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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2021

Unsupervised Resource Allocation with Graph Neural Networks

We present an approach for maximizing a global utility function by learning how to allocate resources in an unsupervised way. We expect interactions between allocation targets to be important and therefore propose to learn the reward structure for near-optimal allocation policies with a GNN. By relaxing the resource constraint, we can employ gradient-based optimization in contrast to more standard evolutionary algorithms. Our algorithm is motivated by a problem in modern astronomy, where one needs to select-based on limited initial information-among $10^9$ galaxies those whose detailed measurement will lead to optimal inference of the composition of the universe. Our technique presents a way of flexibly learning an allocation strategy by only requiring forward simulators for the physics of interest and the measurement process. We anticipate that our technique will also find applications in a range of resource allocation problems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Data efficiency and extrapolation trends in neural network interatomic potentials

Abstract Recently, key architectural advances have been proposed for neural network interatomic potentials (NNIPs), such as incorporating message-passing networks, equivariance, or many-body expansion terms. Although modern NNIP models exhibit small differences in test accuracy, this metric is still considered the main target when developing new NNIP architectures. In this work, we show how architectural and optimization choices influence the generalization of NNIPs, revealing trends in molecular dynamics (MD) stability, data efficiency, and loss landscapes. Using the 3BPA dataset, we uncover trends in NNIP errors and robustness to noise, showing these metrics are insufficient to predict MD stability in the high-accuracy regime. With a large-scale study on NequIP, MACE, and their optimizers, we show that our metric of loss entropy predicts out-of-distribution error and data efficiency despite being computed only on the training set. This work provides a deep learning justification for probing extrapolation and can inform the development of next-generation NNIPs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Open-source generation of sigma profiles: impact of quantum chemistry and solvation treatment on machine learning performance

The combination of machine learning (ML) models with chemistry-related tasks requires the description of molecular structures in a machine-readable way. The nature of these so-called molecular descriptors has a direct and major impact on the performance of ML models and remains an open problem in the field. Structural descriptors like SMILES strings or molecular graphs lack size-independence and can be memory intensive. Machine-learned descriptors can be of low dimensionality and constant size but lack physical significance and human interpretability. Sigma profiles, which are unnormalized histograms of the surface charge distributions of solvated molecules, combine physical significance with low dimensionality and size-independence, making them a suitable candidate for a universal molecular descriptor. However, their widespread adoption in ML applications requires open access to sigma profile generation, which is currently not available. This work details the development of OpenSPGen – an open-source tool for generating sigma profiles. Also presented are studies on the effect of different settings on the efficacy of the generated sigma profiles at predicting thermophysical material properties when used as inputs to a Gaussian process as a simple surrogate ML model. We find that a higher level of theory does not translate to more accurate results. We also provide further recommendations for sigma profile calculation and use in ML models.

Salih, Fathya Y. M. [University of Notre Dame, IN ↗
DOE OSTI2023

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function

Abstract Motivation Millions of protein sequences have been generated by numerous genome and transcriptome sequencing projects. However, experimentally determining the function of the proteins is still a time consuming, low-throughput, and expensive process, leading to a large protein sequence-function gap. Therefore, it is important to develop computational methods to accurately predict protein function to fill the gap. Even though many methods have been developed to use protein sequences as input to predict function, much fewer methods leverage protein structures in protein function prediction because there was lack of accurate protein structures for most proteins until recently. Results We developed TransFun—a method using a transformer-based protein language model and 3D-equivariant graph neural networks to distill information from both protein sequences and structures to predict protein function. It extracts feature embeddings from protein sequences using a pre-trained protein language model (ESM) via transfer learning and combines them with 3D structures of proteins predicted by AlphaFold2 through equivariant graph neural networks. Benchmarked on the CAFA3 test dataset and a new test dataset, TransFun outperforms several state-of-the-art methods, indicating that the language model and 3D-equivariant graph neural networks are effective methods to leverage protein sequences and structures to improve protein function prediction. Combining TransFun predictions and sequence similarity-based predictions can further increase prediction accuracy. Availability and implementation The source code of TransFun is available at https://github.com/jianlin-cheng/TransFun.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Domain Adaptive Graph Neural Networks for Constraining Cosmological Parameters Across Multiple Data Sets

