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At least 415 records · Page 23

Protein Conformational States—A First Principles Bayesian Method

Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naïve Bayes classifier from the machine learning community for use on atom-to-atom pairwise contacts. The result is an unsupervised learning algorithm that samples a ‘distribution’ over potential classification schemes. We apply the classifier to a series of test structures and one real protein, showing that it identifies the conformational transition with >95% accuracy in most cases. A nontrivial feature of our adaptation is a new connection to information entropy that allows us to vary the level of structural detail without spoiling the categorization. This is confirmed by comparing results as the number of atoms and time-samples are varied over 1.5 orders of magnitude. Further, the method’s derivation from Bayesian analysis on the set of inter-atomic contacts makes it easy to understand and extend to more complex cases.

97 MATHEMATICS AND COMPUTING↗

Quantitative Analysis and Prediction of Thermal Runaway Metrics of High-Nickel Oxide Cathodes by Machine Learning Models

The pursuit of higher energy density in lithium-ion batteries has made high-nickel (Ni) layered oxides leading cathode candidates for next-generation electric vehicles. However, their poor thermal stability, particularly at Ni contents ≥ 90%, increases the risk of cathode-initiated thermal runaway. Furthermore, we present a data-driven framework combining linear and nonlinear machine learning models to predict key thermal runaway descriptors from a high-throughput differential scanning calorimetry database. With cathode composition and state of charge (SOC) as input features, the ensemble model accurately predicts peak temperature, heat release, and peak heat flow. SHAP analysis identifies Ni content and SOC as the dominant factors controlling thermal runaway temperature, while SOC primarily governs heat release and peak heat flow. Al, Mg, and Mn improve thermal stability by strengthening metal–oxygen bonding and delaying structural transformation, whereas B mainly reduces heat release through surface passivation. Validation with a new cathode composition confirms accurate prediction of SOC-dependent thermal runaway behavior and critical SOC.

25 ENERGY STORAGE↗

Active Learning Framework

Machine learning (ML) of interatomic potentials show great promise to accelerate scientific simulation, e.g., by emulating expensive computations at a high accuracy but much reduced computational cost. Training datasets are calculated from computationally expensive ab initio quantum mechanics methods, density functional theory (DFT). Trained on this data, an ML model can be very successful in predicting energy and forces for new atomic configurations. A critical factor is the quality and diversity of the training dataset. Thus, a highly automated approach to dataset construction based on active learning framework is designed suitable for material physics. The active learning scheme begins with fully randomized atomic configurations. Then, many Molecular Dynamics (MD) trajectories are simulated using current ML potentials, where each MD trajectory is initialized to a random disordered configuration. The temperature is varied in order to diversify the sampled configuration during these simulations. The variance of predictions for eight neural networks within an ensemble is analyzed to determine whether the model is operating as expected. This helps in determining whether collecting more data would be helpful to the model by checking the ensemble variance is greater than the threshold. In this case, the MD trajectory is terminated and the final atomic configuration is placed on a queue (SQL database) for DFT calculations and added to training dataset. Periodically, ML model is retrained to the updated training model. This Active Learning loop is iterated until the cost of MD simulations becomes prohibitively expensive. The MD simulations will hopefully be sufficiently robust to support nucleation after many active learning iterations. In this sense, active learning scheme must automatically discover the important low energy and nonequilibrium physics.

Nebgen, Benjamin↗

Decoding the proton’s gluonic density with lattice QCD-informed machine learning

We present a first machine learning-based decoding of the gluonic structure of the proton from lattice QCD using a variational autoencoder inverse mapper (VAIM). Harnessing the power of generative AI, we predict the parton distribution function (PDF) of the gluon given information on the reduced pseudo-Ioffe-time distributions (RpITDs) as calculated from an ensemble with lattice spacing a ≈ 0.09 fm and a pion mass of M π ≈ 310 MeV. The resulting gluon PDF is consistent with phenomenological global fits within uncertainties, particularly in the intermediate-to-high-x region where lattice data are most constraining. A subsequent correlation analysis confirms that the VAIM learns a meaningful latent representation, highlighting the potential of generative AI to bridge lattice QCD and phenomenological extractions within a unified analysis framework.

