputs. We propose the Poisson Log-Normal (PoLoN) process, a framework that employs GP to model Poisson log-rates. As in GP regression, our approach relies on the correlations between data points captured via GP kernel structure rather than explicit functional parameterizations. We demonstrate that the PoLoN predictive distribution is Poisson-LogNormal and provide an algorithm for optimizing kernel hyperparameters. Furthermore, we adapt the PoLoN approach to the problem of detecting weak localized signals superimposed on a smoothly varying background - a task of considerable interest in many areas of science and engineering. Our framework allows us to predict the strength, location and width of the detected signals. We evaluate PoLoN's performance using both synthetic and real-world datasets, including the open dataset from CERN which was used to detect the Higgs boson at the Large Hadron Collider. Our results indicate that the PoLoN process can be used as a non-parametric alternative for analyzing, predicting, and extracting signals from integer-valued data.

Saha, Anushka [Rutgers U., Piscataway]↗

Simulation driven adaptive sampling for neutron-diffraction based strain mapping of additively manufactured parts

Neutron diffraction based strain mapping is a useful technique for measuring residual strains in additively manufactured (AM) metal parts. The measurement is traditionally done by scanning the sample in a point-wise raster pattern to extract the strain at each position. Since the overall scan can span several hours, adaptive sampling approaches using Bayesian optimization based on Gaussian process (BO-GP) regression have been introduced—demonstrating that even with a fraction of the typically made measurements the dominant strain patterns in the sample can be reconstructed. However, the parameters of the BO-GP algorithm have to be carefully chosen for best performance, and the movement time between arbitrary points can offset the time savings from a reduced number of measurement locations. In this paper, we propose algorithms to refine the BO-GP based methods by using simulations of strain patterns in AM parts based on the materials and the process used to print them. We demonstrate that the simulated strain patterns can be used to help choose better parameters for the BO-GP based framework—leading to low reconstruction error for the final strain pattern. Furthermore, we show that the strain mapping experiment can be initialized with a sampling pattern learnt from the simulation data and ordered to reduce movement time, dramatically enabling reduction in the overall time required to run the baseline BO-GP method.

Gaussian process regression↗

Examples of Mission-driven Data Science from Jefferson Lab and ACES

This presentation details mission-driven data science initiatives at Jefferson Lab and the Joint Institute for Advanced Computing on Environmental Studies (ACES). JLab, a U.S. Department of Energy Office of Science national laboratory, operates the Continuous Electron Beam Accelerator Facility (CEBAF), and is the lead institute for the new High Performance Data Facility (HPDF) Hub. The Joint Institute for ACES brings together interdisciplinary teams in health informatics, climate modeling, computer science, and physics to address environmental challenges, including flood modeling. The Hampton Roads region, particularly Norfolk and Virginia Beach, faces increasing flood risks, motivating the need for rapid, reliable, and risk-aware decision support. ACES’s flooding work has a focus on uncertainty quantification (UQ) and machine learning (ML) for coastal flood management. The work is motivated by the increasing vulnerability of communities such as Norfolk and Virginia Beach, Virginia, to frequent coastal flooding events, and the need for rapid, reliable decision support. The research develops computationally efficient ML surrogate models to forecast water levels and flooding risk. A central theme is the quantification and calibration of predictive uncertainty, especially for out-of-distribution (OOD) scenarios, using techniques such as Monte Carlo Dropout, Deep Ensembles, Gaussian Processes, and Deep Quantile Regression (DQR). The study demonstrates that distance-aware UQ is critical for reliable scientific AI, particularly in high-dimensional, safety-critical, and real-time applications.

