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At least 127 records · Page 7

Real-time sparse-sampled Ptychographic imaging through deep neural networks

Ptychography has rapidly grown in the fields of X-ray and electron imaging for its unprecedented ability to achieve nano or atomic scale resolution while simultaneously retrieving chemical or magnetic information from a sample. A ptychographic reconstruction is achieved by means of solving a complex inverse problem that imposes constraints both on the acquisition and on the analysis of the data, which typically precludes real-time imaging due to computational cost involved in solving this inverse problem. In this work we propose PtychoNN, a novel approach to solve the ptychography reconstruction problem based on deep convolutional neural networks. We demonstrate how the proposed method can be used to predict real-space structure and phase at each scan point solely from the corresponding far-field diffraction data. The presented results demonstrate how PtychoNN can effectively be used on experimental data, being able to generate high quality reconstructions of a sample up to hundreds of times faster than state-of-the-art ptychography reconstruction solutions once trained. By surpassing the typical constraints of iterative model-based methods, we can significantly relax the data acquisition sampling conditions and produce equally satisfactory reconstructions. Besides drastically accelerating acquisition and analysis, this capability can enable new imaging scenarios that were not possible before, in cases of dose sensitive, dynamic and extremely voluminous samples.

Cherukara, Mathew J↗

Foundation Models of Scientific Knowledge for Chemistry: Opportunities, Challenges and Lessons Learned

Foundation models pre-trained on large corpora demonstrate significant gains across many natural language processing tasks and domains e.g., law, healthcare, education, etc. However, only limited efforts have investigated the opportunities and limitations of applying these powerful models to science and security applications. In this work we develop foundation models of scientific knowledge for chemistry to augment scientists with the advanced ability to perceive and reason at scale previously unimagined. Specifically, we build large-scale (1.47B parameter) general-purpose models for chemistry that can be effectively used to perform a wide range of in-domain and out-of-domain tasks. Evaluating these models in a zero-shot setting, we analyze the effect of model and data scaling, knowledge depth, and temporality on model performance in context of model training efficiency. Our novel findings demonstrate that (1) model size significantly contributes to the task performance when evaluated in a zero-shot setting; (2) data quality (aka diversity) affects model performance more than data quantity; (3) similarly, unlike previous work (Luu et al., 2021) temporal order of the documents in the corpus boosts model performance only for specific tasks, e.g., SciQ; and (4) models pre-trained from scratch perform better on in-domain tasks than those tuned from general-purpose models like Open AI’s GPT-2.

Foundation Models, Chemistry↗

Machine Learning-Based Anomaly Detection for PMT Data Quality Monitoring in the SBN and DUNE

Maintaining high-quality detector data is essential for achieving the scientific objectives of the Short-Baseline Neutrino (SBN) Program at Fermilab. Current data quality monitoring (DQM) procedures rely primarily on threshold-based metrics and manual inspection of detector monitoring plots, making the detection of subtle or gradually developing anomalies both time-consuming and dependent on expert interpretation. This project developed and evaluated a machine-learning workflow for automatically identifying anomalous photomultiplier tube (PMT) channels in the Short-Baseline Near Detector (SBND) using optical-hit amplitude data. A Python-based analysis program was developed to process ROOT files, extract statistical features describing individual PMT amplitude distributions, and generate feature vectors for anomaly detection. These features were used to train an Isolation Forest model using data representing normal detector operation. The trained model was subsequently applied to independent detector runs to identify channels exhibiting statistically unusual behavior relative to the learned reference response. To support expert interpretation, the workflow generated complementary diagnostic products, including anomaly score distributions, normalized amplitude comparisons, decision-tree visualizations, and principal component analysis (PCA) projections. This project demonstrated the feasibility of integrating unsupervised machine learning into detector data-quality monitoring and developed a complete workflow for automated PMT performance assessment to aid expert-driven review. Beyond its technical contributions, the VFP appointment fostered a research collaboration between Aurora University and Fermilab and provided direct workforce development benefits by training the visiting faculty member in detector-scale machine-learning methods that are now being incorporated into undergraduate coursework and research. The methodology developed here provides a foundation for future applications to ProtoDUNE and other liquid argon time projection chamber (LArTPC) detectors, contributing to ongoing efforts to improve detector reliability, reduce manual monitoring requirements, and enable scalable data quality monitoring for future large-scale neutrino experiments, including the Deep Underground Neutrino Experiment (DUNE).

