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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Multi-Edge Graph Convolutional Networks for Power Systems

The exponential electrification of transportation has contributed to highly intermittent load variations in the distribution grid. This uncertainty has raised challenges for distribution system operation and control. Accurate nodal voltage estimation is highly essential for the safe and reliable operation of the grid. Graph convolutional networks have been used in machine-learning-based models for power grid applications like voltage estimation for their ability to capture the network topology of the grid. This paper presents a novel multi-edge graph convolutional layer that considers resistance and reactance as edge attributes. This layer is created by modifying the message-passing function within the graph convolutional network. The novel layer is then used to create a multi-edge graph convolutional network-based surrogate model for estimating voltage in the distribution network with highly uncertain electric vehicle loads. Results indicate improved performance of the multi-edge graph convolutional network model when compared to a standard graph convolutional network model.

Ravi, Abhijith↗
DOE OSTI2023

Session Introduction: Graph Representations and Algorithms in Biomedicine

Connectivity is a fundamental property of biological systems: on the cellular level, proteins interact with each other to form protein-protein interaction networks (PPIs); on the organism level, neurons are arranged in a network; and on a community-level, species can have complex relationships with one another that drive the development and balance of an ecosystem. Graphs, representations of systems consisting of entities as vertices and their connections as edges, are a useful structure to characterize many such systems. Such models can be used to understand biological systems that naturally have a network structure, including PPIs, biological neurons, and ecosystems. In today’s information age, graph representations and algorithms (often in combination with machine learning techniques) are used to organize massive amounts of related data, much of which may be heterogeneous or unstructured, and identify patterns that represent novel biological insights. PSB’s 2023 session “Graph Representations and algorithms in Biomedicine,” encompasses modern developments in graph theory and its applications to various fields of biomedicine. This session includes a wide range of research - knowledge graphs built from text-mined health data, heterogeneous networks using multi-omic databases, and graphs refined to represent uncertainty or improve memory usage.

Chrisman, Brianna S.↗
DOE OSTI2024

Portable Parallel Algorithms and Frameworks for Exascale Graph Analytics

Graphs (or networks) are a tool used to model the interactions among various entities. Efficiently processing large graphs has recently attracted significant attention due to the applications of graphs in various domains, such as biology, chemistry, and cyber-security. Analyzing the structure and properties of these graphs is an important component of many scientific computing pipelines. With the explosion in the volume of data, graphs have become very large and can contain hundreds of billions of vertices and trillions of edges. Therefore, it is crucial to develop high-performance methods to enable graph analysis to be done quickly and energy-efficiently. Furthermore, these solutions should be highly parallel in order to take advantage of modern parallel machines. However, designing efficient solutions is not enough. With the wide variety of computing environments available, each with different programmability and performance characteristics, it is necessary to develop solutions that are portable in terms of both performance (i.e., provide theoretical guarantees) and programmability (i.e., provide high level abstractions).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

FPGA Acceleration of GCN in Light of the Symmetry of Graph Adjacency Matrix

Graph Convolutional Neural Networks (GCNs) are widely used to process large-scale graph data. Different from deep neural networks (DNNs), GCNs are sparse, irregular, and unstructured, posing unique challenges to hardware acceleration with regular processing elements (PEs). In particular, the adjacency matrix of a GCN is extremely sparse, leading to frequent but irregular memory access, low spatial/temporal data locality and poor data reuse. Furthermore, a realistic graph usually consists of unstructured data (e.g., unbalanced distributions), creating significantly different processing times and imbalanced workload for each node in GCN acceleration. To overcome these challenges, we propose an end-to-end hardware-software co-design to accelerate GCNs on resource-constrained FPGAs with the features including: (1) A custom dataflow that leverages symmetry along the diagonal of the adjacency matrix to accelerate feature aggregation for undirected graphs. We utilize either the upper or the lower triangular matrix of the adjacency matrix to perform aggregation in GCN to improve data reuse. (2) Unified compute cores for both aggregation and transform phases, with full support to the symmetry-based dataflow. These cores can be dynamically reconfigured to the systolic mode for transformation or as individual accumulators for aggregation in GCN processing. (3) Preprocessing of the graph in software to rearrange the edges and features to match the custom dataflow. This step improves the regularity in memory access and data reuse in the aggregation phase. Moreover, we quantize the GCN precision from FP32 to INT8 to reduce the memory footprint without losing the inference accuracy. We implement our accelerator design in Intel Stratix10 MX FPGA board with HBM2, and demonstrate 1.3x-110.5x improvement in end-to-end GCN latency as compared to the state-of the-art FPGA implementations, on the graph datasets of Cora, Pubmed, Citeseer and Reddit.