State of the art astronomical simulations have provided datasets which enabled the training of novel deep learning techniques for constraining cosmological parameters. However, differences in subgrid physics implementation and numerical approximations among simulation suites lead to differences in simulated datasets, which pose a hard challenge when trying to generalize across diverse data domains and ultimately when applying models to observational data. Recent work reveals deep learning algorithms are able to extract more information from complex cosmological simulations than summary statistics like power spectra. We introduce Domain Adaptive Graph Neural Networks (DA-GNNs), trained on CAMELS data, inspired by CosmoGraphNet (Villanueva-Domingo et al 2023). By utilizing GNNs, we can capitalize on their capacity to capture both astrophysical and topological features of galaxy distributions. Mixing these capabilities with domain adaptation techniques such as Maximum Mean Discrepancy (MMD), which enable extraction of domain-invariant features, our framework demonstrates enhanced accuracy and robustness. We present experimental results, including the alignment of distributions across domains through data visualization. These findings suggest that DA-GNNs are an efficient way of extracting domain independent cosmological information, a vital step toward robust deep learning for real cosmic survey data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

MOFSimplify, machine learning models with extracted stability data of three thousand metal–organic frameworks

Abstract We report a workflow and the output of a natural language processing (NLP)-based procedure to mine the extant metal–organic framework (MOF) literature describing structurally characterized MOFs and their solvent removal and thermal stabilities. We obtain over 2,000 solvent removal stability measures from text mining and 3,000 thermal decomposition temperatures from thermogravimetric analysis data. We assess the validity of our NLP methods and the accuracy of our extracted data by comparing to a hand-labeled subset. Machine learning (ML, i.e. artificial neural network) models trained on this data using graph- and pore-geometry-based representations enable prediction of stability on new MOFs with quantified uncertainty. Our web interface, MOFSimplify, provides users access to our curated data and enables them to harness that data for predictions on new MOFs. MOFSimplify also encourages community feedback on existing data and on ML model predictions for community-based active learning for improved MOF stability models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Attention-Augmented Parametric Kernel Graph Neural Network (APKGNN) for Node Classification

We present a new graph neural network, the Attention-based Parametric-Kernel augmented Graph Neural Network (APKGNN), developed for node classification tasks. Despite extensive work on modeling multi-faceted relationships between connected nodes of a graph, the effect of attention on edge features mapped to relationships has not yet been analyzed through learning representation. This study derives such an attention vector by first calculating node features corresponding to endpoints of an edge and then aggregating these with extracted local intrinsic patches of a given graph to generate augmented local patch vectors. This process uses a parametric kernel based on Gaussian mixture models (GMMs) to embed local neighborhoods of the graph in local patches. The patch vectors then convolve with the above node features to produce an updated node representation. We show that this new learning representation (APKGNN) achieves higher node classification accuracy on tasks - both standard benchmarks (Cora, PubMed, Citeseer) and new experimental short text corpora where nodes correspond to text documents and words. This implementation of the GNN convolution layer outperforms state-of-the-art (SOTA) algorithms, achieving higher training, validation, and test accuracy by a significant margin on three standard benchmark data sets under both SOTA experimental settings and those for new testbeds.

Bose, Avishek↗
DOE OSTI2022

On the integration of molecular dynamics, data science, and experiments for studying solvent effects on catalysis

Computational workflows that combine molecular dynamics (MD) simulations and emerging data-centric (DC) methods can accelerate the screening and analysis of solvent systems experimentally and computationally. Here, MD simulations provide atomic positions and velocities of reactant, solvent, and catalyst materials that can be manipulated into data representations that in turn can be used by DC techniques to conduct predictive modeling, feature extraction, and experimental design. For liquid-phase catalytic applications, emerging DC techniques such as Convolutional and Graph Neural Networks (CNN/GNN), Topological Data Analysis (TDA), and Active Learning (AL) can leverage MD and experimental data to quickly predict solvent effects on reaction outcomes. For instance, in recent studies, 3D solvent environments obtained with MD have been exploited by CNNs to predict experimental reaction rates for homogeneous acid-catalyzed lignocellulosic processes. In this perspective, we discuss basic principles of DC methods and how these can be combined with MD to enable high-throughput screening of solvent selection for diverse catalysis applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

ARCH: Large-scale knowledge graph via aggregated narrative codified health records analysis

Objective: Electronic health record (EHR) systems contain a wealth of clinical data stored as both codified data and free-text narrative notes (NLP). The complexity of EHR presents challenges in feature representation, information extraction, and uncertainty quantification. Here, to address these challenges, we proposed an efficient Aggregated naRrative Codified Health (ARCH) records analysis to generate a large-scale knowledge graph (KG) for a comprehensive set of EHR codified and narrative features. Methods: Using data from 12.5 million Veterans Affairs patients, ARCH first derives embedding vectors and generates similarities along with associated p-values to measure the strength of relatedness between clinical features with statistical certainty quantification. Next, ARCH performs a sparse embedding regression to remove indirect linkage between features to build a sparse KG. Finally, ARCH was validated on various clinical tasks, including detecting known relationships between entity pairs, predicting drug side effects, disease phenotyping, as well as sub-typing Alzheimer’s disease patients. Results: ARCH produces high-quality clinical embeddings and KG for over 60,000 codified and narrative EHR concepts. The KG and embeddings are visualized in the R-shiny powered web-API.3 ARCH achieved high accuracy in detecting EHR concept relationships, with AUCs of 0.926 (codified) and 0.861 (NLP) for similar EHR concepts, and 0.810 (codified) and 0.843 (NLP) for related pairs. It detected drug side effects with a 0.723 AUC, which improved to 0.826 after fine-tuning. Using both codified and NLP features, the detection power increased significantly. Compared to other methods, ARCH has superior accuracy and enhances weakly supervised phenotyping algorithms’ performance. Notably, it successfully categorized Alzheimer’s patients into two subgroups with varying mortality rates. Conclusion: The proposed ARCH algorithm generates large-scale high-quality semantic representations and knowledge graph for both codified and NLP EHR features, useful for a wide range of predictive modeling tasks.

