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At least 829 records · Page 46

Enabling Predictive Scale-Bridging Simulations through Active Learning (Institutional Computing Annual Report (Project w21_alscalebridging)) [Slides]

The goal of this project was to develop, demonstrate, and provide a new capability to achieve greater physical fidelity in large-scale simulations, rather than the usual brute-force increases in the number of mesh elements or particles. Transport in nanoporous media, critical to hydrocarbon extraction from tight shale formations, is affected by molecular-level interactions. Several coarse-scale Lattice Boltzmann model (LBM) parameters cannot be directly computed, so instead we calibrate them to molecular dynamics (MD) simulations, by building emulators that mimic MD and LBM behavior and then training an upscaler. The resulting machine learning (ML)-based scale-bridging framework is up to 7 orders of magnitude faster than direct MD.

74 ATOMIC AND MOLECULAR PHYSICS↗

End-to-End Optimization for Battery Materials and Molecules by Combining Graph Neural Networks and Reinforcement Learning

The National Renewable Energy Laboratory (NREL), together with the Colorado School of Mines (CSM) and Colorado State University (CSU), has developed a machine learning-enhanced approach to the design of new battery materials. Currently, such materials are designed in part via numerous expensive high-fidelity computational simulations that predict the performance of a given composition. Even with computational screening tools, the vast landscape of possible molecular or crystal structures exceeds current and future computational capacity. Improving the efficiency by which new materials can be optimized will therefore disrupt the cost, risk, and time required to bring new energy solutions to the marketplace. Predicting the properties of an organic molecule or periodic crystalline material given its structure has grown increasingly common. These approaches leverage large-scale computational and experimental databases and ML approaches such as graph neural networks. The inverse design problem of finding a material that possesses desired properties is substantially more challenging, since enumerating all valid material structures is not feasible. In this project, we leveraged recent success in reinforcement learning to efficiently navigate this high-dimensional search space. Just as algorithms can find the optimal chess moves from nearly limitless options, we train an approach to evolve a simple starting structure into a complex structure that possess the desired properties. Our solution has been demonstrated by applying it to two related design application tasks for short- and long-term energy storage, respectively: (1) the design of solid-state ion conductors and (2) the design of organic redox-active materials. The project has resulted an open-source software library for material design, documented examples of applying the library to both organic and inorganic material optimization, and peer-reviewed publications detailing the data, computational models, and resulting candidate materials.

25 ENERGY STORAGE↗

Evaluation of normalization strategies for mass spectrometry-based multi-omics datasets

Introduction Data normalization is crucial for multi-omics integration, reducing systematic errors and maximizing the likelihood of discovering true biological variation. Most studies assess normalization for a single omics type or use datasets from separate experiments. Few address time-course data, where normalization might bias temporal differentiation. In this study, we compared common normalization methods and a machine learning approach, Systematical Error Removal using Random Forest (SERRF), using multi-omics datasets generated from the same experiment—even from the same cell lysate. Objectives To develop a straightforward process to assess normalization effects and identify the most robust methods across multi-omics datasets. Methods We analyzed metabolomics, lipidomics, and proteomics datasets from primary human cardiomyocytes and motor neurons exposed to acetylcholine-active compounds over time. Normalization effectiveness was evaluated based on improvement in QC features consistency and observing the change in treatment and time-related variance. Results Probabilistic Quotient Normalization (PQN) and Locally Estimated Scatterplot Smoothing (LOESS) QC were identified as optimal for metabolomics and lipidomics, while PQN, Median, and LOESS normalization excelled for proteomics. These methods consistently enhanced QC feature consistency in metabolomics and lipidomics, and preserved time-related variance or treatment-related variance in proteomics, demonstrating their effectiveness and robustness. SERRF normalization, applied only to metabolomics in this study, outperformed other methods in some datasets but inadvertently masked treatment-related variance in others. Conclusion Our evaluation identified PQN and LoessQC as the top methods for metabolomics and lipidomics, and PQN, Median, and Loess normalization for proteomics, in multi-omics integration in a temporal study.