Nair, Gopikrishnan R.↗
DOE OSTI2024

A Comparison between Invariant and Equivariant Classical and Quantum Graph Neural Networks

Machine learning algorithms are heavily relied on to understand the vast amounts of data from high-energy particle collisions at the CERN Large Hadron Collider (LHC). The data from such collision events can naturally be represented with graph structures. Therefore, deep geometric methods, such as graph neural networks (GNNs), have been leveraged for various data analysis tasks in high-energy physics. One typical task is jet tagging, where jets are viewed as point clouds with distinct features and edge connections between their constituent particles. The increasing size and complexity of the LHC particle datasets, as well as the computational models used for their analysis, have greatly motivated the development of alternative fast and efficient computational paradigms such as quantum computation. In addition, to enhance the validity and robustness of deep networks, we can leverage the fundamental symmetries present in the data through the use of invariant inputs and equivariant layers. In this paper, we provide a fair and comprehensive comparison of classical graph neural networks (GNNs) and equivariant graph neural networks (EGNNs) and their quantum counterparts: quantum graph neural networks (QGNNs) and equivariant quantum graph neural networks (EQGNN). The four architectures were benchmarked on a binary classification task to classify the parton-level particle initiating the jet. Based on their area under the curve (AUC) scores, the quantum networks were found to outperform the classical networks. However, seeing the computational advantage of quantum networks in practice may have to wait for the further development of quantum technology and its associated application programming interfaces (APIs).

Forestano, Roy T. (ORCID:0000000203552076)↗
DOE OSTI2025

Nature-GL: A Revolutionary Learning Paradigm Unleashing Nature’s Power in Real-World Spatial-Temporal Graph Learning

Spatial-Temporal Graph Learning (ST-GL) is a prominent research area due to its unique capability to effectively learn real-world graphs. Applications of ST-GL pose stringent and various demands on not only real-time inference with low energy cost and high ac- curacy but also fast training. Unfortunately, as Moore’s Law approaches its limits and ST-GL model complexity drastically grows, the gap between digital hardware’s computational power and ST- GL application demands is widening. In response, this paper introduces Nature-GL, a nature-powered graph learning paradigm that exploits the principle of entropy increase to advance graph learning. In particular, Nature-GL transforms both the training and inference of real-valued ST-GL into electron-speed natural anneal- ing processes of a parameterized dynamical system that represents the target graphs. Experimental results across four real-world ap- plications with six datasets demonstrate that Nature-GL achieves orders-of-magnitude speedups in both training and inference, delivering higher accuracy compared to Graph Neural Networks.

Liu, Chuan [University of Rochester]↗
DOE OSTI2025

Scalable training of trustworthy and energy-efficient predictive graph foundation models for atomistic materials modeling: a case study with HydraGNN