McSpadden, Diana [Thomas Jefferson National Accele↗

Machine Learning Accelerated First-Principles Study of the Hydrodeoxygenation of Propanoic Acid

The complex reaction network of catalytic biomass conversions often involves hundreds of surface intermediates and thousands of reaction steps, greatly hindering the rational design of metal catalysts for these conversions. Here, we present a framework of machine learning (ML)-accelerated first-principles studies for the hydrodeoxygenation (HDO) of propanoic acid over transition metal surfaces. The microkinetic model (MKM) is initially parametrized by ML-predicted energies and iteratively improved by identifying the rate-determining species and steps (RDS), computing their energies by density functional theory (DFT), and reparameterizing the MKM until all the RDS are computed by DFT. The Gaussian process (GP) model performs significantly better than the linear ridge regression model for predicting both the adsorption free energies and transition state free energies. Parameterized with energies from the GP model, only 5–20% of the full reaction network has to be computed by DFT for the MKM to possess DFT-level accuracy for the TOF and dominant reaction pathway. While the linear ridge regression model performs worse than the GP model, its performance is greatly improved when only transition states are predicted by the regression model and adsorption energies are computed by DFT. Overall, we find that a high accuracy in adsorption free energies is more important for a reliable MKM than a high accuracy in TS free energies. Lastly, based on the GP model with GOH and GCHCHCO as catalyst descriptors, we build two-dimensional volcano plots in activity and selectivity that can help design promising alloy catalysts for HDO reactions of organic acids.

adsorption↗

Latent space dynamics identification for interface tracking with application to shock-induced pore collapse

Capturing sharp, evolving interfaces remains a central challenge in reduced-order modeling, especially when data is limited and the system exhibits localized nonlinearities or discontinuities. Here, we propose LaSDI-IT (Latent Space Dynamics Identification for Interface Tracking), a data-driven framework that combines low-dimensional latent dynamics learning with explicit interface-aware encoding to enable accurate and efficient modeling of physical systems involving moving material boundaries. At the core of LaSDI-IT is a revised autoencoder architecture that jointly reconstructs the physical field and an indicator function representing material regions or phases, allowing the model to track complex interface evolution without requiring detailed physical models or mesh adaptation. The latent dynamics are learned through linear regression in the encoded space and generalized across parameter regimes using Gaussian process interpolation with greedy sampling. We demonstrate LaSDI-IT on the problem of shock-induced pore collapse in high explosives, a process characterized by sharp temperature gradients and dynamically deforming pore geometries. The method achieves relative prediction errors below 9% across the parameter space, accurately recovers key quantities of interest such as pore area and hot spot formation, and matches the performance of dense training with only half the data. This latent dynamics prediction was 10 6 times faster than the conventional high-fidelity simulation, proving its utility for multi-query applications. These results highlight LaSDI-IT as a general, data-efficient framework for modeling discontinuity-rich systems in computational physics, with potential applications in multiphase flows, fracture mechanics, and phase change problems.

Gaussian process↗

Accurate and uncertainty-aware multi-task prediction of HEA properties using prior-guided deep Gaussian processes

Surrogate modeling techniques have become indispensable in accelerating the discovery and optimization of high-entropy alloys (HEAs), especially when integrating computational predictions with sparse experimental observations. This study systematically evaluates the training and testing performance of four prominent surrogate models—conventional Gaussian processes (cGP), Deep Gaussian processes (DGP), encoder-decoder neural networks for multi-output regression and eXtreme Gradient Boosting (XGBoost)—applied to a hybrid dataset of experimental and computational properties of the 8-component HEA system Al-Co-Cr-Cu-Fe-Mn-Ni-V. We specifically assess their capabilities in predicting correlated material properties, including yield strength, hardness, modulus, ultimate tensile strength, elongation, and average hardness under dynamic/quasi-static conditions, alongside auxiliary computational properties. The comparison highlights the strengths of hierarchical deep modeling approaches in handling heteroscedastic, heterotopic, and incomplete data commonly encountered in materials science. Our findings illustrate that combined surrogate models such as DGPs infused with machine-learned priors outperform other surrogates by effectively capturing inter-property correlations and by assimilating prior knowledge. This enhanced predictive accuracy positions the combined surrogate models as powerful tools for robust and data-efficient materials design.