Gluon parton distribution function↗

Estimation of sensor measurement errors in reactor coolant systems using multi-sensor fusion

A nuclear power plant is typically instrumented with a variety of sensors to continually monitor its variables, and their sensor’s measurements may be used to assess the plant state and initiate safety actions, if needed. Errors in sensor measurements, due to factors such as calibration drifts, critically affect such state assessments. Here, we address a problem of estimating sensor errors using physics-informed machine learning methods that use measurements collected under known plant conditions. For a given sensor, we propose an information fusion method that uses measurements from other sensors to estimate its output assuming it is error-free and provides its difference from an actual measurement as an error estimate. We present the ensemble of trees and support vector machine fusers, and evaluate their performance using measurements collected over an emulated test loop of a pressurized water reactor. The plant variables are related to each other through the underlying physical laws under inertial constraints that place bounds on their derivatives, which analytically justify the applicability of machine learning methods for computing these fusers. Under twenty scenarios, we assess their sensor error estimates for pressure sensors of the heat exchanger of a reactor’s primary coolant system. Multiple types of errors are captured by both fusers under externally induced calibration drifts, blockages, minor leaks and air gaps in sensing lines, and electromagnetic interference; the root mean square error of the estimation of error is under 2.2% percent of the maximum measurement. We present generalization equations, in the framework of statistical learning theory, for these methods that characterize the confidence probability that the estimation error is bounded by a specified parameter in future test scenarios.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations

Abstract Motivation Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in noncoding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. Results We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of nonrandom interactions from all Hi-C interactions. Using these nonrandom interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization. Availability and implementation It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci.

Du, Lin (ORCID:0009000289869812)↗

Creating ground truth for nanocrystal morphology: a fully automated pipeline for unbiased transmission electron microscopy analysis

Control over colloidal nanocrystal morphology (size, size distribution, and shape) is important for tailoring the functionality of individual nanocrystals and their ensemble behavior. Despite this, traditional methods to quantify nanocrystal morphology are laborious. New developments in automated morphology classification will accelerate these analyses but the assessment of machine learning models is limited by human accuracy for ground truth, causing even unsupervised machine learning models to have inherent bias. Herein, we introduce synthetic image rendering to solve the ground truth problem of nanocrystal morphology classification. By simulating 2D images of nanocrystal shapes via a function of high-dimensional parameter space, we trained a convolutional neural network to link unique morphologies to their simulated parameters, defining nanocrystal morphology quantitatively rather than qualitatively. An automated pipeline then processes, quantitatively defines, and classifies nanocrystal morphology from experimental transmission electron microscopy (TEM) images. Using improved computer vision techniques, 42,650 nanocrystals were identified, assessed, and labeled with quantitative parameters, offering a 600-fold improvement in efficiency over best-practice manual measurements. Further, a classification algorithm was trained with a prediction accuracy of 99.5%, which can successfully analyze a range of concave, convex, and irregular nanocrystal shapes. The resulting pipeline was applied to differentiating two syntheses of nominally cuboidal CsPbBr 3 nanocrystals and uniquely classifying binary nickel sulfide nanocrystal phase based on morphology. This pipeline provides a simple, efficient, and unbiased method to quantify nanocrystal morphology and represents a practical route to construct large datasets with an absolute ground truth for training unbiased morphology-based machine learning algorithms.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

An Ensemble Neural Network Model for Predicting Rare-Earth Oxide and Silicate Heat Capacities at High Temperature

In this work, a neural network model was developed to predict the constant pressure heat capacity for materials in the rare-earth oxide—silica material space. Several model architectures were trained and tested on heat capacity data generated from first-principles density functional theory calculations. Hyperparameter optimization was performed, and the optimal model was selected for heat capacity predictions. The optimal model architecture was found to have a root-mean-squared error of 5.12 ± 3.37 J/mol-K. The optimal model architecture was then used in a bagging ensemble model trained using the leave-one-group-out method to provide error estimates for model predictions. The out-of-bag score for the ensemble model was 0.997. The predicted heat capacities agree well with the DFT and experimental results and were computed orders of magnitude faster than DFT simulations. Machine learning shows the potential to provide a suitable surrogate model for thermochemical property predictions for candidate environmental barrier coating materials but refining of input material features and model architectures could further improve accuracy for these models.

environmental barrier coatings↗

Active operator learning with predictive uncertainty quantification for partial differential equations