We present our work on developing and training scalable, trustworthy, and energy-efficient predictive graph foundation models (GFMs) using HydraGNN, a multi-headed graph convolutional neural network architecture. HydraGNN expands the boundaries of graph neural network (GNN) computations in both training scale and data diversity. It abstracts over message passing algorithms, allowing both reproduction of and comparison across algorithmic innovations that define nearest-neighbor convolution in GNNs. This work discusses a series of optimizations that have allowed scaling up the GFMs training to tens of thousands of GPUs on datasets consisting of hundreds of millions of graphs. Our GFMs use multitask learning (MTL) to simultaneously learn graph-level and node-level properties of atomistic structures, such as energy and atomic forces. Using over 154 million atomistic structures for training, we illustrate the performance of our approach along with the lessons learned on two state-of-the-art US Department of Energy (US-DOE) supercomputers, namely the Perlmutter petascale system at the National Energy Research Scientific Computing Center and the Frontier exascale system at Oak Ridge Leadership Computing Facility. The HydraGNN architecture enables the GFM to achieve near-linear strong scaling performance using more than 2000 GPUs on Perlmutter and 16,000 GPUs on Frontier.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Powers of magnetic graph matrix: Fourier spectrum, walk compression, and applications

Magnetic graphs, originally developed to model quantum systems under magnetic fields, have recently emerged as a powerful framework for analyzing complex directed networks. Existing research has primarily used the spectral properties of the magnetic graph matrix to study global and stationary network features. However, their capacity to model local, nonequilibrium behaviors, often described by matrix powers, remains largely unexplored. We present a combinatorial interpretation of the magnetic graph matrix powers through directed walk profiles—counts of graph walks indexed by the number of edge reversals. Crucially, we establish that walk profiles correspond to a Fourier transform of magnetic matrix powers. The connection allows exact reconstruction of walk profiles from magnetic matrix powers at multiple discrete potentials, and more importantly, an even smaller number of potentials often suffices for accurate approximate reconstruction in real networks. This shows the empirical compressibility of the information captured by the magnetic matrix. This fresh perspective suggests further applications; for example, we illustrate how powers of the magnetic matrix can identify frustrated directed cycles (e.g., feedforward loops) and can be effectively employed for link prediction by encoding local structural details in directed graphs.

complex networks↗
DOE OSTI2026

Knowledge Graph for End-to-End Traceability of an Integrated Human-Earth System Model

Integrated human-Earth system models inform energy-water-land system dynamics and policies, yet their results are difficult to trace through input-data, model structure, scenario configurations, and solved outputs. Because this information is siloed across disconnected artifacts, process-based IAMs have historically lacked a unified, queryable representation. Such lack of traceability prevents researchers from systematically isolating the multi-sector drivers of complex outcomes (such as tracing water-scarcity results back to distant energy-system dynamics) or conducting holistic uncertainty attribution across hundreds of interacting parameters. To address this concern, our work documents the software engineering process of a knowledge graph that unifies these four layers for the Global Change Analysis Model (GCAM-USA_Reference scenario, GCAM v9.1). The graph was built as a relational property graph in DuckDB from the run’s own artifacts: the input-preparation dependency map (gcamdata chunk map), the model’s XML input files, the run configuration, and the results database (BaseX), successfully mapping the model’s declared structure. The resulting graph comprises 204,321 nodes and 1,687,814 edges across 16 node types and 15 edge types, with approximately 16.3 million time-series values stored separately to maintain structural efficiency. To ensure representation fidelity, every edge carries an epistemic-status annotation recording the warrant for the relationship (structural, provenance, dependency, or model-derived), and a machine-readable provenance ledger classifying the origin of every schema element. Evaluation against a fixed five-benchmark suite with locked baselines reports zero structural orphans, zero dangling edge endpoints, and 100% of output-producing technologies traceable to raw input files. Two interactive interfaces present the graph, including a serverless browser application built on DuckDB-Wasm. By establishing the first end-to-end provenance framework for an IAM, this work enables researchers and scientists to systematically audit complex policy scenarios, debug model structures, and trace policy-relevant outputs to their data origins in real time.