36 MATERIALS SCIENCE↗

Machine learning enhanced predictions of ICRF heating: Overcoming numerical limitations via data curation

In this work, we present the development of robust surrogate models for Ion Cyclotron Range of Frequencies (ICRF) and High-Harmonic Fast Wave (HHFW) heating predictions in fusion plasmas. Building upon our previous efforts to achieve real-time capable models, we identify the cause of the outliers found using TORIC in certain HHFW heating scenarios. The outliers are observed to be spurious ion Bernstein wave (IBW)-like modes caused by a wavelength control algorithm designed to address challenging scenarios with high perpendicular wavenumbers. The effect arises from the modulation in the perpendicular susceptibility, which can induce sign reversal and IBW-like propagation for scenarios featuring normalized ion Larmor radius λ i ≫ 1. We use TORIC with this algorithm disabled to generate a novel HHFW-NSTX database that is free of outliers. Surrogate models trained on this database, including Random Forest Regressor (RFR), Multi-Layer Perceptrons, and Gaussian Process Regressors (GPR), demonstrate the ability to accurately predict HHFW heating profiles, with regression scores of R 2 ∈[0.93−0.99]. Additionally we demonstrate that it is possible to generalize predictions beyond training data by the use of both RFR and GPR models, enabling the prediction of scenarios previously limited to the original model. GPR models also provide uncertainty quantification, offering insights into model confidence. This work introduces a comprehensive Verification, Validation, and Uncertainty Quantification methodology for surrogate modeling, applicable not only to ICRF heating but also to other RF heating challenges and fusion physics problems. Beyond accelerated inference, these models show effective extrapolation capabilities, providing an alternative for addressing numerical challenges.

Artificial neural networks↗

Bayesian learning with Gaussian processes for low-dimensional representations of time-dependent nonlinear systems

This work presents a data-driven method for learning low-dimensional time-dependent physics-based surrogate models whose predictions are endowed with uncertainty estimates. We use the operator inference approach to model reduction that poses the problem of learning low-dimensional model terms as a regression of state space data and corresponding time derivatives by minimizing the residual of reduced system equations. Standard operator inference models perform well with accurate training data that are dense in time, but producing stable and accurate models when the state data are noisy and/or sparse in time remains a challenge. Another challenge is the lack of uncertainty estimation for the predictions from the operator inference models. Our approach addresses these challenges by incorporating Gaussian process surrogates into the operator inference framework to (1) probabilistically describe uncertainties in the state predictions and (2) procure analytical time derivative estimates with quantified uncertainties. The formulation leads to a generalized least-squares regression and, ultimately, reduced-order models that are described probabilistically with a closed-form expression for the posterior distribution of the operators. The resulting probabilistic surrogate model propagates uncertainties from the observed state data to reduced-order predictions. Furthermore, we demonstrate the method is effective for constructing low-dimensional models of two nonlinear partial differential equations representing a compressible flow and a nonlinear diffusion–reaction process, as well as for estimating the parameters of a low-dimensional system of nonlinear ordinary differential equations representing compartmental models in epidemiology.

Data-driven model reduction↗

Short-Term Probabilistic Solar Forecasting via Reinforcement Learning over ECMWF

In this paper, we present an innovative reinforcement learning approach for short-term solar forecasting, leveraging data from the European Centre for Medium-Range Weather Forecasts (ECMWF). The methodology begins with the application of the System Advisor Model (SAM) to transform various ECMWF numerical weather prediction members into predictive photovoltaic power generation. To enhance the precision of deterministic forecasting, we introduce a dynamic model selection algorithm based on Q-learning. This algorithm dynamically identifies and utilizes the most accurate ensemble member for forecasting purposes. Furthermore, we employ a support vector regression surrogate model with a Gaussian distribution to generate probabilistic forecasts, providing a holistic view of solar energy generation uncertainty. To expedite the training process and make it more practical for real-world applications, we integrate a rolling update workflow. This innovative workflow reduces the training period from months to a mere 19 days, making our method highly efficient. Numerical results of the case study show that in comparison to benchmark models, the proposed method improves the deterministic and probabilistic solar forecasting accuracy by up to 40.84% and 48.42%, respectively.