Colón Santana, Juan A. [Unlisted, US, IL]↗

Machine Learning Automated Analysis of Enormous Synchrotron X-ray Diffraction Datasets

X-ray diffraction (XRD) data analysis can be a time-consuming and laborious task. Deep neural network (DNN) based models trained with synthetic XRD patterns have been proven to be a highly efficient, accurate, and automated method for analyzing common XRD data collected from solid samples in ambient environments. However, it remains unclear whether synthetic XRD-based models can be effective in solving micro(μ)-XRD mapping data for in situ experiments involving liquid phases, which always have lower quality and significant artifacts. In this study, we collected μ-XRD mapping data from a LaCl 3 -calcite hydrothermal fluid system and trained two categories of models to analyze the experimental XRD patterns. Here, the models trained solely with synthetic XRD patterns showed low accuracy (as low as 64%) when solving experimental μ-XRD mapping data. However, the accuracy of the DNN models significantly improved (90% or above) when we trained them with a data set containing both synthetic and a small number of labeled experimental μ-XRD patterns. This study highlights the importance of labeled experimental patterns in training DNN models to solve μ-XRD mapping data from in situ experiments involving liquid phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Beam Hardening Artifact Reduction in X-Ray CT Reconstruction of 3D Printed Metal Parts Leveraging Deep Learning and CAD Models

Nondestructive evaluation (NDE) of additively manufactured (AM) parts is important for understanding the impacts of various process parameters and qualifying the built part. X-ray computed tomography (XCT) has played a critical role in rapid NDE and characterization of AM parts. However, XCT of metal AM parts can be challenging because of artifacts produced by standard reconstruction algorithms as a result of a confounding effect called “beam hardening.” Beam hardening artifacts complicate the analysis of XCT images and adversely impact the process of detecting defects, such as pores and cracks, which is key to ensuring the quality of the parts being printed. In this work, we propose a novel framework based on using available computer-aided design (CAD) models for parts to be manufactured, accurate XCT simulations, and a deep-neural network to produce high-quality XCT reconstructions from data that are affected by noise and beam hardening. Using extensive experiments with simulated data sets, we demonstrate that our method can significantly improve the reconstruction quality, thereby enabling better detection of defects compared with the state of the art. We also present promising preliminary results of applying the deep networks trained using CAD models to experimental data obtained from XCT of an AM jet-engine turbine blade.

Ziabari, Amir↗

Machine learning for improved current-density reconstruction from two-dimensional vector magnetic images

The reconstruction of electrical current densities from magnetic field measurements is an important technique with applications in materials science, circuit design, quality control, plasma physics, and biology. Analytic reconstruction methods exist for planar currents, but break down in the presence of high-spatial-frequency noise or large standoff distance, restricting the types of systems that can be studied. Here, we demonstrate the use of a deep convolutional neural network for current density reconstruction from two-dimensional images of vector magnetic fields acquired by a quantum diamond microscope . Trained network performance significantly exceeds analytic reconstruction for data with high noise or large standoff distances. This machine learning technique can perform quality inversions on lower-signal-to-noise-ratio data, significantly reducing the data collection time and permitting reconstructions of weaker and three-dimensional current sources. Published by the American Physical Society 2025

Reed, Niko R. (ORCID:0009000305222403)↗

Star–Galaxy Image Separation with Computationally Efficient Gaussian Process Classification

Abstract We introduce a novel method for discerning optical telescope images of stars from those of galaxies using Gaussian processes (GPs). Although applications of GPs often struggle in high-dimensional data modalities such as optical image classification, we show that a low-dimensional embedding of images into a metric space defined by the principal components of the data suffices to produce high-quality predictions from real large-scale survey data. We develop a novel method of GP classification hyperparameter training that scales approximately linearly in the number of image observations, which allows for application of GP models to large-size Hyper Suprime-Cam Subaru Strategic Program data. In our experiments, we evaluate the performance of a principal component analysis embedded GP predictive model against other machine-learning algorithms, including a convolutional neural network and an image photometric morphology discriminator. Our analysis shows that our methods compare favorably with current methods in optical image classification while producing posterior distributions from the GP regression that can be used to quantify object classification uncertainty. We further describe how classification uncertainty can be used to efficiently parse large-scale survey imaging data to produce high-confidence object catalogs.

