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Enabling Efficient Sparse Computations using Linear Algebra Aware Compilers

This project developed the LAPIS compiler framework, built on the Multilevel Intermediate Representation (MLIR), to optimize sparse linear algebra operations and support performance portability across diverse architectures. The main innovation of LAPIS is the Kokkos dialect, which allows for lowering codes from a high productivity language to different architectures in an elegant way. The dialect also allows the conversion of lower-level MLIR code to C++ Kokkos code, facilitating the integration of scientific machine learning (SciML) models into applications. To extend LAPIS for distributed memory architectures, a new partition dialect was created to manage the distribution of sparse tensors and express communication patterns for sparse linear algebra operations. This dialect also supports the distributed execution of operators and includes algorithmic optimizations to minimize communication to improve performance. The project also demonstrates that MLIR can enable effective linear algebra-level optimizations, improving performance on different GPUs for both sparse and dense linear algebra kernels. Key applications of LAPIS include sparse linear algebra and graph kernels, TenSQL, a relational database management solution built on GraphBLAS, and the development of subgraph isomorphism and monomorphism kernels, showcasing performance portability. In summary, the LAPIS framework supports productivity, performance, portability, and distributed memory execution, while also enabling linear algebra-level optimizations that are challenging in traditional programming languages, with successful applications ranging from simple sparse linear algebra to complex graph kernels.

97 MATHEMATICS AND COMPUTING

Constraining Galaxy-Halo connection using machine learning

We investigate the potential of machine learning (ML) methods to model small-scale galaxy clustering for constraining Halo Occupation Distribution (HOD) parameters. Our analysis reveals that while many ML algorithms report good statistical fits, they often yield likelihood contours that are significantly biased in both mean values and variances relative to the true model parameters. This highlights the importance of careful data processing and algorithm selection in ML applications for galaxy clustering, as even seemingly robust methods can lead to biased results if not applied correctly. ML tools offer a promising approach to exploring the HOD parameter space with significantly reduced computational costs compared to traditional brute-force methods if their robustness is established. Using our ANN-based pipeline, we successfully recreate some standard results from recent literature. Properly restricting the HOD parameter space, transforming the training data, and carefully selecting ML algorithms are essential for achieving unbiased and robust predictions. Among the methods tested, artificial neural networks (ANNs) outperform random forests (RF) and ridge regression in predicting clustering statistics, when the HOD prior space is appropriately restricted. We demonstrate these findings using the projected two-point correlation function (w p (r p )), angular multipoles of the correlation function (ξ ℓ (r)), and the void probability function (VPF) of Luminous Red Galaxies from Dark Energy Spectroscopic Instrument mocks. Our results show that while combining w p (r p ) and VPF improves parameter constraints, adding the multipoles ξ 0 , ξ 2 , and ξ 4 to w p (r p ) does not significantly improve the constraints.

cosmology

Maximizing efficiency of dataset compression for machine learning potentials with information theory

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.

36 MATERIALS SCIENCE

Microscopic insights into the solvation of polyethylene glycol chains in water: A machine learning potential approach

Polyethylene glycol (PEG) is a structurally simple, nontoxic, and water-soluble polymer widely utilized in medical and pharmaceutical applications. Notably, when a PEG chain is immersed in water, the surrounding water molecules play a key role in driving conformational changes of this macromolecule. In this study, we explore the solvation behavior of PEG under mechanical strain using molecular dynamics simulations, with an interatomic potential obtained from machine learning. Our focus is on the transition from the favored coil-like conformation to an extended one under external force. Through analyses of radial distribution functions, hydrogen bonding, and solvation dynamics, we uncover how mechanical stretching influences the local hydration environment. Furthermore, we disentangle the enthalpic and entropic contributions to the conformational stability of PEG in water. Surprisingly, our neural network potential model identifies dewetting of PEG C-atoms, and not water H-bonding with PEG O-atoms, as the main enthalpic driving force for the coiling of PEG in water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Machine Learning-Driven Solvent Screening for Biobased 2,3-Butanediol Extraction

Biobased 2,3-butanediol (2,3-BDO) is a valuable biomass-derived chemical due to its versatility in being transformed into a wide variety of products. However, the separation and purification of 2,3-BDO from fermentation broth remain a significant challenge owing to its high boiling point and hydrophilic nature. Herein, we developed a machine learning (ML)-based screening workflow that uses molecular calculations as training data and requires only a small number of experimental measurements for validation to identify alternative solvent candidates for the liquid–liquid extraction (LLE) of 2,3-BDO from aqueous solution. In particular, 130 density functional theory (DFT) calculations with the implicit solvation method not only built a correlation between the computational partition coefficient and the experimental distribution coefficient of 2,3-BDO but also parameterized an Extra-Trees ML model to screen the distribution coefficient for a wider range of 6717 organic solvents. The experimental measurements of only 24 solvents were needed to validate the computational results. A list of 50 prioritized solvents was proposed for 2,3-BDO LLE, and seven additional experimental measurements were conducted to further verify our selected solvents. The impact of the extraction temperature and solvent-to-feed ratio was also investigated for selected solvents in experiments. Furthermore, this work suggested alternative solvents for 2,3-BDO LLE and proposed a versatile workflow that requires fewer experiments and can be applied to a broader range of LLE studies.