Electronic health records↗
DOE OSTI2025

Graph neural networks for mechanical property prediction of 2D fiber composites

This work investigates the ability of graph neural networks (GNNs) to homogenize 2D fiber composite microstructures. We use different inhomogeneity and anisotropy indices to motivate and show that the Volume Elements (VEs) used in ML methods should ideally be far from their Representative Volume Element (RVE) size limit and, consequently, are notably anisotropic. Hence, training only the isotropic limit properties may not be acceptable. Another aspect is the need to normalize elastic stiffness values for ML, especially when high elastic contrast ratios are encountered between composite phases or in the material set. We introduce a normalization technique based on the mean-field method (MFM) to handle such high contrast ratios and train for the entire stiffness tensor. We show that the proposed GNN approaches exhibit high accuracy and efficiency compared to traditional methods and convolutional neural networks, utilizing unstructured graphs constructed from microstructure topology. Our model successfully predicts the stiffness tensor, peak strength under bulk damage, and brittle fracture initiation strength across diverse microstructure configurations while maintaining high accuracy even for extreme material contrasts and volume fractions. We also present a method to improve prediction accuracy for small dataset sizes using Voronoi partitioning.

Brittle strength↗
DOE OSTI2023

Accelerating network layouts using graph neural networks

Graph layout algorithms used in network visualization represent the first and the most widely used tool to unveil the inner structure and the behavior of complex networks. Current network visualization software relies on the force-directed layout (FDL) algorithm, whose high computational complexity makes the visualization of large real networks computationally prohibitive and traps large graphs into high energy configurations, resulting in hard-to-interpret “hairball” layouts. Here we use Graph Neural Networks (GNN) to accelerate FDL, showing that deep learning can address both limitations of FDL: it offers a 10 to 100 fold improvement in speed while also yielding layouts which are more informative. We analytically derive the speedup offered by GNN, relating it to the number of outliers in the eigenspectrum of the adjacency matrix, predicting that GNNs are particularly effective for networks with communities and local regularities. Finally, we use GNN to generate a three-dimensional layout of the Internet, and introduce additional measures to assess the layout quality and its interpretability, exploring the algorithm’s ability to separate communities and the link-length distribution. The novel use of deep neural networks can help accelerate other network-based optimization problems as well, with applications from reaction-diffusion systems to epidemics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Accelerating the Inference of the Exa.TrkX Pipeline

Recently, graph neural networks (GNNs) have been successfully used for a variety of particle reconstruction problems in high energy physics, including particle tracking. The Exa.TrkX pipeline based on GNNs demonstrated promising performance in reconstructing particle tracks in dense environments. It includes five discrete steps: data encoding, graph building, edge filtering, GNN, and track labeling. All steps were written in Python and run on both GPUs and CPUs. In this work, we accelerate the Python implementation of the pipeline through customized and commercial GPU-enabled software libraries, and develop a C++ implementation for inferencing the pipeline. The implementation features an improved, CUDA-enabled fixed-radius nearest neighbor search for graph building and a weakly connected component graph algorithm for track labeling. GNNs and other trained deep learning models are converted to ONNX and inferenced via the ONNX Runtime C++ API. The complete C++ implementation of the pipeline allows integration with existing tracking software. We report the memory usage and average event latency tracking performance of our implementation applied to the TrackML benchmark dataset.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Virtual node graph neural network for full phonon prediction

Understanding the structure-property relationship is crucial for designing materials with desired properties. The past few years have witnessed remarkable progress in machine-learning methods for this connection. However, substantial challenges remain, including the generalizability of models and prediction of properties with materials-dependent output dimensions. Here we present the virtual node graph neural network to address the challenges. By developing three virtual node approaches, we achieve Γ-phonon spectra and full phonon dispersion prediction from atomic coordinates. We show that, compared with the machine-learning interatomic potentials, our approach achieves orders-of-magnitude-higher efficiency with comparable to better accuracy. This allows us to generate databases for Γ-phonon containing over 146,000 materials and phonon band structures of zeolites. Additionally, our work provides an avenue for rapid and high-quality prediction of phonon band structures enabling materials design with desired phonon properties. The virtual node method also provides a generic method for machine-learning design with a high level of flexibility. In this study, the authors present a virtual node graph neural network to enable the prediction of material properties with variable output dimensions. This method offers fast and accurate predictions of phonon band structures in complex solids.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Direction-optimizing Label Propagation Framework for Structure Detection in Graphs: Design, Implementation, and Experimental Analysis