60 APPLIED LIFE SCIENCES↗

Neoclassical toroidal viscosity torque prediction via deep learning

GPECnet is a densely connected neural network that has been trained on GPEC data, to predict the plasma stability, neoclassical toroidal viscosity (NTV) torque, and optimized 3D coil current distributions for desired NTV torque profiles. Using NTV torque, driven by non-axisymmetric field perturbations in a tokamak, can be vital in optimizing pedestal performance by controlling the rotation profile in both the core, to ensure tearing stability, and the edge, to avoid edge localized modes (ELMs). The generalized perturbed equilibrium code (GPEC) software package can be used to calculate the plasma stability to 3D perturbations and the NTV torque profile generated by applied 3D magnetic fields. These calculations, however, involve complex integrations over space and energy distributions, which takes time to compute. Initially, GPECnet has been trained solely on data representative of the quiescent H-mode (QH) scenario, in which neutral beams are often balanced and toroidal rotation is low across the plasma profile. Lastly, this work provides the foundation for active control of the rotation shear using a combination of beams and 3D fields for robust and high performance QH mode operation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Earth Sciences Applications for Energy and Global Security: A Few Vignettes [Slides]

Understanding the physics of flow and transport in the subsurface environment is crucial to several National Security applications. In the Energy Security realm, some examples include characterizing radioactive waste disposal, exploring natural gas extraction and sequestering CO2. An example in the Global Security arena is to be able to distinguish between anthropogenic and naturally occurring seismic disturbances, the former being of particular concern as underground nuclear testing activity has seen an increase in recent years. A common theme across these applications is the ability to accurately model fluid flow in porous and/or fractured subsurface media. For decades, researchers have grappled with how to include the effects of uncertainties in these models, including but not limited to heterogeneity, unknown initial and boundary conditions and issues with scalability. More recently advances in computing and machine learning methodologies have allowed a broader exploration of the uncertainty space as we strive for real time decision making. I will present an overview of the field and discuss a few examples of how my own research in these topics has evolved over nearly two decades.

58 GEOSCIENCES↗

Data-driven modeling of dislocation mobility from atomistics using physics-informed machine learning

Dislocation mobility, which dictates the response of dislocations to an applied stress, is a fundamental property of crystalline materials that governs the evolution of plastic deformation. Traditional approaches for deriving mobility laws rely on phenomenological models of the underlying physics, whose free parameters are in turn fitted to a small number of intuition-driven atomic scale simulations under varying conditions of temperature and stress. This tedious and time-consuming approach becomes particularly cumbersome for materials with complex dependencies on stress, temperature, and local environment, such as body-centered cubic crystals (BCC) metals and alloys. In this paper, we present a novel, uncertainty quantification-driven active learning paradigm for learning dislocation mobility laws from automated high-throughput large-scale molecular dynamics simulations, using Graph Neural Networks (GNN) with a physics-informed architecture. We demonstrate that this Physics-informed Graph Neural Network (PI-GNN) framework captures the underlying physics more accurately compared to existing phenomenological mobility laws in BCC metals.

36 MATERIALS SCIENCE↗

The case for digital twins in metal additive manufacturing

The digital twin (DT) is a relatively new concept that is finding increased acceptance in industry. A DT is generally considered as comprising a physical entity, its virtual replica, and two-way digital data communications in-between. Its primary purpose is to leverage the process intelligence captured within digital models—or usually their faster-solving surrogates—towards generating increased value from the physical entities. The surrogate models are created using machine learning based on data obtained from the field, experiments and digital models, which may be physics-based or statistics-based. Anomaly detection and correction, and diagnostic closed-loop process control are examples of how a process DT can be deployed. In the manufacturing industry, its use can achieve improvements in product quality and process productivity. Metal additive manufacturing (AM) stands to gain tremendously from the use of DTs. This is because the AM process is inherently chaotic, resulting in poor repeatability. However, a DT acting in a supervisory role can inject certainty into the process by actively keeping it within bounds through real-time control commands. Closed-loop feedforward control is achieved by observing the process through sensors that monitor critical parameters and, if there are any deviations from their respective optimal ranges, suitable corrective actions are triggered. The type of corrective action (e.g. a change in laser power or a modification to the scanning speed) and its magnitude are determined by interrogating the surrogate models. Because of their artificial intelligence (AI)-endowed predictive capabilities, which allow them to foresee a future state of the physical twin (e.g. the AM process), DTs proactively take context-sensitive preventative steps, whereas traditional closed-loop feedback control is usually reactive. Apart from assisting a build process in real-time, a DT can help with planning the build of a part by pinpointing the optimum processing window relevant to the desired outcome. Again, the surrogate models are consulted to obtain the required information. In this article, we explain how the application of DTs to the metal AM process can significantly widen its application space by making the process more repeatable (through quality assurance) and cheaper (by getting builds right the first time).