Artifical Intelligence↗
DOE OSTI2021

Fast GPU-Based Generation of Large Graph Networks From Degree Distributions

Synthetically generated, large graph networks serve as useful proxies to real-world networks for many graph-based applications. The ability to generate such networks helps overcome several limitations of real-world networks regarding their number, availability, and access. Here, we present the design, implementation, and performance study of a novel network generator that can produce very large graph networks conforming to any desired degree distribution. The generator is designed and implemented for efficient execution on modern graphics processing units (GPUs). Given an array of desired vertex degrees and number of vertices for each desired degree, our algorithm generates the edges of a random graph that satisfies the input degree distribution. Multiple runtime variants are implemented and tested: 1) a uniform static work assignment using a fixed thread launch scheme, 2) a load-balanced static work assignment also with fixed thread launch but with cost-aware task-to-thread mapping, and 3) a dynamic scheme with multiple GPU kernels asynchronously launched from the CPU. The generation is tested on a range of popular networks such as Twitter and Facebook, representing different scales and skews in degree distributions. Results show that, using our algorithm on a single modern GPU (NVIDIA Volta V100), it is possible to generate large-scale graph networks at rates exceeding 50 billion edges per second for a 69 billion-edge network. GPU profiling confirms high utilization and low branching divergence of our implementation from small to large network sizes. For networks with scattered distributions, we provide a coarsening method that further increases the GPU-based generation speed by up to a factor of 4 on tested input networks with over 45 billion edges.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Mesh-based super-resolution of fluid flows with multiscale graph neural networks

A graph neural network (GNN) approach is introduced in this work which enables mesh-based three-dimensional super-resolution of fluid flows. In this framework, the GNN is designed to operate not on the full mesh-based field at once, but on localized meshes of elements (or cells) directly. To facilitate mesh-based GNN representations in a manner similar to spectral (or finite) element discretizations, a baseline GNN layer (termed a message passing layer, which updates local node properties) is modified to account for synchronization of coincident graph nodes, rendering compatibility with commonly used element-based mesh connectivities. Furthermore, the architecture is multiscale in nature, and is comprised of a combination of coarse-scale and fine-scale message passing layer sequences (termed processors) separated by a graph unpooling layer. The coarse-scale processor embeds a query element (alongside a set number of neighboring coarse elements) into a single latent graph representation using coarse-scale synchronized message passing over the element neighborhood, and the fine-scale processor leverages additional message passing operations on this latent graph to correct for interpolation errors. Demonstration studies are performed using hexahedral mesh-based data from Taylor–Green Vortex and backward-facing step flow simulations at Reynolds numbers of 1600 and 3200. Through analysis of both global and local errors, the results ultimately show how the GNN is able to produce accurate super-resolved fields compared to targets in both coarse-scale and multiscale model configurations. Reconstruction errors for fixed architectures were found to increase in proportion to the Reynolds number. Geometry extrapolation studies on a separate cavity flow configuration show promising cross-mesh capabilities of the super-resolution strategy.

Backward-facing step↗
DOE OSTI2025

Learning to Simulate Aerosol Dynamics with Graph Neural Networks

Aerosol effects on climate, weather, and air quality depend on characteristics of individual particles, which are tremendously diverse and change in time. Particle-resolved models are the only models able to capture this diversity in particle physiochemical properties, and these models are computationally expensive. As a strategy for accelerating particle-resolved microphysics models, we introduce Graph-based Learning of Aerosol Dynamics (GLAD) and use this model to train a surrogate of the particle-resolved model PartMC-MOSAIC. GLAD implements a Graph Network-based Simulator (GNS), a machine learning framework that has been used to simulate particle-based fluid dynamics models. In GLAD, each particle is represented as a node in a graph, and the evolution of the particle population over time is simulated through learned message passing. Here, we demonstrate our GNS approach on a simple aerosol system that includes condensation of sulfuric acid onto particles composed of sulfate, black carbon, organic carbon, and water. A graph with particles as nodes is constructed, and a graph neural network (GNN) is then trained using the model output from PartMC-MOSAIC. The trained GNN can then be used for simulating and predicting aerosol dynamics over time. Results demonstrate the framework's ability to accurately learn chemical dynamics and generalize across different scenarios, achieving efficient training and prediction times. We evaluate the performance across four scenarios, highlighting the framework's robustness and adaptability in modeling aerosol microphysics and chemistry.