ensemble forecasting↗

Data-Efficient Methods for Determining Flory–Huggins χ Parameters in Multicomponent Polymer Formulations

Polymer formulations are essential in diverse applications including personal care products, coatings, paints, adhesives, and plastic materials. Designing these formulations requires navigating large, complex design spaces, where phase and self-assembly behavior critically impact performance. The Flory–Huggins χ parameter, which quantifies segmental miscibility, is widely used to parametrize the excess free energy of mixing in formulation models. In this work, we introduce two data-efficient, top-down methods for estimating χ parameters using the Random Phase Approximation (RPA): (i) Boundary Nonlinear Regression (Boundary-NLR), which fits theoretical spinodal boundaries to experimental phase boundaries, and (ii) Surrogate Model Inverse Parameter Estimation (SMIPE), which uses a Gaussian Process Classifier to fit sparse phase maps via a surrogate model. Both methods allow rapid parametrization of polymer field-theoretic models without the need for additional experiments. We evaluate these approaches on data sets involving polymer–solvent–nonsolvent ternary mixtures and block copolymer–solvent systems, demonstrating their robustness to experimental noise and their relevance for real-world formulation design.

copolymers↗

Automated Bayesian high-throughput estimation of plasma temperature and density from emission spectroscopy

Here, this paper introduces a novel approach for automated high-throughput estimation of plasma temperature and density using atomic emission spectroscopy, integrating Bayesian inference with sophisticated physical models. We provide an in-depth examination of Bayesian methods applied to the complexities of plasma diagnostics, supported by a robust framework of physical and measurement models. Our methodology is demonstrated using experimental observations in the field of magneto-inertial fusion, focusing on individual and sequential shot analyses of the Plasma Liner Experiment at LANL. The results demonstrate the effectiveness of our approach in enhancing the accuracy and reliability of plasma parameter estimation and in using the analysis to reveal the deep hidden structure in the data. This study not only offers a new perspective of plasma analysis but also paves the way for further research and applications in nuclear instrumentation and related domains.

Bayesian inference↗

Sparse Cholesky factorization for solving nonlinear PDEs via Gaussian processes

In recent years, there has been widespread adoption of machine learning-based approaches to automate the solving of partial differential equations (PDEs). Among these approaches, Gaussian processes (GPs) and kernel methods have garnered considerable interest due to their flexibility, robust theoretical guarantees, and close ties to traditional methods. They can transform the solving of general nonlinear PDEs into solving quadratic optimization problems with nonlinear, PDE-induced constraints. However, the complexity bottleneck lies in computing with dense kernel matrices obtained from pointwise evaluations of the covariance kernel, and its partial derivatives, a result of the PDE constraint and for which fast algorithms are scarce. The primary goal of this paper is to provide a near-linear complexity algorithm for working with such kernel matrices. We present a sparse Cholesky factorization algorithm for these matrices based on the near-sparsity of the Cholesky factor under a novel ordering of pointwise and derivative measurements. The near-sparsity is rigorously justified by directly connecting the factor to GP regression and exponential decay of basis functions in numerical homogenization. We then employ the Vecchia approximation of GPs, which is optimal in the Kullback-Leibler divergence, to compute the approximate factor. This enables us to compute ϵ-approximate inverse Cholesky factors of the kernel matrices with complexity O(N log d (N/ϵ)) in space and O(N log 2d (N/ϵ)) in time. We integrate sparse Cholesky factorizations into optimization algorithms to obtain fast solvers of the nonlinear PDE. We numerically illustrate our algorithm’s near-linear space/time complexity for a broad class of nonlinear PDEs such as the nonlinear elliptic, Burgers, and Monge-Ampère equations. In summary, we provide a fast, scalable, and accurate method for solving general PDEs with GPs and kernel methods.