36 MATERIALS SCIENCE↗

A machine learning approach for identifying variables associated with risk of developing neutralizing antidrug antibodies to factor VIII

A key unmet need in the management of hemophilia A (HA) is the lack of clinically validated markers that are associated with the development of neutralizing antibodies to Factor VIII (FVIII) (commonly referred to as inhibitors). This study aimed to identify relevant biomarkers for FVIII inhibition using Machine Learning (ML) and Explainable AI (XAI) using the My Life Our Future (MLOF) research repository. The dataset includes biologically relevant variables such as age, race, sex, ethnicity, and the variants in the F8 gene. In addition, we previously carried out Human Leukocyte Antigen Class II (HLA-II) typing on samples obtained from the MLOF repository. Using this information, we derived other patient-specific biologically and genetically important variables. These included identifying the number of foreign FVIII derived peptides, based on the alignment of the endogenous FVIII and infused drug sequences, and the foreign-peptide HLA-II molecule binding affinity calculated using NetMHCIIpan. The data were processed and trained with multiple ML classification models to identify the top performing models. The top performing model was then chosen to apply XAI via SHAP, (SHapley Additive exPlanations) to identify the variables critical for the prediction of FVIII inhibitor development in a hemophilia A patient. Using XAI we provide a robust and ranked identification of variables that could be predictive for developing inhibitors to FVIII drugs in hemophilia A patients. These variables could be validated as biomarkers and used in making clinical decisions and during drug development. The top five variables for predicting inhibitor development based on SHAP values are: (i) the baseline activity of the FVIII protein, (ii) mean affinity of all foreign peptides for HLA DRB 3, 4, & 5 alleles, (iii) mean affinity of all foreign peptides for HLA DRB1 alleles), (iv) the minimum affinity among all foreign peptides for HLA DRB1 alleles, and (v) F8 mutation type.

60 APPLIED LIFE SCIENCES↗

3D reconstruction of an inertial-confinement fusion implosion with neural networks using multiple heterogeneous data sources

3D asymmetries are major degradation mechanisms in inertial-confinement fusion implosions at the National Ignition Facility (NIF). These asymmetries can be diagnosed and reconstructed with the neutron imaging system (NIS) on three lines of sight around the NIF target chamber. Conventional tomographic reconstructions are used to reconstruct the 3D morphology of the implosion using NIS [Volegov et al., J. Appl. Phys. 127, 083301 (2020)], but the problem is ill-posed with only three imaging lines of sight. Asymmetries can also be diagnosed with the real-time neutron activation diagnostics (RTNAD) and the neutron time-of-flight (nToF) suite. Since the NIS, RTNAD, and nToF each sample a different part of the implosion using different physical principles, we propose that it is possible to overcome the limitations of too few imaging lines of sight by performing 3D reconstructions that combine information from all three heterogeneous data sources. This work presents a new machine learning-based reconstruction technique to do just this. By using a simple physics model and group of neural networks to map 3D morphologies to data, this technique can easily account for data of multiple different types. A simple proof-of-principle is presented, demonstrating that this technique can accurately reconstruct a hot-spot shape using synthetic primary neutron images and a hot-spot velocity vector. In particular, the hot-spot’s asymmetry, quantified as spherical harmonic coefficients, is reconstructed to within ±4% of the radius in 90% of test cases. In the future, this technique will be applied to actual NIS, RTNAD, and nToF data to better understand 3D asymmetries at the NIF.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Deterministic High-Fidelity Neutronics Simulation of Pebble Bed Reactors Using Pebble Tracking Transport