With the increased prevalence of neural operators being used to provide rapid solutions to partial differential equations (PDEs), understanding the accuracy of model predictions and the associated error levels is necessary for deploying reliable surrogate models in scientific applications. Existing uncertainty quantification (UQ) frameworks employ ensembles or Bayesian methods, which can incur substantial computational costs during both training and inference. Here, we propose a lightweight predictive UQ method tailored for Deep operator networks (DeepONets) that also generalizes to other operator networks. Numerical experiments on linear and nonlinear PDEs demonstrate that the framework’s uncertainty estimates are unbiased and provide accurate out-of-distribution uncertainty predictions with a sufficiently large training dataset. Our framework provides fast inference and uncertainty estimates that can efficiently drive outer-loop analyses that would be prohibitively expensive with conventional solvers. We demonstrate how predictive uncertainties can be used in the context of Bayesian optimization and active learning problems to yield improvements in accuracy and data-efficiency for outer-loop optimization procedures. In the active learning setup, we extend the framework to Fourier Neural Operators (FNO) and describe a generalized method for other operator networks. To enable real-time deployment, we introduce an inference strategy based on precomputed trunk outputs and a sparse placement matrix, reducing evaluation time by more than a factor of five. Our method provides a practical route to uncertainty-aware operator learning in time-sensitive settings.

97 MATHEMATICS AND COMPUTING↗

Spotlight: efficient automated global optimization in rietveld analysis of diffraction data

Performing reliable Rietveld analysis on tens or hundreds of powder diffraction datasets from parametric or time-resolved experiments often poses a bottleneck in extracting meaningful results from the data. While automated analysis of data has recently been demonstrated, high temperature annealing studies, during which phase transformations occur and lattice parameters may change due to repartitioning of elements, are prime examples where automation by a simple phase identification from a database of room temperature structures or automation by sequential refinements is likely to fail. To enable reliable, efficient, automated Rietveld analysis, we present a Python package named Spotlight , building on established Rietveld packages such as MAUD, GSAS , or GSAS-II , which extends the refinement of best fit parameters to a global optimization using an ensemble of optimizers leveraging hierarchical parallel execution on high-performance computing clusters. Spotlight further enables the efficient design of refinement plans through the iterative automated machine-learning of a surrogate for the refinement on which the global optimizations are performed until results from the surrogate converge to the response surface data. We demonstrate Spotlight with the analysis of uranium molybdenum and Ti–6Al–4V datasets, as well as in two open-source tutorials analyzing aluminium oxide and lead sulphate.

36 MATERIALS SCIENCE↗

EFIT-Prime: Probabilistic and physics-constrained reduced-order neural network model for equilibrium reconstruction in DIII-D

We introduce EFIT-Prime, a novel machine learning surrogate model for EFIT (Equilibrium FIT) that integrates probabilistic and physics-informed methodologies to overcome typical limitations associated with deterministic and ad hoc neural network architectures. EFIT-Prime utilizes a neural architecture search-based deep ensemble for robust uncertainty quantification, providing scalable and efficient neural architectures that comprehensively quantify both data and model uncertainties. Physically informed by the Grad–Shafranov equation, EFIT-Prime applies a constraint on the current density J tor and a smoothness constraint on the first derivative of the poloidal flux, ensuring physically plausible solutions. Furthermore, the spatial location of the diagnostics is explicitly incorporated in the inputs to account for their spatial correlation. Extensive evaluations demonstrate EFIT-Prime's accuracy and robustness across diverse scenarios, most notably showing good generalization on negative-triangularity discharges that were excluded from training. Timing studies indicate an ensemble inference time of 15 ms for predicting a new equilibrium, offering the possibility of plasma control in real-time, if the model is optimized for speed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Improving Prediction of Surface Solar Irradiance Variability by Integrating Observed Cloud Characteristics and Machine Learning

A 5-year, 1-minute resolution observational dataset of clouds and solar radiation was produced that includes two metrics of the variability in surface solar irradiance due to cloud type and fractional sky cover. Multiple regression models were trained to fit observations of surface solar irradiance variability from those two cloud property predictors. We found that ensemble tree-based methods, Random Forest and Gradient Boosting Machine, have the least overfitting issues and showed the best performance with an R2 of 0.42. While the observational data trained in this study was only from one site, the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) site in Oklahoma, initial comparisons of the seasonality of the statistics suggest that these results are relatively weather regime independent; the generality of such a finding across sites will be tested in future work. The observational data and developed machine learning model are being used to create a numerical weather prediction model parameterization to enable day-ahead solar variability prediction in a computationally efficient way. This is a first step towards creating a new paradigm of predicting day-ahead variability with the potential to provide a new tool to improve grid operation, planning, and resilience.