97 MATHEMATICS AND COMPUTING↗

Uncertainty-Aware Machine Learning for Small-Angle X-ray Scattering Analysis in Autonomous Experimentation

Small-angle X-ray scattering (SAXS) is a powerful high-throughput characterization tool for probing nanoscale structure in native sample environments, providing real-time morphological information such as nanoparticle size and shape during synthesis. However, automated SAXS data analysis for extracting meaningful structural parameters is non-trivial and remains a bottleneck in closed-loop experimentation towards autonomous materials discovery, which demands fast, reliable, and uncertainty-aware data analysis. Here, we develop a machine-learning approach for automated SAXS analysis tailored to closed-loop nanoparticle synthesis. A Random Forest (RF) regression model is trained on 100,000 synthetic SAXS curves generated from polydisperse spherical nanoparticles with realistic background contributions. Using normalized one-dimensional SAXS intensity profiles as input, the RF model directly predicts nanoparticle radius, size polydispersity, and background parameters, while the ensemble standard deviation across trees provides built-in uncertainty quantification (UQ). On synthetic data, we show that combining fit-quality metrics (R 2 , MAE) with thresholds on prediction uncertainty reliably identifies accurate parameter estimates without access to ground truth. We then apply the trained model to 365 experimental SAXS profiles of citrate-reduced gold nanoparticles synthesized using an automated droplet-flow microreactor with in situ SAXS at a synchrotron beamline, classifying the results into high- and low-confidence subsets based on UQ metrics. Finally, we integrate RF-based SAXS analysis into a simulated closed-loop optimization campaign using Gaussian process Bayesian optimization to minimize nanoparticle polydispersity, benchmarking against conventional automated Levenberg–Marquardt fitting. The RF-guided campaign exhibits substantially faster convergence and lower relative opportunity cost (∼0.07 vs ∼0.3), demonstrating that uncertainty-aware machine-learning SAXS analysis significantly enhances the efficiency and robustness of autonomous nanomaterials synthesis workflows.

Bayesian optimization↗

Bayesian Optimization of Catalysis with In-Context Learning

Large language models (LLMs) can perform accurate classification with zero or few examples through in-context learning (ICL), allowing the model to observe query-relevant examples at inference time and eliminating the need for additional weight updates to generalize beyond its original training data. We extend this capability to regression with uncertainty estimation using frozen LLMs (e.g., GPT-4o, Gemini), enabling Bayesian optimization (BO) in natural language without explicit model training or feature engineering. We apply this to materials discovery by representing materials as synthesis and testing procedures for use in natural language prompts. This Bayesian, design-first approach prioritizes optimization toward target material properties before detailed characterization, in contrast to conventional experimental workflows that often emphasize characterization of suboptimal materials. On benchmarks like aqueous solubility and oxidative coupling of methane (OCM), BO-ICL matches or outperforms Gaussian processes. In live experiments on the reverse water–gas shift (RWGS) reaction, BO-ICL identifies multimetallic catalysts that approach equilibrium CO yield within 6 and 10 iterations from a pool of 3,700 and 360,000 candidates, respectively. Our method redefines materials representation and accelerates discovery, with broad applications across catalysis, materials science, and AI.

Calibration↗

Probabilistic projections of the Amery Ice Shelf catchment, Antarctica, under conditions of high ice-shelf basal melt