Extraction

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 Enabled Process Optimization for Pharmacologically Relevant Dependent Variables: CRADA Final Report

ABPDU staff worked with Teselagen to provide expertise and perform literature searches for therapeutic carrying strains to maximize fermentation parameters for Teselagen's machine learning platform. The goal was to overcome the COVID-19 crisis and plan for a future where molecules can be detected, diagnosed, built, manufactured, and distributed within months.

59 BASIC BIOLOGICAL SCIENCES

A Probabilistic Reasoner Based on Bayes Risk for Damage Detection in Structural Systems

Structural health monitoring (SHM) systems are used to inform operation of structural systems subject to loads and environments that may affect their integrity. SHM systems rely on continuous monitoring of the structure to determine its health state. These systems are often coupled with a model of the deployed structure to determine the consequences of changes in the system by forecasting the response to future states. These models, which may be thought of as digital twins, need to be updated to reflect the latest state of the structural system. This work makes use of an uncertainty-aware machine learning model that enforces distance preservation of the original input space to determine deviations from the training data input space distributions. This workflow enables domain shift detection to determine whether damage is present in the structure. The uncertainty metrics generated by this network are then used in a Bayes risk framework to design an optimal damage detector given cost and risk considerations. The approach is demonstrated on a computational example with simulated damage.

Najera-Flores, David [ATA Engineering, Inc.]

2024 Second Half Semi Annual Report: Modeling plasticity-mediated flow in metals with pressurized cavities

The objective is to better predict the bulk-scale mechanical behavior of porous metals that have over pressurized cavities (e.g., irradiated metals with helium bubbles) by quantifying the complex coupling among cavity aspects (e.g., size distribution, inhomogeneous overpressure values, spatial arrangement) and metal properties (e.g., rate-dependency, crystallographic lattice). This requires up-scaling local mechanical fields from the single crystal scale and will be accomplished using a homogenization approach that combines full-field numerical simulations, analytical formalisms, and physics-informed machine learning to produce symbolically-defined constitutive equations (e.g., gauge functions). These equations will satisfy the objective because they enable computationally efficient predictions that approach the accuracy of computationally expensive full-field numerical simulations, abide by theoretical requirements (e.g., conservation of energy, work conjugacy), and retain the transparency of analytical models.

36 MATERIALS SCIENCE

Circumventing data imbalance in magnetic ground state data for magnetic moment predictions

Abstract Magnetic materials play a crucial role in the transition to more sustainable forms of energy and electric vehicles. There is an anticipated shortage in magnetic materials in the future, and as a result there is an urgent need to discover and design new magnetic materials. Computational magnetic material design using density functional theory is daunting because of the challenge in identifying magnetic ground states from a combinatorially large set of possibilities. Machine learning offers a path forward by enabling efficient surrogate models that can more readily enumerate these states, but there is a dearth of training data available, and what is available tends to be imbalanced with too much non-magnetic data. In this work we show that the discrete and previously tackled data imbalance that exists at the level of the magnetic ordering leads to an imbalanced continuous distribution with many zeros when the data is unraveled at the atomic magnetic moment level, which subsequently leads to models with low accuracy for magnetic properties. We mitigate this by using a two-part model framework. Our scheme is able to classify atoms into magnetic and non-magnetic with an F1 score and Matthew’s correlation coefficient (MCC) of ~91% and then to provide an implicit embedding representation that maps directly onto the magnitude of the magnetic moment with a mean absolute error of 0.1 μ B . Beyond screening for new magnetic materials, we demonstrate an additional practical use case of our scheme: the provision of good initial guesses for magnetic moments in first-principles electronic relaxations. Such initialization is shown to lead to faster convergence to configurations that lie closer to the ground state.