The pebble tracking transport (PTT) algorithm offers a high-fidelity deterministic approach for neutron transport for pebble bed reactors (PBRs). This approach requires the mesh for the active-core region to consist exclusively of tetrahedral elements, where each node in the pebble-packing region represents a pebble centroid. This paper investigates the application of PTT for full-scale PBRs, considering both the isothermal and the temperature-dependent core conditions. Macroscopic cross sections are generated using Serpent 2 full-core eigenvalue simulations where pebbles are grouped into disjoint subsets using machine learning. To minimize the need for individual cross-section sets for each pebble in the core, K-means clustering is used to group pebbles by temperature and neutronic environment parameters. Here, we compare the multiplication factor and power rate distributions between PTT simulations using the Griffin reactor physics software and reference solutions from Serpent 2. Our analysis shows that a full-core, high-fidelity PTT calculation produces accurate results with minimal local (pebblewise) errors. Additionally, timing results indicate that PTT simulations converge rapidly on modern supercomputing platforms.

Griffin↗

D–MOPH–25: diverse MOF–molecule pairs for Henry’s constants prediction

Computational methods like grand-canonical Monte Carlo simulations and machine learning (ML) have accelerated metal–organic frameworks (MOF) exploration but are typically limited to a narrow range of adsorbates due to data availability and force field constraints. In this study, we introduce a dataset of diverse MOF–molecule pairs for Henry’s constant prediction, D–MOPH–25, which systematically explores a diverse chemical space by combining 113 molecular adsorbates with over 5000 MOF structures through an active learning process. D–MOPH–25 constitutes the most diverse adsorbate dataset used in any ML study of molecular adsorption in MOFs to date. Our workflow builds a benchmark for predicting Henry’s constants at 300 K, leveraging conformal prediction for uncertainty quantification. Assessment through Shannon entropy and uniform manifold approximation and projection confirms the comprehensiveness of D–MOPH–25 while highlighting the importance of robust classification to filter out unphysical data points in regression tasks. Although future enhancements in model architecture and sampling criteria could improve predictive performance, our dataset already spans the target space using only 2.31% of total possibilities. This comprehensive dataset facilitates assessment of model generalizability across adsorbate species and can establish a foundation for high-throughput MOF screening and ML-driven separation processes.

active learning↗

Toward Justifiable Trust in Autonomous Systems Incorporating Human Knowledge in Autonomous Systems through Machine Learning

Trust in Autonomous Systems is largely about humans trusting the decisions made by autonomous systems. This trust can be increased through learning from domain experts. In particular, autonomous systems can learn offline from past mission operations before conducting any operations of its own. Additionally, autonomous systems can learn online by obtaining human feedback during operations. We will discuss several classes of machine learning methods and our application of them to autonomous systems. The first class of methods is anomaly detection, which uses operations data to identify examples of anomalous operations. The second class of methods is inverse reinforcement learning, also known as apprenticeship learning, that takes past operations data as input and yields a controller that is able to duplicate the operations described by the data. The third class is active learning, which identifies examples on which the model is most uncertain and requests domain expert feedback.

Oza, Nikunj C.↗

Understanding and design of interstitial oxygen conductors

Highly efficient oxygen-active materials that react with, absorb, and transport oxygen is essential for fuel cells, electrolyzers and related applications. While vacancy-mediated oxygen-ion conductors have long been the focus of research, they are limited by high migration barriers at intermediate temperatures (400–600 °C), which hinder their practical applications. In contrast, interstitial oxygen conductors exhibit significantly lower migration barriers enabling higher ionic conductivity at lower temperatures. This review systematically examines both well-established and recently identified families of interstitial oxygen-ion conductors, focusing on how their unique structural motifs such as corner-sharing polyhedral frameworks, isolated polyhedral, and cage-like architectures, facilitate low migration barriers through interstitial and/or interstitialcy diffusion mechanisms. A central discussion of this review focuses on the evolution of design strategies, from targeted donor doping, element screening, to physical-intuition descriptor material screening and machine learning approach, which leverage computational tools to explore vast chemical spaces in search for new interstitial conductors. The success of these strategies demonstrates that a significant, largely unexplored space remains for discovering high-performing interstitial oxygen conductors. Crucial features enabling high-performance interstitial oxygen diffusion include the availability of electrons for oxygen reduction and sufficient structural flexibility with accessible volume for interstitial accommodation and migration. This review concludes with a forward-looking perspective, proposing a knowledge-driven methodology that integrates current understanding with data-centric approaches to identify promising interstitial oxygen conductors outside traditional search paradigms. These approaches are expected to significantly accelerate the development of high-performance interstitial oxygen conductors for a variety of oxygen-active applications, ultimately paving the way for more efficient and sustainable energy technologies.

