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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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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

An improved hyperbolic embedding algorithm

Because hyperbolic space has properties that make it amenable to graph representations, there is significant interest in scalable hyperbolic-space embedding methods. These embeddings enable constant-time approximation of shortest-path distances, and so are significantly more efficient than full shortest-path computations. In this article, we improve on existing landmark-based hyperbolic embedding algorithms for large-scale graphs. Whereas previous methods compute the embedding by using the derivative-free Nelder–Mead simplex optimization method, our approach uses the limited-memory BFGS (LBFGS) method, which is quasi-Newton optimization, with analytic gradients. Our method is not only significantly faster but also produces higher-quality embeddings. Moreover, we are able to include the hyperbolic curvature as a variable in the optimization. We compare our hyperbolic embedding method implementation in Python (called Hypy) against the best publicly available software, Rigel. Our method is an order of magnitude faster and shows significant improvements in the accuracy of the shortest-path distance calculations. Furthermore, tests are performed on a variety of real-world networks, and we show the scalability of our method by embedding a graph with 1.8 billion edges and 65 million nodes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Improving Performance of Multi-Area State Estimation Using Spectral Clustering

This paper investigates the problem of dividing a large power system into several areas to be solved by a state estimator which coordinates locally obtained decentralized estimates. By applying automatic partitioning to the utility system, the performance of the distributed state estimator can be improved as compared to the pre-defined utility control areas. The presented approach utilizes the spectral properties of the un-directed graph formed by assigning a vertex to every bus and an edge to every pair of buses connected by a line. The graph Laplacian matrix and associated eigenvectors and eigenvalues are used to cluster the graph vertices in such a way that each area has a large number of internal connections, but a small number of external connections. This approach is demonstrated using the IEEE 118 bus system.

Kelle, David↗
DOE OSTI2024

pnnl/emp-gnn

Efficient Graph Neural Network for Predicting Molecular Properties software can compare the prediction quality with ab initio DFT results reported by the high-performance state-of-theart NWChem quantum chemistry package [1] through Mean Absolute Error (MAE) obtained by the fitting between DFT and model predictions i.e, MPNN [2]. We also demonstrated the performance benefits by grouping large molecules by atom sizes, and executing GNN models on different types of resources. Since the training times depend on the number of atoms, we demonstrate the impact of distributing the workloads on two GPUs with varying capabilities (e.g., NVIDIA A100 vs. GeForce RTX 2080 Ti) to optimize the efficiency. We are at the precipice of broad adoption of GNNs for molecular property prediction tasks; hence, our work is timely by comparing model prediction against classical approaches with the intent of providing initial screening for specific classes of molecules.

Lee, Hyungro↗
DOE OSTI2016

Solving Graph Laplacian Systems Through Recursive Bisections and Two-Grid Preconditioning

We present a parallelizable direct method for computing the solution to graph Laplacian-based linear systems derived from graphs that can be hierarchically bipartitioned with small edge cuts. For a graph of size n with constant-size edge cuts, our method decomposes a graph Laplacian in time O(n log n), and then uses that decomposition to perform a linear solve in time O(n log n). We then use the developed technique to design a preconditioner for graph Laplacians that do not have this property. Finally, we augment this preconditioner with a two-grid method that accounts for much of the preconditioner's weaknesses. We present an analysis of this method, as well as a general theorem for the condition number of a general class of two-grid support graph-based preconditioners. Numerical experiments illustrate the performance of the studied methods.