79 ASTRONOMY AND ASTROPHYSICS↗

An Open-Access Repository of Synchrophasor Data Quality Examples: Curation and Example Applications

Synchrophasor measurements are critical in providing wide-area situational awareness to power system operators. However, data artifacts may be introduced due to various issues such as loss of communication, loss of GPS signal, internal clock error, and vendor-specific implementation of phasor estimation algorithms. Tools designed to provide actionable insights from synchrophasor data, hence, must be designed to be robust to these data quality issues. In this work, two years of synchrophasor data sourced from multiple electric utilities in the United States were analyzed to identify examples of data quality problems. These examples were then labeled and published in the Grid Event Signature Library, a publicly available repository of power system measurements hosted by the Oak Ridge National Laboratory. This paper describes the data curation process, and illustrates two application use cases where the dataset can be valuable to the research community. In the first use case, a random forest classifier is trained to distinguish power system disturbance signatures from data anomalies introduced in synchrophasor measurements due to clock errors. The second use case studies the impact of data quality issues on an example synchrophasor application (specifically, event start time determination). The choice of data quality problems investigated is informed by the examples in the repository curated in this work.

24 POWER TRANSMISSION AND DISTRIBUTION↗

ChatPORT: Fine-Tuned LLM for Easy Code {PORT}ing

Fine-tuning existing LLMs for specialized tasks has become a very attractive alternative due to its low cost and quick development cycle. With many pre-trained LLMs available, it is an increasingly complex task to choose the correct model as the starting point or base model. In this work we discuss ChatPORT - a specialized fine-tuned LLM geared towards providing correctly translated codes from one programming model to another. We evaluate a number of base models and compare and contrast their features and characteristics that make them a viable starting point. In this paper, we focus on the OpenMP offload porting capabilities of ChatPORT. We build our training data using kernels from the Heterogeneous Computing Benchmarks (HeCBench) [12] and the OpenMP Validation and Verification suite [5] to fine-tune the base models. We then test the model using unseen kernels extracted from the HeCBench benchmark suite. Our results show that: (1) not all open LLMs geared towards HPC are aware of programming models like OpenMP, (2) although all base models benefit from fine-tuning they learn differently and produce different correctness rates, (3) depending on the memory size and compute resource available, different base models can be used for fine-tuning without significantly affecting the quality of transpiled code they generate, (4) fine-tuning improved the correctness rate of the LLM by an average of 43.2%, and (5) feedback-based training data further increased the correctness rate by an average of 6% over the LLMs tested.

Pophale, Swaroop [ORNL] (ORCID:0000000185446367)↗

Smart Preprocessing & Robust Integration Emulator

To achieve the desired particle size of biomass feedstocks during preprocessing for trouble-free handling and conversion to produce biofuels and bioproducts, the raw materials must undergo a crucial milling process. The particle size of biomass plays a critical role in subsequent biofuel manufacturing, where a larger area-to-volume ratio facilitates efficient synthesis while balancing the impact of moisture on biomass storage. To optimize biofuel production efficiency and overcome these challenges, it is imperative to accurately predict the particle size distribution (PSD) of the biomass in the design of efficient preprocessing systems. The population balance model (PBM), upon empirical calibration and validation, can provide rapid prediction of post-milling PSD of granular biomass. However, PSD has limitations related to mass conservation and the absence of moisture considerations. To overcome these drawbacks, a deep learning model called the enhanced deep neural operator (DNO+) is implemented in the code. This model not only retains the capabilities of the PBM in handling complex mapping functions but also incorporates additional factors influencing the system. By considering various experimental conditions such as sieve size and moisture content, the trained DNO+ model can effectively predict the PSD after milling for any given feed PSD. To further reduce the reliance on experimental data, the PBM is integrated into the DNO+ model, resulting in a physics-informed DNO+ (PIDNO+). The PIDNO+ model addresses the non-conservation of quality exhibited by the PBM while inheriting the advantages of the DNO+ model in considering multiple influencing factors. Moreover, the PIDNO+ model significantly reduces the amount of data required for model training. Both deep learning models, i.e., DNO+ and PIDNO+, are excellent in predictive performance, offering swift and accurate machine learning-based predictions. The use of this code that contains these models will assist in guiding the proper milling equipment selection and operational conditions to achieve the desired biomass particle sizes, ensuring the efficiency of subsequent biofuel and bioproduct production processes.