Interstitial oxygen conductors↗

On the feasibility of using physics-informed machine learning for underground reservoir pressure management

In this work, we evaluate the feasibility of using physics-informed machine learning (PIML) for underground energy-related pressure management. To this end, we develop a PIML framework to manage underground reservoir pressures by training neural networks to determine fluid extraction rates for dedicated extraction wells during fluid injection operations given a range of reservoir conditions (e.g., transmissivity and storativity). We implement an automatically-differentiable analytical physics model of fluid flow in porous media within the PIML framework as a proxy for more complicated models. This allows us to execute a sufficient number of training scenarios to fully evaluate the feasibility of using PIML to support pressure management activities. We quantify the number of physics-model parameters required for automatic differentiation to become more efficient than finite-difference gradient calculations. We use a simple scenario with a single injector, extractor, and critical location for our feasibility analysis. We evaluate the effect of the size of the training dataset (i.e., the number of reservoir condition samples) on the accuracy and efficiency of the PIML framework. For an equivalent number of model evaluations, the larger training dataset took less time to train and produced a neural network that was able to more accurately manage reservoir pressures. We also evaluate the effect of the training dataset batch size (i.e., number of reservoir condition samples used to update the neural network coefficients during training; i.e., how the training dataset is partitioned). While training ran faster with larger batch sizes, they produced neural networks that managed pressures less accurately. We demonstrate the approach on a more complex scenario involving 10 injectors, 10 extractors, and 4 critical locations (a relatively high well density of 20 wells/km2). We provide the number of forward and adjoint model evaluations required in each case as an indication of the feasibility of using PIML for pressure management when more complicated physics models with longer execution times are used.

54 ENVIRONMENTAL SCIENCES↗

A detailed study of interpretability of deep neural network based top taggers

Abstract Recent developments in the methods of explainable artificial intelligence (XAI) allow researchers to explore the inner workings of deep neural networks (DNNs), revealing crucial information about input–output relationships and realizing how data connects with machine learning models. In this paper we explore interpretability of DNN models designed to identify jets coming from top quark decay in high energy proton–proton collisions at the Large Hadron Collider. We review a subset of existing top tagger models and explore different quantitative methods to identify which features play the most important roles in identifying the top jets. We also investigate how and why feature importance varies across different XAI metrics, how correlations among features impact their explainability, and how latent space representations encode information as well as correlate with physically meaningful quantities. Our studies uncover some major pitfalls of existing XAI methods and illustrate how they can be overcome to obtain consistent and meaningful interpretation of these models. We additionally illustrate the activity of hidden layers as neural activation pattern diagrams and demonstrate how they can be used to understand how DNNs relay information across the layers and how this understanding can help to make such models significantly simpler by allowing effective model reoptimization and hyperparameter tuning. These studies not only facilitate a methodological approach to interpreting models but also unveil new insights about what these models learn. Incorporating these observations into augmented model design, we propose the particle flow interaction network model and demonstrate how interpretability-inspired model augmentation can improve top tagging performance.