Riihimaki, Laura↗

Ensemble flow reconstruction in the atmospheric boundary layer from spatially limited measurements through latent diffusion models

Due to costs and practical constraints, field campaigns in the atmospheric boundary layer typically only measure a fraction of the atmospheric volume of interest. Machine learning techniques have previously successfully reconstructed unobserved regions of flow in canonical fluid mechanics problems and two-dimensional geophysical flows, but these techniques have not yet been demonstrated in the three-dimensional atmospheric boundary layer. Here, we conduct a numerical analogue of a field campaign with spatially limited measurements using large-eddy simulation. We pose flow reconstruction as an inpainting problem, and reconstruct realistic samples of turbulent, three-dimensional flow with the use of a latent diffusion model. The diffusion model generates physically plausible turbulent structures on larger spatial scales, even when input observations cover less than 1% of the volume. Through a combination of qualitative visualization and quantitative assessment, we demonstrate that the diffusion model generates meaningfully diverse samples when conditioned on just one observation. These samples successfully serve as initial conditions for a large-eddy simulation code. We find that diffusion models show promise and potential for other applications for other turbulent flow reconstruction problems.

17 WIND ENERGY↗

Crystal Orientation and Defect Mapping in Electron-Beam-Sensitive Zeolites with Near-Axis Transmission Kikuchi Diffraction

Porous materials are vital in catalysis, energy conversion, and environmental remediation. Understanding structural heterogeneity in zeolites is key to linking synthesis, framework intergrowths, and catalytic performance, yet current methods for phase identification and spatial mapping lack sufficient resolution or throughput. We present a high-throughput approach using near-axis transmission Kikuchi diffraction in a scanning electron microscope, achieving high phase and spatial resolution for electron-beam-sensitive zeolites, including ZSM-5 and, for the first time, Zeolite A. Here, this method enables direct visualization of intergrowth features that critically affect catalytic and adsorption behavior, bridging the gap between ensemble-averaged X-ray diffraction and high-resolution but low-throughput transmission electron microscopy. Combining nanoscale mapping with statistical sampling is highly suited for machine-learning pipelines guiding new structure function understanding and could be extended to other beam-sensitive porous materials such as metal–organic or covalent–organic frameworks.

crystallography↗

A unified ensemble soil moisture dataset across the continental United States

Abstract A unified ensemble soil moisture (SM) package has been developed over the Continental United States (CONUS). The data package includes 19 products from land surface models, remote sensing, reanalysis, and machine learning models. All datasets are unified to a 0.25-degree and monthly spatiotemporal resolution, providing a comprehensive view of surface SM dynamics. The statistical analysis of the datasets leverages the Koppen-Geiger Climate Classification to explore surface SM’s spatiotemporal variabilities. The extracted SM characteristics highlight distinct patterns, with the western CONUS showing larger coefficient of variation values and the eastern CONUS exhibiting higher SM values. Remote sensing datasets tend to be drier, while reanalysis products present wetter conditions. In-situ SM observations serve as the basis for wavelet power spectrum analyses to explain discrepancies in temporal scales across datasets facilitating daily SM records. This study provides a comprehensive soil moisture data package and an analysis framework that can be used for Earth system model evaluations and uncertainty quantification, quantifying drought impacts and land–atmosphere interactions and making recommendations for drought response planning.

54 ENVIRONMENTAL SCIENCES↗

Study of Overfitting by Machine Learning Methods Using Generalization Equations

The training error of Machine Learning (ML) methods has been extensively used for performance assessment, and its low values have been used as a main justification for complex methods such as estimator fusion and ensembles, and hyper parameter tuning. We present two practical cases where independent tests indicate that the low training error is more of a reflection of over-fitting rather than the generalization ability. We derive a generic form of the generalization equations that separates the training error terms of ML methods from their epistemic terms that correspond to approximation and learnability properties. It provides a framework to separately account for both terms to ensure an overall high generalization performance. For regression estimation tasks, we derive conditions for performance enhancements achieved by hyper parameter tuning, and fusion and ensemble methods over their constituent methods. We present experimental measurements and ML estimates that illustrate the analytical results for the throughput profile estimation of a data transport infrastructure.