aerosol chemistry dynamics↗
DOE OSTI2024

Gene-Metabolite Association Prediction with Interactive Knowledge Transfer Enhanced Graph for Metabolite Production

Identifying gene targets for enhancing metabolite production in metabolic engineering is challenging due to the vast research literature and the approximation in genome-scale metabolic model (GEM) simulations. Here, to address this, we propose the Gene-Metabolite Association Prediction task, which automates gene discovery for given metabolite-gene pairs, accompanied by a benchmark dataset of 2474 metabolites and 1947 genes for Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is complicated by incomplete metabolic graphs and metabolic heterogeneity. We introduce an Interactive Knowledge Transfer mechanism based on Metabolism Graphs (IKT4Meta) to enhance prediction accuracy by integrating cross-metabolism knowledge. Using Pretrained Language Models (PLMs) to generate inter-graph links mitigates heterogeneity issues, while intra-graph links are propagated via these anchors. Gene-metabolite predictions are then performed on the enriched graphs integrating multiple microorganisms’ knowledge. Experiments show that IKT4Meta outperforms baselines by up to 12.3% in link prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Tackling the Challenges in Scene Graph Generation With Local-to-Global Interactions

In this work, we seek new insights into the underlying challenges of the scene graph generation (SGG) task. Quantitative and qualitative analysis of the visual genome (VG) dataset implies: 1) ambiguity: even if interobject relationship contains the same object (or predicate), they may not be visually or semantically similar; 2) asymmetry: despite the nature of the relationship that embodied the direction, it was not well addressed in previous studies; and 3) higher-order contexts: leveraging the identities of certain graph elements can help generate accurate scene graphs. Motivated by the analysis, we design a novel SGG framework, Local-to-global interaction networks (LOGINs). Locally, interactions extract the essence between three instances of subject, object, and background, while baking direction awareness into the network by explicitly constraining the input order of subject and object. Globally, interactions encode the contexts between every graph component (i.e., nodes and edges). Finally, Attract and Repel loss is utilized to fine-tune the distribution of predicate embeddings. By design, our framework enables predicting the scene graph in a bottom-up manner, leveraging the possible complementariness. To quantify how much LOGIN is aware of relational direction, a new diagnostic task called Bidirectional Relationship Classification (BRC) is also proposed. Overall, experimental results demonstrate that LOGIN can successfully distinguish relational direction than existing methods (in BRC task), while showing state-of-the-art results on the VG benchmark (in SGG task).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Comparing Mapper Graphs of Artificial Neuron Activations

The mapper graph is a popular tool from topological data analysis that provides a graphical summary of point cloud data. It has been used to study data from cancer research, sports analytics, neurosciences, and machine learning. In particular, mapper graphs have been used recently to visualize the topology of high-dimensional artificial neural activations from convolutional neural networks and large language models. However, a key question that arises from using mapper graphs across applications is how to compare mapper graphs to study their structural differences. In this paper, we introduce a distance between mapper graphs using tools from optimal transport. We demonstrate the utility of such a distance by studying the topological changes of neural activations across convolutional layers in deep learning, as well as by capturing the loss of structural information for multiscale mapper.

mapper graphs, computational topology, machine lea↗
DOE OSTI2022

Scalable training of graph convolutional neural networks for fast and accurate predictions of HOMO-LUMO gap in molecules