Xia, Yidong [Idaho National Laboratory (INL), Idah↗

Advancements on Multi-Fidelity Random Fourier Neural Networks: Application to Hurricane Modeling for Wind Energy

Multi-fidelity approaches are emerging as effective strategies in computational science to handle otherwise intractable tasks like Uncertainty Quantification (UQ), training of Machine Learning (ML) models, and optimization, for expensive high-fidelity applications in which the amount of available simulations or data is limited. The main idea is simple: large datasets generated for low-fidelity approximations of the problem at hand are fused with a much sparser dataset for the target (high-fidelity) system. In this paper, we build on our recent success in designing random Fourier Neural Networks (rFNNs) [1] to target problems arising in wind energy applications and in particular problems of interest for hurricane modeling. In this context, data for the high-fidelity models are limited and lower fidelity alternatives are needed. In this work, we introduce a novel multi-fidelity training approach for our rFNNs and demonstrate its use on a simple verification problem and on a hurricane modeling problem in which high-fidelity data are generated via Large-Eddy Simulations (LES), while low-fidelity data are given by a mesoscale model. Initial results demonstrate how the multi-fidelity training approach can improve the quality of the resulting surrogate.

Fourier Neural Networks↗

HPC-FAIR: A Framework Managing Data and AI Models for Analyzing and Optimizing Scientific Applications

The increasing reliance on machine learning (ML) to analyze and optimize large-scale scientific applications on supercomputers faces a significant bottleneck: the lack of readily available, high-quality training datasets and the difficulty in reusing existing AI models. This project was motivated by the urgent need to address the “FAIR” principles (Findability, Accessibility, Interoperability, Reusability) for both training datasets and AI models in the high-performance computing (HPC) domain. The project developed HPC-FAIR, a high-performance computing data management framework designed to centralize HPC-related datasets and AI models within a unified hub. To ensure interoperability, the framework established a standardized representation and vocabulary (ontology) for both data and models. HPC-FAIR also implemented automated workflows to streamline data processing, model access, and benchmarking. Additionally, the project focused on optimizing data harnessing efficiency through advanced techniques like deep reuse and compression-based analytics.

97 MATHEMATICS AND COMPUTING↗

Evaluating Limits of Machine Learning-Assisted Raman Spectroscopy in Classification of Biological Samples

Machine learning (ML)-assisted Raman spectroscopy has become a powerful analytical tool for the classification and identification of analytes; however, technical challenges impacting its detection accuracy have not been thoroughly investigated. This study explores experimental factors affecting classification performance. Among the evaluated ML models, ML algorithms show minimal impact on classification accuracy. Instead, experimental factors, including spectral similarity between tested samples and data quality, dominate detection performance. Increases in spectral noise and spectral similarity significantly reduce classification accuracy. In well-controlled samples with low experimental noise, ML-assisted Raman spectroscopy can discriminate lipid mixtures with a composition difference of 1.85 mol %. To assess the effect of biological heterogeneity, we analyzed single-cell Raman spectra from Saccharomyces cerevisiae strains carrying single, double, or triple gene mutations. Intrinsic cell-to-cell variability introduced substantial spectral differences, severely reducing the accuracy of multiclass classification of these genetically similar strains at the single-cell level. Averaging Raman spectra across multiple cells improved classification accuracy by reducing this spectral variability. We also assess the effectiveness of transfer learning across different Raman spectrometers, specifically by applying an ML model trained on one instrument to another Raman spectrometer. Transfer learning can be improved with proper instrument calibration, highlighting the importance of instrument standardization. Overall, our results demonstrate that data quality and spectral similarity are the primary bottlenecks in ML-assisted Raman spectroscopy. Careful attention to sample preparation, data acquisition, measurement conditions, and instrument calibration is critical to achieving robust and reliable classification performance.