97 MATHEMATICS AND COMPUTING↗
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 OSTI2020

A Guide to Conquer the Biological Network Era Using Graph Theory

Networks are one of the most common ways to represent biological systems as complex sets of binary interactions or relations between different bioentities. In this article, we discuss the basic graph theory concepts and the various graph types, as well as the available data structures for storing and reading graphs. In addition, we describe several network properties and we highlight some of the widely used network topological features. We briefly mention the network patterns, motifs and models, and we further comment on the types of biological and biomedical networks along with their corresponding computer- and human-readable file formats. Finally, we discuss a variety of algorithms and metrics for network analyses regarding graph drawing, clustering, visualization, link prediction, perturbation, and network alignment as well as the current state-of-the-art tools. We expect this review to reach a very broad spectrum of readers varying from experts to beginners while encouraging them to enhance the field further.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Scaling Laws of Graph Neural Networks for Atomistic Materials Modeling

Atomistic materials modeling is a critical task with wide-ranging applications, from drug discovery to materials science, where accurate predictions of the target material property can lead to significant advancements in scientific discovery. Graph Neural Networks (GNNs) represent the state-of-the-art approach for modeling atomistic material data thanks to their capacity to capture complex relational structures. While machine learning performance has historically improved with larger models and datasets, GNNs for atomistic materials modeling remain relatively small compared to large language models (LLMs), which leverage billions of parameters and terabyte-scale datasets to achieve remarkable performance in their respective domains. To address this gap, we explore the scaling limits of GNNs for atomistic materials modeling by developing a foundational model with billions of parameters, trained on extensive datasets in terabytescale. Our approach incorporates techniques from LLM libraries to efficiently manage large-scale data and models, enabling both effective training and deployment of these large-scale GNN models. This work addresses three fundamental questions in scaling GNNs: the potential for scaling GNN model architectures, the effect of dataset size on model accuracy, and the applicability of LLM-inspired techniques to GNN architectures. Specifically, the outcomes of this study include (1) insights into the scaling laws for GNNs, highlighting the relationship between model size, dataset volume, and accuracy, (2) a foundational GNN model optimized for atomistic materials modeling, and (3) a GNN codebase enhanced with advanced LLM-based training techniques. Our findings lay the groundwork for large-scale GNNs with billions of parameters and terabyte-scale datasets, establishing a scalable pathway for future advancements in atomistic materials modeling.

Li, Chaojian [ORNL] (ORCID:0000000340309777)↗
DOE OSTI2018

Isolation and Connectivity in Random Geometric Graphs with Self-similar Intensity Measures

Random geometric graphs consist of randomly distributed nodes (points), with pairs of nodes within a given mutual distance linked. In the usual model the distribution of nodes is uniform on a square, and in the limit of infinitely many nodes and shrinking linking range, the number of isolated nodes is Poisson distributed, and the probability of no isolated nodes is equal to the probability the whole graph is connected. Here we examine these properties for several self-similar node distributions, including smooth and fractal, uniform and nonuniform, and finitely ramified or otherwise. We show that nonuniformity can break the Poisson distribution property, but it strengthens the link between isolation and connectivity. It also stretches out the connectivity transition. Finite ramification is another mechanism for lack of connectivity. The same considerations apply to fractal distributions as smooth, with some technical differences in evaluation of the integrals and analytical arguments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

User Manual - HydraGNN: Distributed PyTorch Implementation of Multi-Headed Graph Convolutional Neural Networks

This document serves as user manual for HydraGNN, a scalable graph neural network (GNN) architecture that allows for a simultaneous prediction of multiple target properties using multi-task learning (MTL). The HydraGNN architecture is constructed by successive superposition of three different sets of layers. The first set is made of message-passing layers to exchange information across nodes in the graph and use this to update the nodal features. The second set is made of global pooling layers that aggregate information from all the nodes in the graph and map it into a scalar, and is needed only for global target properties that are related to the entire graph. The third set of layers is dedicated to the implementation of MTL, which is enabled by forking of the architecture into separate heads, each one of them dedicated to the predictive task of one specific target property. Through an object-oriented programming paradigm, HydraGNN is templated over different message-passing policies, which allows for a user-friendly hyperparameter study to assess the sensitivity of the predictive performance of the HydraGNN architecture on a specific dataset with respect to the choice of the message-passing policy. The object-oriented paradigm used by HydraGNN also allows for a user-friendly inclusion of newly developed message passing policies within the existing framework. HydraGNN supports distributed computing capabilities for scalable data reading and scalable training on leadership-class supercomputers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2010

Finding cycles and trees in sublinear time.