Computer Science

Machine learning-driven predictive resource management in complex science workflows

Here, the collaborative efforts of large communities in science experiments, often comprising thousands of global members, reflect a monumental commitment to exploration and discovery. Recently, advanced and complex data processing has gained increasing importance in science experiments. Data processing workflows typically consist of multiple intricate steps, and the precise specification of resource requirements is crucial for each step to allocate optimal resources for effective processing. Estimating resource requirements in advance is challenging due to a wide range of analysis scenarios, varying skill levels among community members, and the continuously increasing spectrum of computing options. One practical approach to mitigate these challenges involves initially processing a subset of each step to measure precise resource utilization from actual processing profiles before completing the entire step. While this two-staged approach enables processing on optimal resources for most of the workflow, it has drawbacks such as initial inaccuracies leading to potential failures and suboptimal resource usage, along with overhead from waiting for initial processing completion, which is critical for fast-turnaround analyses. In this context, our study introduces a novel pipeline of machine learning models within a comprehensive workflow management system, the Production and Distributed Analysis (PanDA) system. These models employ advanced machine learning techniques to predict key resource requirements, overcoming challenges posed by limited upfront knowledge of characteristics at each step. Accurate forecasts of resource requirements enable informed and proactive decision-making in workflow management, enhancing the efficiency of handling diverse, complex workflows across heterogeneous resources.

97 MATHEMATICS AND COMPUTING

Satellite Embedding-Based Population Imputation for Areas with Missing Building Footprint Data: A Computer Vision-Based Approach

High-resolution population modeling is important for supporting effective decision-making across diverse sectors. LandScan Mosaic generates population estimates at the level of individual buildings and aggregates them to 3 arc-second grids, and this approach performs well in regions where building footprint data are comprehensive and reliable. However, large portions of the globe still suffer from incomplete, sparse, or entirely missing building stock datasets, creating a structural limitation for strictly building-based population models. To address this research gap, this study proposes a computer vision-based framework that employs Google Earth Engine satellite embeddings and UNet, which allows us to directly impute grid-level population estimates in building-data-deficient areas. Applied to Taiwan as a case study, the framework achieved strong predictive performance with R$^{2}$ of 0.89, RMSE of 18.70, and MAE of 8.41, outperforming traditional machine learning approaches. Notably, the proposed framework effectively addressed building false-positive errors inherent in Global Human Settlement Layer (GHSL) data, correctly identifying uninhabited areas that were erroneously classified as populated. The framework also offers significant advantages for global population mapping, particularly in terms of scalability and temporal consistency, thereby extending the coverage and accuracy of high-resolution population products in data-scarce regions worldwide. Urban planners, decision makers, and related stakeholders can obtain granular population distributions to support more accurate and targeted infrastructure investment, service delivery, resource allocation, and risk assessment decisions.

97 MATHEMATICS AND COMPUTING

An Active Learning-Based Streaming Pipeline for Reduced Data Training of Structure Finding Models in Neutron Diffractometry

Structure determination workloads in neutron diffractometry are computationally expensive and routinely require several hours to many days to determine the structure of a material from its neutron diffraction patterns. The potential for machine learning models trained on simulated neutron scattering patterns to significantly speed up these tasks have been reported recently. However, the amount of simulated data needed to train these models grows exponentially with the number of structural parameters to be predicted and poses a significant computational challenge. To overcome this challenge, we introduce a novel batch-mode active learning (AL) policy that uses uncertainty sampling to simulate training data drawn from a probability distribution that prefers labelled examples about which the model is least certain. We confirm its efficacy in training the same models with ∼ 75% less training data while improving the accuracy. We then discuss the design of an efficient stream-based training workflow that uses this AL policy and present a performance study on two heterogeneous platforms to demonstrate that, compared with a conventional training workflow, the streaming workflow delivers ∼ 20% shorter training time without any loss of accuracy.

Wang, Tianle [Brookhaven National Laboratory (BNL)

LTAU-FF: Loss Trajectory Analysis for Uncertainty in atomistic Force Fields

Model ensembles are effective tools for estimating prediction uncertainty in deep learning atomistic force fields. However, their widespread adoption is hindered by high computational costs and overconfident error estimates. In this work, we address these challenges by leveraging distributions of per-sample errors obtained during training and employing a distance-based similarity search in the model latent space. Our method, which we call LTAU (Loss Trajectory Analysis for Uncertainty), efficiently estimates the full probability distribution function of errors for any test point using the logged training errors, achieving speeds that are 2–3 orders of magnitudes faster than typical ensemble methods and allowing it to be used for tasks where training or evaluating multiple models would be infeasible. We apply LTAU towards estimating parametric uncertainty in atomistic force fields (LTAU-FF), demonstrating that it produces well-calibrated confidence intervals and predicts errors that correlate strongly with the true errors for data near the training domain. Furthermore, we show that the errors predicted by LTAU-FF can be used in practical applications for detecting out-of-domain data, tuning model performance, and predicting failure during simulations. We believe that LTAU will be a valuable tool for uncertainty quantification in atomistic force fields and is a promising method that should be further explored in other domains of machine learning.