Fungi↗

Protein model quality assessment using rotation–equivariant transformations on point clouds

Machine learning research concerning protein structure has seen a surge in popularity over the last years with promising advances for basic science and drug discovery. Working with macromolecular structure in a machine learning context requires an adequate numerical representation, and researchers have extensively studied representations such as graphs, discretized 3D grids, and distance maps. As part of CASP14, we explored a new and conceptually simple representation in a blind experiment: atoms as points in 3D, each with associated features. These features—initially just the basic element type of each atom—are updated through a series of neural network layers featuring rotation-equivariant convolutions. Starting from all atoms, we further aggregate information at the level of alpha carbons before making a prediction at the level of the entire protein structure. We find that this approach yields competitive results in protein model quality assessment despite its simplicity and despite the fact that it incorporates minimal prior information and is trained on relatively little data. As a result, its performance and generality are particularly noteworthy in an era where highly complex, customized machine learning methods such as AlphaFold 2 have come to dominate protein structure prediction.

59 BASIC BIOLOGICAL SCIENCES↗

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↗

Temporal Subsampling Diminishes Small Spatial Scales in Recurrent Neural Network Emulators of Geophysical Turbulence

The immense computational cost of traditional numerical weather and climate models has sparked the development of machine learning (ML) based emulators. Because ML methods benefit from long records of training data, it is common to use data sets that are temporally subsampled relative to the time steps required for the numerical integration of differential equations. Here, we investigate how this often overlooked processing step affects the quality of an emulator's predictions. We implement two ML architectures from a class of methods called reservoir computing: (a) a form of Nonlinear Vector Autoregression (NVAR), and (b) an Echo State Network (ESN). Despite their simplicity, it is well documented that these architectures excel at predicting low dimensional chaotic dynamics. We are therefore motivated to test these architectures in an idealized setting of predicting high dimensional geophysical turbulence as represented by Surface Quasi-Geostrophic dynamics. In all cases, subsampling the training data consistently leads to an increased bias at small spatial scales that resembles numerical diffusion. Interestingly, the NVAR architecture becomes unstable when the temporal resolution is increased, indicating that the polynomial based interactions are insufficient at capturing the detailed nonlinearities of the turbulent flow. The ESN architecture is found to be more robust, suggesting a benefit to the more expensive but more general structure. Spectral errors are reduced by including a penalty on the kinetic energy density spectrum during training, although the subsampling related errors persist. Future work is warranted to understand how the temporal resolution of training data affects other ML architectures.

58 GEOSCIENCES↗

Operator learning for energy-efficient building ventilation control with computational fluid dynamics simulation of a real-world classroom

Energy-efficient ventilation control plays an important role in reducing building energy consumption while ensuring occupant health and comfort. While Computational Fluid Dynamics (CFD) simulations provide detailed and physically accurate representations of indoor airflow, their high computational cost limits their use in real-time building control. In this work, we present a neural operator learning framework that combines the physical accuracy of CFD with the computational efficiency of machine learning to enable building ventilation control with the high-fidelity fluid dynamics models. Our method jointly optimizes the airflow supply rates and vent angles to reduce energy use and adhere to air quality constraints. We train an ensemble of neural operator transformer models to learn the mapping from building control actions to airflow fields using high-resolution CFD data. This learned neural operator is then embedded in an optimization-based control framework for building ventilation control. Experimental results show that our approach achieves significant energy savings compared to maximum airflow rate control, rule-based control, as well as data-driven control methods using spatially averaged CO 2 prediction and deep learning–based reduced-order models, while consistently maintaining safe indoor air quality. These results highlight the practicality and scalability of our method in maintaining energy efficiency and indoor air quality in real-world buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

NRAP-Open-IAM Multisegmented Wellbore Reduced-Order Model: Improvement and Quality Assurance

The multisegmented wellbore model (MSW) semi-analytically estimates the amount of CO 2 and brine leakage from a leaking legacy well by segmenting it into intervals to simulate site-specific stratigraphic and hydrogeologic properties. The model is a component of the National Risk Assessment Partnership Open-Source Integrated Assessment Model (NRAP-Open-IAM), which was developed to perform risk assessment for geologic CO 2 storage. The new wellbore leakage model, which uses deep learning networks for a caprock segment, was developed to enhance the analytical MSW. The model was trained and validated using a synthetic data set of Subsurface Transport Over Multiple Phases (STOMP) multiphase flow simulations from various geological, well attribute, and operational conditions to ensure its quality. The results demonstrate that the model is more accurate than the existing model in predicting the transport of two-phase fluids (brine and injected CO 2 ) through the well. This report provides a detailed explanation of the model development and quality assurance.

58 GEOSCIENCES↗