We present sublinear-time (randomized) algorithms for finding simple cycles of length at least k {ge} 3 and tree-minors in bounded-degree graphs. The complexity of these algorithms is related to the distance of the graph from being C{sub k}-minor-free (resp., free from having the corresponding tree-minor). In particular, if the graph is far (i.e., {Omega}(1)-far) from being cycle-free, i.e. if one has to delete a constant fraction of edges to make it cycle-free, then the algorithm finds a cycle of polylogarithmic length in time {tilde O}({radical}N), where N denotes the number of vertices. This time complexity is optimal up to polylogarithmic factors. The foregoing results are the outcome of our study of the complexity of one-sided error property testing algorithms in the bounded-degree graphs model. For example, we show that cycle-freeness of N-vertex graphs can be tested with one-sided error within time complexity {tilde O}(poly(1/{epsilon}) {center_dot} {radical}N). This matches the known {Omega}({radical}N) query lower bound, and contrasts with the fact that any minor-free property admits a two-sided error tester of query complexity that only depends on the proximity parameter {epsilon}. For any constant k {ge} 3, we extend this result to testing whether the input graph has a simple cycle of length at least k. On the other hand, for any fixed tree T, we show that T -minor-freeness has a one-sided error tester of query complexity that only depends on the proximity parameter {epsilon}. Our algorithm for finding cycles in bounded-degree graphs extends to general graphs, where distances are measured with respect to the actual number of edges. Such an extension is not possible with respect to finding tree-minors in o({radical}N) complexity.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Acceleration of Graph Neural Network-Based Prediction Models in Chemistry via Co-Design Optimization on Intelligence Processing Units

Atomic structure prediction and associated property calculations are the bedrock of chemical physics. Since high-fidelity ab initio modeling techniques for computing the structure and properties can be prohibitively expensive, this motivates the development of machine-learning (ML) models that make these predictions more efficiently. Training graph neural networks over large atomistic databases introduces unique computational challenges such as the need to process millions of small graphs with variable size and support communication patterns that are distinct from learning over large graphs such as social networks. We demonstrate a novel hardware-software co-design approach to scale up the training of atomistic graph neural networks (GNN) for structure and property prediction. First, to eliminate redundant computation and memory associated with alternative padding techniques and to improve throughput via minimizing communication, we formulate the effective coalescing of the batches of variable-size atomistic graphs as the bin packing problem and introduce a hardware-agnostic algorithm to pack these batches. In addition, we propose hardware-specific optimizations including a planner and vectorization for the gather-scatter operations targeted for Graphcore’s Intelligence Processing Unit (IPU), as well as model-specific optimizations such as merged communication collectives and optimized softplus. Putting these all together, we demonstrate the effectiveness of the proposed co-design approach by providing an implementation of a well-established atomistic GNN on the Graphcore IPUs. We evaluate the training performance on multiple atomistic graph databases with varying degrees of graph counts, sizes and sparsity. Here, we demonstrate that such a co-design approach can reduce the training time of atomistic GNNs and can improve the performance by up to 1.5× compared to the baseline implementation of the model on the IPUs. Additionally, we compare our IPU implementation with a Nvidia GPU-based implementation and show that our atomistic GNN implementation on the IPUs can run 1.8× faster on average compared to the execution time on the GPUs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Accurate Prediction of Voltage of Battery Electrode Materials Using Attention-Based Graph Neural Networks