Rao, Nageswara↗

Advances in Hyperspectral Image Classification Methods for Vegetation and Agricultural Cropland Studies

Hyperspectral data are becoming more widely available via sensors on airborne and unmanned aerial vehicle (UAV) platforms, as well as proximal platforms. While space-based hyperspectral data continue to be limited in availability, multiple spaceborne Earth-observing missions on traditional platforms are scheduled for launch, and companies are experimenting with small satellites for constellations to observe the Earth, as well as for planetary missions. Land cover mapping via classification is one of the most important applications of hyperspectral remote sensing and will increase in significance as time series of imagery are more readily available. However, while the narrow bands of hyperspectral data provide new opportunities for chemistry-based modeling and mapping, challenges remain. Hyperspectral data are high dimensional, and many bands are highly correlated or irrelevant for a given classification problem. For supervised classification methods, the quantity of training data is typically limited relative to the dimension of the input space. The resulting Hughes phenomenon, often referred to as the curse of dimensionality, increases potential for unstable parameter estimates, overfitting, and poor generalization of classifiers. This is particularly problematic for parametric approaches such as Gaussian maximum likelihood–based classifiers that have been the backbone of pixel-based multispectral classification methods. This issue has motivated investigation of alternatives, including regularization of the class covariance matrices, ensembles of weak classifiers, development of feature selection and extraction methods, adoption of nonparametric classifiers, and exploration of methods to exploit unlabeled samples via semi-supervised and active learning. Data sets are also quite large, motivating computationally efficient algorithms and implementations. This chapter provides an overview of the recent advances in classification methods for mapping vegetation using hyperspectral data. Three data sets that are used in the hyperspectral classification literature (e.g., Botswana Hyperion satellite data and AVIRIS airborne data over both Kennedy Space Center and Indian Pines) are described in Section 3.2 and used to illustrate methods described in the chapter. An additional high-resolution hyperspectral data set acquired by a SpecTIR sensor on an airborne platform over the Indian Pines area is included to exemplify the use of new deep learning approaches, and a multiplatform example of airborne hyperspectral data is provided to demonstrate transfer learning in hyperspectral image classification. Classical approaches for supervised and unsupervised feature selection and extraction are reviewed in Section 3.3. In particular, nonlinearities exhibited in hyperspectral imagery have motivated development of nonlinear feature extraction methods in manifold learning, which are outlined in Section 3.3.1.4. Spatial context is also important in classification of both natural vegetation with complex textural patterns and large agricultural fields with significant local variability within fields. Approaches to exploit spatial features at both the pixel level (e.g., co-occurrence–based texture and extended morphological attribute profiles [EMAPs]) and integration of segmentation approaches (e.g., HSeg) are discussed in this context in Section 3.3.2. Recently, classification methods that leverage nonparametric methods originating in the machine learning community have grown in popularity. An overview of both widely used and newly emerging approaches, including support vector machines (SVMs), Gaussian mixture models, and deep learning based on convolutional neural networks is provided in Section 3.4. Strategies to exploit unlabeled samples, including active learning and metric learning, which combine feature extraction and augmentation of the pool of training samples in an active learning framework, are outlined in Section 3.5. Integration of image segmentation with classification to accommodate spatial coherence typically observed in vegetation is also explored, including as an integrated active learning system. Exploitation of multisensor strategies for augmenting the pool of training samples is investigated via a transfer learning framework in Section 3.5.1.2. Finally, we look to the future, considering opportunities soon to be provided by new paradigms, as hyperspectral sensing is becoming common at multiple scales from ground-based and airborne autonomous vehicles to manned aircraft and space-based platforms.

Pasolli, Edoardo↗

CANShield: Signal-based Intrusion Detection for Controller Area Networks

Modern vehicles rely on complex cyber-physical systems made up of hundreds of electronic control units (ECUs) connected through controller area network (CAN) buses. However, the CAN bus attack surface is increasing due to advanced features in automobiles, making it prone to injection attacks. The ordinary injection attacks disrupt the typical timing properties of the CAN data stream, and the rule-based intrusion detection systems (IDS) can easily detect them. However, advanced attackers can inject false data to the signal level, maintaining the regular pattern/frequency of the CAN messages. Such attacks can bypass the rule-based IDS or any anomaly-based IDS built on binary payload data. To make the vehicles robust against such intelligent attacks, we propose CANShield, a signal-based intrusion detection framework for the CAN bus that consists of three modules. A data preprocessing module handles the high-dimensional CAN data stream at the signal level and make them suitable for any machine learning model. A data analyzer module consists of multiple deep autoencoder networks, each analyzing the time series data from a different perspective. Finally, an attack detection module uses an ensemble method to make the final decision. Evaluation results on a standard signal-based dataset show the effectiveness of the CANShield in detecting five advanced attacks.

Shahriar, Md Hasan↗