Abstract Graph Convolutional Neural Network (GCNN) is a popular class of deep learning (DL) models in material science to predict material properties from the graph representation of molecular structures. Training an accurate and comprehensive GCNN surrogate for molecular design requires large-scale graph datasets and is usually a time-consuming process. Recent advances in GPUs and distributed computing open a path to reduce the computational cost for GCNN training effectively. However, efficient utilization of high performance computing (HPC) resources for training requires simultaneously optimizing large-scale data management and scalable stochastic batched optimization techniques. In this work, we focus on building GCNN models on HPC systems to predict material properties of millions of molecules. We use HydraGNN, our in-house library for large-scale GCNN training, leveraging distributed data parallelism in PyTorch. We use ADIOS, a high-performance data management framework for efficient storage and reading of large molecular graph data. We perform parallel training on two open-source large-scale graph datasets to build a GCNN predictor for an important quantum property known as the HOMO-LUMO gap. We measure the scalability, accuracy, and convergence of our approach on two DOE supercomputers: the Summit supercomputer at the Oak Ridge Leadership Computing Facility (OLCF) and the Perlmutter system at the National Energy Research Scientific Computing Center (NERSC). We present our experimental results with HydraGNN showing (i) reduction of data loading time up to 4.2 times compared with a conventional method and (ii) linear scaling performance for training up to 1024 GPUs on both Summit and Perlmutter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Multitask graph neural networks for elastoplastic response prediction in dual-phase polycrystals

Microstructure-sensitive prediction of elastoplastic response remains a recurring bottleneck in multiscale damage and fatigue modeling, where large ensembles of statistically distinct polycrystals are required to quantify variability and extreme-value behavior. In this work, we develop a multitask graph neural network (GNN) surrogate that maps dual-phase ferrite–martensite polycrystal microstructures to Statistical Volume Element (SVE)-level elastoplastic Quantities of Interest (QoIs). Each SVE is represented as a grain-adjacency graph, with node features encoding phase, geometry, and crystallographic orientation, and edge features encoding relative misorientation. A message-passing graph convolution generates node embeddings, which are pooled into a graph representation and passed to a multitask regression head that jointly predicts 10 scalar QoIs and vector-valued stress–strain responses in orthogonal loading directions across multiple martensite volume fractions and SVE sizes. Results show high accuracy for scalar QoIs and strong agreement for full stress–strain trajectories, with population envelopes reproducing both median behavior and finite-SVE variability across compositions and partition scales. A unified model trained on pooled volume-fraction data preserves most within-regime accuracy relative to regime-specific models while also capturing the broader cross-regime variation reflected in the pooled test set. Distributional comparisons further demonstrate that the surrogate preserves heterogeneity under SVE partitioning, enabling statistically consistent block-wise random-field construction for mesoscale analyses. Overall, the proposed grain-graph surrogate provides a practical pathway to accelerate ensemble-based studies of SVE-level constitutive variability in dual-phase polycrystals.

Crystal plasticity↗
DOE OSTI2023

Graph-based machine learning improves just-in-time defect prediction

The increasing complexity of today’s software requires the contribution of thousands of developers. This complex collaboration structure makes developers more likely to introduce defect-prone changes that lead to software faults. Determining when these defect-prone changes are introduced has proven challenging, and using traditional machine learning (ML) methods to make these determinations seems to have reached a plateau. In this work, we build contribution graphs consisting of developers and source files to capture the nuanced complexity of changes required to build software. By leveraging these contribution graphs, our research shows the potential of using graph-based ML to improve Just-In-Time (JIT) defect prediction. We hypothesize that features extracted from the contribution graphs may be better predictors of defect-prone changes than intrinsic features derived from software characteristics. We corroborate our hypothesis using graph-based ML for classifying edges that represent defect-prone changes. This new framing of the JIT defect prediction problem leads to remarkably better results. We test our approach on 14 open-source projects and show that our best model can predict whether or not a code change will lead to a defect with an F1 score as high as 77.55% and a Matthews correlation coefficient (MCC) as high as 53.16%. This represents a 152% higher F1 score and a 3% higher MCC over the state-of-the-art JIT defect prediction. We describe limitations, open challenges, and how this method can be used for operational JIT defect prediction.

59 BASIC BIOLOGICAL SCIENCES↗