Performing first-principles calculations to discover electrodes’ properties in the large chemical space is a challenging task. While machine learning (ML) has been applied to effectively accelerate those discoveries, most of the applied methods ignore the materials’ spatial information and only use predefined features: based only on chemical compositions. Here, we propose two attention-based graph convolutional neural network techniques to learn the average voltage of electrodes. Our proposed methods, which combine both atomic composition and atomic coordinates in 3D-space, improve the accuracy in voltage prediction significantly when compared to composition-based ML models. The first model directly learns the chemical reaction of electrodes and metal ions to predict their average voltage, whereas the second model combines electrodes’ ML predicted formation energy (E form ) to compute their average voltage. Our E form -based model demonstrates improved accuracy in transferability from our subset of learned Li ions to Na ions. Moreover, we predicted the theoretical voltage of 10 Na x MPO 4 F (M = Ti, Cr, Fe, Cu, Mn, Co, and Ni) fluorophosphate battery frameworks, which are unavailable in the Material Project database. It could be shown that we can expect average voltages higher than 3.1 V from those Na battery frameworks except from the NaTiPO 4 F and TiPO 4 F pair of electrodes, which offer an average voltage of 1.32 V.

25 ENERGY STORAGE↗
DOE OSTI2023

Perfecting one-loop BCJ numerators in SYM and supergravity

We take a major step towards computing D-dimensional one-loop amplitudes in general gauge theories, compatible with the principles of unitarity and the color-kinematics duality. For n-point amplitudes with either supersymmetry multiplets or generic non-supersymmetric matter in the loop, simple all-multiplicity expressions are obtained for the maximal cuts of kinematic numerators of n-gon diagrams. At n = 6, 7 points with maximal supersymmetry, we extend the cubic-diagram numerators to encode all contact terms, and thus solve the long-standing problem of simultaneously realizing the following properties: color-kinematics duality, manifest locality, optimal power counting of loop momenta, quadratic rather than linearized Feynman propagators, compatibility with double copy as well as all graph symmetries. Color-kinematics dual representations with similar properties are presented in the half-maximally supersymmetric case at n = 4, 5 points. The resulting gauge-theory integrands and their supergravity counterparts obtained from the double copy are checked to reproduce the expected ultraviolet divergences.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Medical diagnoses using three-way fuzzy concept lattice and their Euclidean distance

Searching the closest symptoms of a particular disease in the given patient is a major concern for medical diagnoses expert. In most cases, this problem arises due to large number of incomplete, uncertain, or inconsistent information generated in medical diagnoses data set. Recently, some of the researchers tried to pay attention towards precise measurement of uncertainty and vagueness in medical data set using the properties of applied abstract algebra. In this process, researchers noticed that calculus of three-way decision space is more useful to characterize the uncertainty and vagueness in medical data set based on truth, indeterminacy, and falsity membership-values. However, searching some relevant query based on user requirement to diagnoses the disease is a major issue in three-way decision space. To encounter this problem, current paper tried to analyze the medical data set using the properties of single-valued neutrosophic graph-based concept lattice. In addition, another method is proposed to select some of the interesting three-way fuzzy concepts at user-defined granulation for their computed Euclidean distance with an illustrative example.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials

Accurate molecular property predictions require 3D geometries, which are typically obtained using expensive methods such as density functional theory (DFT). Here, we attempt to obtain molecular geometries by relying solely on machine learning interatomic potential (MLIP) models. To this end, we first curate a large-scale molecular relaxation dataset comprising 3.5 million molecules and 300 million snapshots. Then MLIP pre-trained models are trained with supervised learning to predict energy and forces given 3D molecular structures. Once trained, we show that the pre-trained models can be used in different ways to obtain geometries either explicitly or implicitly. First, it can be used to obtain approximate low-energy 3D geometries via geometry optimization. While these geometries do not consistently reach DFT-level chemical accuracy or convergence, they can still improve downstream performance compared to non-relaxed structures. To mitigate potential biases and enhance downstream predictions, we introduce geometry fine-tuning based on the relaxed 3D geometries. Second, the pre-trained models can be directly fine-tuned for property prediction when ground truth 3D geometries are available. Our results demonstrate that MLIP pre-trained models trained on relaxation data can learn transferable molecular representations to improve downstream molecular property prediction and can provide practically valuable but approximate molecular geometries that benefit property predictions. Our code is publicly available at: https://github.com/divelab/AIRS/.