Abstract. Antarctica's Lambert Glacier drains about one-sixth of the ice from the East Antarctic Ice Sheet and is considered stable due to the strong buttressing provided by the Amery Ice Shelf. While previous projections of the sea-level contribution from this sector of the ice sheet have predicted significant mass loss only with near-complete removal of the ice shelf, the ocean warming necessary for this was deemed unlikely. Recent climate projections through 2300 indicate that sufficient ocean warming is a distinct possibility after 2100. This work explores the impact of parametric uncertainty on projections of the response of the Lambert–Amery system (hereafter “the Amery sector”) to abrupt ocean warming through Bayesian calibration of a perturbed-parameter ice-sheet model ensemble. We address the computational cost of uncertainty quantification for ice-sheet model projections via statistical emulation, which employs surrogate models for fast and inexpensive parameter space exploration while retaining critical features of the high-fidelity simulations. To this end, we build Gaussian process (GP) emulators from simulations of the Amery sector at a medium resolution (4–20 km mesh) using the Model for Prediction Across Scales (MPAS)-Albany Land Ice (MALI) model. We consider six input parameters that control basal friction, ice stiffness, calving, and ice-shelf basal melting. From these, we generate 200 perturbed input parameter initializations using space filling Sobol sampling. For our end-to-end probabilistic modeling workflow, we first train emulators on the simulation ensemble and then calibrate the input parameters using observations of the mass balance, grounding line movement, and calving front movement with priors assigned via expert knowledge. Next, we use MALI to project a subset of simulations to 2300 using ocean and atmosphere forcings from a climate model for both low- and high-greenhouse-gas-emission scenarios. From these simulation outputs, we build multivariate emulators by combining GP regression with principal component dimension reduction to emulate multivariate sea-level contribution time series data from the MALI simulations. We then use these emulators to propagate uncertainty from model input parameters to predictions of glacier mass loss through 2300, demonstrating that the calibrated posterior distributions have both greater mass loss and reduced variance compared to the uncalibrated prior distributions. Parametric uncertainty is large enough through about 2130 that the two projections under different emission scenarios are indistinguishable from one another. However, after rapid ocean warming in the first half of the 22nd century, the projections become statistically distinct within decades. Overall, this study demonstrates an efficient Bayesian calibration and uncertainty propagation workflow for ice-sheet model projections and identifies the potential for large sea-level rise contributions from the Amery sector of the Antarctic Ice Sheet after 2100 under high-greenhouse-gas-emission scenarios.

54 ENVIRONMENTAL SCIENCES↗

Evolution of intermittent filaments in the scrape-off layer of NSTX

Filamentary structures naturally arise from background turbulence in the scrape-off layer (SOL) of plasmas, leading to significant particle and heat transport that can degrade overall plasma confinement. This enhanced transport can contribute to unacceptably high heat loads on plasma-facing components. As such, understanding the physics of SOL plasma filaments is critical for predicting and mitigating their effects in future fusion devices. On the National Spherical Torus Experiment (NSTX), plasma filaments—commonly referred to as “blobs”—were investigated using the gas-puff imaging (GPI) diagnostic in the edge and SOL regions. The analysis involved identifying, segmenting, and tracking the characteristic contours of the blobs in each frame of the GPI video sequences. Their evolution was characterized through shape descriptors, velocity, and angular velocity derived from their contour coordinates. The results indicate that as the blob area increases, their shapes become more concave and less circular, suggesting reduced structural stability in larger blobs. This result aligns with previous theoretical results where it was shown that larger blobs are more susceptible to instabilities [Krasheninnikov et al., J. Plasma Phys. 74, 679–717 (2008) and D'Ippolito et al., Phys. Plasmas 18, 060501 (2011)]. A positive correlation was observed between radial velocity and radial position, suggesting radially outward acceleration of the filaments, potentially driven by decreasing viscous drag toward the far SOL. Interestingly, blobs in background SOL turbulence exhibited minimal spinning in contrast to filaments originating from edge localized modes, which show substantial rotation during their paths [Lampert et al., Phys. Plasmas 29, 102502 (2022)]. Statistical analysis of the solidity and total curvature shape descriptors, along with their temporal evolution, revealed relatively broad, near-Gaussian distributions. This suggests that blob morphology is strongly influenced by stochastic turbulent processes in the surrounding plasma environment. Blob parameters were also compared with bulk plasma and radial profile measurements. Notable trends were found between blob rotation and poloidal velocity with collisionality and line-integrated density. These findings contribute to a deeper understanding of blob dynamics and provide valuable insights for refining SOL turbulence models.

Covariance and correlation↗