97 MATHEMATICS AND COMPUTING↗

Predicting resistive wall mode stability in NSTX through balanced random forests and counterfactual explanations

Abstract Recent progress in the disruption event characterization and forecasting framework has shown that machine learning guided by physics theory can be easily implemented as a supporting tool for fast computations of ideal stability properties of spherical tokamak plasmas. In order to extend that idea, a customized random forest (RF) classifier that takes into account imbalances in the training data is hereby employed to predict resistive wall mode (RWM) stability for a set of high beta discharges from the NSTX spherical tokamak. More specifically, with this approach each tree in the forest is trained on samples that are balanced via a user-defined over/under-sampler. The proposed approach outperforms classical cost-sensitive methods for the problem at hand, in particular when used in conjunction with a random under-sampler, while also resulting in a threefold reduction in the training time. In order to further understand the model’s decisions, a diverse set of counterfactual explanations based on determinantal point processes (DPP) is generated and evaluated. Via the use of DPP, the underlying RF model infers that the presence of hypothetical magnetohydrodynamic activity would have prevented the RWM from concurrently going unstable, which is a counterfactual that is indeed expected by prior physics knowledge. Given that this result emerges from the data-driven RF classifier and the use of counterfactuals without hand-crafted embedding of prior physics intuition, it motivates the usage of counterfactuals to simulate real-time control by generating the β N levels that would have kept the RWM stable for a set of unstable discharges.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Biological Research and Space Health Enabled by Machine Learning to Support Deep Space Missions

A key science goal of the NASA “Moon to Mars” campaign is to understand how biology responds to the Lunar, Martian, and deep space environments in order to advance fundamental knowledge, reduce risk, and support safe, productive human space missions. Through the powerful emerging computer science approaches of artificial intelligence (AI) and machine learning (ML), a paradigm shift has begun in biomedical science and engineered astronaut health systems, to enable Earth-independence and autonomy of mission operations. We present a decadal view of AI/ML architecture to support deep space mission goals, developed in concert with leaders in the field. We describe current AI/ML methods to support 1) fundamental biology, 2) in situ analytics, 3) high performance computing hardware, 4) automated science, 5) self-driving labs, 6) remote data management, 7) integrated real-time mission biomonitoring, and 8) a Precision Space Health system. Cutting-edge AI/ML approaches that can be integrated to support these domains include active learning, explainable AI, adaptive learning, causal inference, knowledge graphs, federated learning, transfer learning, and large language models. Finally, we present results from several current ML projects that are underway in the field to address key challenges of small sample n, high feature count, heterogeneity, and sparse data. These include 1) connecting omics data to phenotypic data using an ensemble model to infer causality of spaceflight rodent liver health disruption, 2) usage of explainable ML to interrogate the muscular underpinnings of spaceflight muscle atrophy, 3) ML models analyzing and determining directed acyclic graphs of human space health risk leveraging rodent bone datasets, 4) usage of large pre-trained models connecting biomedical knowledgebases with small spaceflight datasets to understand gene-to-gene interaction networks, and 5) a suite of benchmarked open science datasets (spaceflight mouse liver; radiation DNA damage) enabling programmers to identify the best ML algorithms to answer space biological science questions.

space biology↗

A Comprehensive Review of Latent Space Dynamics Identification Algorithms for Intrusive and Non-Intrusive Reduced-Order-Modeling

Numerical solvers of partial differential equations (PDEs) have been widely employed for simulating physical systems. However, the computational cost remains a major bottleneck in various scientific and engineering applications, which has motivated the development of reduced-order models (ROMs). Recently, machine-learning-based ROMs have gained significant popularity and are promising for addressing some limitations of traditional ROM methods, especially for advection dominated systems. In this chapter, we focus on a particular framework known as Latent Space Dynamics Identification (LaSDI), which transforms the high-fidelity data, governed by a PDE, to simpler and low-dimensional latent-space data, governed by ordinary differential equations (ODEs). These ODEs can be learned and subsequently interpolated to make ROM predictions. Each building block of LaSDI can be easily modulated depending on the application, which makes the LaSDI framework highly flexible. In particular, we present strategies to enforce the laws of thermodynamics into LaSDI models (tLaSDI), enhance robustness in the presence of noise through the weak form (WLaSDI), select high-fidelity training data efficiently through active learning (gLaSDI, GPLaSDI), and quantify the ROM prediction uncertainty through Gaussian processes (GPLaSDI). We demonstrate the performance of different LaSDI approaches on Burgers equation, a non-linear heat conduction problem, and a plasma physics problem, showing that LaSDI algorithms can achieve relative errors of less than a few percent and up to thousands of times speed-ups.

Computational Engineering, Finance, and Science (c↗