Fu, Cong [Texas A & M Univ., College Station, TX (↗
DOE OSTI2020

Transient flow modeling in fractured media using graphs

In this work, we describe a method to simulate transient fluid flows in fractured media using an approach based on graph theory. Our approach builds on past work where the graph-based approach was successfully used to simulate steady-state fluid flows in fractured media. We find a mean computational speedup of the order of 1400 from an ensemble of a 100 discrete fracture networks in contrast to the O(10 4 ) speedup that was obtained for steady-state flows earlier. However, the transient flows considered here involve an additional degree of complexity that was not present in the steady-state flows considered previously with a graph-based approach, that of time marching and solution of the flow equations within a time-stepping scheme. We verify our method with an analytical test case and demonstrate its use on a practical problem related to fluid flows in hydraulically fractured reservoirs. By enabling the study of transient flows, we create an opportunity for a wide set of possibilities where a steady-state approximation is not sufficient, such as the example motivated by hydraulic fracturing that we present here. This work validates the concept that graphs are able to reliably capture the topological properties of the fracture network and serve as effective surrogates in an uncertainty-quantification framework.

58 GEOSCIENCES↗
DOE OSTI2019

A three-phase workflow for general and expressive representations of nondeterminism in HPC applications

Nondeterminism is an increasingly entrenched property of high-performance computing (HPC) applications and has recently been shown to seriously hamper debugging and reproducibility efforts. Additionally, tools for addressing the nondeterministic debugging problem have emerged, but they do not provide methods for systematically cataloging the nondeterminism in a given application. We propose a three-phase workflow for representing executions of nondeterministic message passing interface programs as event graphs, quantifying their structural similarity with graph kernels, and applying machine learning techniques to investigate shared properties across applications. We present an empirical study comparing two graph kernels’ suitability for this task and propose future uses of the methodology.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Advancing energy storage through solubility prediction: leveraging the potential of deep learning

Solubility prediction plays a crucial role in energy storage applications, such as redox flow batteries, because it directly affects the efficiency and reliability. Researchers have developed various methods that utilize quantum calculations and descriptors to predict the aqueous solubilities of organic molecules. Notably, machine learning models based on descriptors have shown promise for solubility prediction. As deep learning tools, graph neural networks (GNNs) have emerged to capture complex structure–property relationships for material property prediction. Specifically, MolGAT, a type of GNN model, was designed to incorporate n-dimensional edge attributes, enabling the modeling of intricacies in molecular graphs and enhancing the prediction capabilities. In a previous study, MolGAT successfully screened 23 467 promising redox-active molecules from a database of over 500 000 compounds, based on redox potential predictions. This study focused on applying the MolGAT model to predict the aqueous solubility (log S) of a broad range of organic compounds, including those previously screened for redox activity. The model was trained on a diverse sample of 8494 organic molecules from AqSolDB and benchmarked against literature data, demonstrating superior accuracy compared with other state of the art graph-based and descriptor-based models. Subsequently, the trained MolGAT model was employed to screen redox-active organic compounds identified in the first phase of high-throughput virtual screening, targeting favorable solubility in energy storage applications. The second round of screening, which considered solubility, yielded 12 332 promising redox-active and soluble organic molecules suitable for use in aqueous redox flow batteries. Thus, the two-phase high-throughput virtual screening approach utilizing MolGAT, specifically trained for redox potential and solubility, is an effective strategy for selecting suitable intrinsically soluble redox-active molecules from extensive databases, potentially advancing energy storage through reliable material development. This indicates that the model is reliable for predicting the solubility of various molecules and provides valuable insights for energy storage, pharmaceutical, environmental, and chemical applications.

25 ENERGY STORAGE↗