Label Propagation is not only a well-known machine learning algorithm for classification but also an effective method for discovering communities and connected components in networks. We propose a new Direction-optimizing Label Propagation Algorithm (DOLPA) framework that enhances the performance of the standard Label Propagation Algorithm (LPA), increases its scalability, and extends its versatility and application scope. As a central feature, the DOLPA framework relies on the use of frontiers and alternates between label push and label pull operations to attain high performance. It is formulated in such a way that the same basic algorithm can be used for finding communities or connected components in graphs by only changing the objective function used. Additionally, DOLPA has parameters for tuning the processing order of vertices in a graph to reduce the number of edges visited and improve the quality of solution obtained. We present the design and implementation of the enhanced algorithm as well as our shared-memory parallelization of it using OpenMP. We also present an extensive experimental evaluation of our implementations using the LFR benchmark and real-world networks drawn from various domains. Compared with an implementation of LPA for community detection available in a widely used network analysis software, we achieve at most five times the F-Score while maintaining similar runtime for graphs with overlapping communities. We also compare DOLPA against an implementation of the Louvain method for community detection using the same LFR-graphs and show that DOLPA achieves about three times the F-Score at just 10% of the runtime. For connected component decomposition, our algorithm achieves orders of magnitude speedups over the basic LP-based algorithm on large-diameter graphs, up to 13.2× speedup over the Shiloach-Vishkin algorithm, and up to 1.6× speedup over Afforest on an Intel Xeon processor using 40 threads.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A Two-Stage Quantum Reinforcement Learning Method for Multi-Objective Transmission Switching

Multi-objective transmission switching (MO-TS) problems involve the strategic reconfiguration of network topology to simultaneously optimize multiple objectives. As the system scale increases, finding feasible solutions becomes increasingly challenging due to the problem's nonlinearity and high computational complexity. To address these challenges, this paper proposes a two-stage quantum reinforcement learning method that leverages potential quantum advantages for MO-TS. In the first stage, candidate switching lines are identified using a graph-theoretical approach to reduce the problem's dimensionality. The second stage introduces a quantum-classical reinforcement learning framework, where a learnable measurement-based CNN-ResVQC architecture is developed to effectively reduce the input dimension for quantum processing, mitigate vanishing gradients, and enhance trainability while improving the quantum circuit's flexibility in modeling complex decision policies for MO-TS. Numerical studies on IEEE 14-bus, 57-bus, and 118-bus systems demonstrate that the proposed algorithm achieves superior training stability and faster convergence with approximately 1% of the network parameters required by classical algorithms, highlighting its effectiveness, efficiency, and scalability. Furthermore, the practicality is validated through its stable convergence under three common quantum noise channels.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2020

Predicting Elastic Properties of Materials from Electronic Charge Density Using 3D Deep Convolutional Neural Networks

Materials representation plays a key role in machine learning-based prediction of materials properties and new materials discovery. Currently both graph and three-dimensional (3D) voxel representation methods are based on the heterogeneous elements of the crystal structures. Here, we propose to use electronic charge density (ECD) as a generic unified 3D descriptor for materials property prediction with the advantage of possessing close relation with the physical and chemical properties of materials. We developed an ECD-based 3D convolutional neural networks (CNNs) for predicting the elastic properties of materials, in which CNNs can learn effective hierarchical features with multiple convolving and pooling operations. Extensive benchmark experiments over 2170 $Fm\bar3m$ face-centered-cubic materials show that our ECD-based CNNs can achieve good performance for elasticity prediction. Especially, our CNN models based on the fusion of elemental Materials-Agnostic Platform for Informatics and Exploration features and ECD descriptors achieved the best fivefold cross-validation performance. More importantly, we showed that our ECD-based CNN models can achieve significantly better extrapolation performance when evaluated over nonredundant data sets, where there are few neighbor-training samples around test samples. As an additional validation, we evaluated the predictive performance of our models on 329 materials of space group $Fm\bar3m$ by comparing to density functional theory calculated values, which shows a better prediction power of our model for bulk modulus than shear modulus. Because of the unified representation power of ECD, it is expected that our ECD-based CNN approach can also be applied to predict other physical and chemical properties of crystalline materials.

36 MATERIALS SCIENCE↗