97 MATHEMATICS AND COMPUTING

An investigation on machine learning predictive accuracy improvement and uncertainty reduction using VAE-based data augmentation

The confluence of ultrafast computers with large memory, rapid progress in Machine Learning (ML) algorithms, and the availability of large datasets place multiple engineering fields at the threshold of dramatic progress. However, a unique challenge in nuclear engineering is data scarcity because experimentation on nuclear systems is usually more expensive and time-consuming than most other disciplines. One potential way to resolve the data scarcity issue is deep generative learning, which uses certain ML models to learn the underlying distribution of existing data and generate synthetic samples that resemble the real data. In this way, one can significantly expand the dataset to train more accurate predictive ML models. In this study, our objective is to evaluate the effectiveness of data augmentation using variational autoencoder (VAE)-based deep generative models. We investigated whether the data augmentation leads to improved accuracy in the predictions of a deep neural network (DNN) model trained using the augmented data. Additionally, the DNN prediction uncertainties are quantified using Bayesian Neural Networks (BNN) and conformal prediction (CP) to assess the impact on predictive uncertainty reduction. To test the proposed methodology, we used TRACE simulations of steady-state void fraction data based on the NUPEC Boiling Water Reactor Full-size Fine-mesh Bundle Test (BFBT) benchmark. Here, we found that augmenting the training dataset using VAEs has improved the DNN model’s predictive accuracy, improved the prediction confidence intervals, and reduced the prediction uncertainties.

Bayesian neural network

Parameter uncertainties for imperfect surrogate models in the low-noise regime

Abstract Bayesian regression determines model parameters by minimizing the expected loss, an upper bound to the true generalization error. However, this loss ignores model form error, or misspecification, meaning parameter uncertainties are significantly underestimated and vanish in the large data limit. As misspecification is the main source of uncertainty for surrogate models of low-noise calculations, such as those arising in atomistic simulation, predictive uncertainties are systematically underestimated. We analyze the true generalization error of misspecified, near-deterministic surrogate models, a regime of broad relevance in science and engineering. We show that posterior parameter distributions must cover every training point to avoid a divergence in the generalization error and design a compatible ansatz which incurs minimal overhead for linear models. The approach is demonstrated on model problems before application to thousand-dimensional datasets in atomistic machine learning. Our efficient misspecification-aware scheme gives accurate prediction and bounding of test errors in terms of parameter uncertainties, allowing this important source of uncertainty to be incorporated in multi-scale computational workflows.

Swinburne, Thomas D. (ORCID:0000000232554257)

Physics-coupled data-driven design of high-temperature alloys

We present a materials design loop, which streamlines physics-coupled machine learning (ML) surrogate models to discover new alloy chemistries with improved properties. The efficacy is demonstrated by discovering a high-temperature alumina-forming austenitic (AFA) stainless steel with enhanced creep, followed by experimental validation. The ML models have been trained using a well-curated, highly consistent experimental dataset augmented with synthetic microstructural features from a computational thermodynamic approach. We have populated a large number of hypothetical AFA alloys to explore the high-dimensional composition space and have predicted their creep properties by providing the same synthetic input features obtained from the trained ML models. Uncertainties from the ML training were taken as thresholds for truncating predicted results to identify alloys with improved or deteriorated creep. Individual elemental compositions have been determined via probability density distribution analysis from the group of alloys at the top and bottom of the predicted creep values for further virtual and experimental validations. In conclusion, we anticipate that this workflow can be applied to screen desired conditions, such as chemistry and processing parameters, in high-dimensional space through physics-guided data analytics.

Alloy design

Physics vs structure: A systematic benchmark of learning strategies for multi-zone building thermal dynamics

Recent advances in physics-informed and data-driven machine learning promise improved thermal models for advanced building control, yet there is limited quantitative evidence on when added physics structure and architectural complexity are beneficial. Here, this work presents a systematic benchmark of five representative system identification methods for modeling multi-zone building thermal dynamics: linear state-space models, multi-layer perceptrons, neural state-space models, neural ordinary differential equations, and physically-consistent neural networks. The methods are evaluated across multiple data regimes and zone coupling strategies. Using a high-fidelity multi-zone commercial building emulator, we examine short-term and long-term prediction accuracy, computational efficiency, and ease of development. Our results reveal critical trade-offs between prediction performance, model complexity, and physical consistency. We demonstrate that decoupled, nonlinear black-box models consistently outperform coupled physics-constrained architectures in both predictive accuracy and out-of-distribution robustness in majority of the test cases for the building type considered in the study. Our findings quantify the cost of complexity in building thermal modeling and provide concrete, actionable, scenario-based guidelines for selecting model classes for control-oriented applications.

Building thermal modeling