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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Impact of Water Extraction on Malonamide Aggregation: A Molecular Dynamics and Graph Theoretic Approach

Solution structure in liquid-liquid extraction affects the efficacy of separation; however, even for simplified organic phases, structural characterization and attribution of aggregation to intermolecular interactions are fundamental challenges. We investigate water uptake into organic phases for two malonamides commonly applied to actinide and lanthanide separations. Extracted water induces reorganization of the amphiphilic extractant molecules, although we find this rearrangement is not strongly manifested in small-angle X-ray scattering making it challenging to probe without methods such as atomistic simulation. Using a graph theoretic approach to define hydrogen bonded water/malonamide aggregates from molecular dynamics simulations, we find evidence of a characteristic aggregate size by water number that results from geometric accommodation of the surrounding malonamide molecules. Furthermore, this implies a degree of size selectivity inherent to these water-in-oil aggregates. Conversely, we find no evidence of a characteristic size of the aggregates with respect to their malonamide number. By defining a separate graphical representation of self-association of the amphiphilic malonamides, we quantify how water affects the local and nonlocal topology of the malonamide network, providing a basis for characterization of the structure and impact of polar solutes in increasingly complex organic phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2018

Robust system size reduction of discrete fracture networks: a multi-fidelity method that preserves transport characteristics

In this paper, we propose a multi-fidelity system reduction technique that uses weighted graphs paired with three-dimensional discrete fracture network (DFN) modelling for efficient simulation of subsurface flow and transport in fractured media. DFN models are used to simulate flow and transport in subsurface fractured rock with low-permeability. One method to alleviate the heavy computational overhead associated with these simulations is to reduce the size of the DFN using a graph representation of it to identify the primary flow sub-network and only simulate flow and transport thereon. The first of these methods used unweighted graphs constructed solely on DFN topology and could be used for accurate predictions of first-passage times. However, these techniques perform poorly when predicting later stages of the mass breakthrough. We utilize a weighted-graph representation of the DFN where edge weights are based on hydrological parameters in the DFN that allows us to exploit the kinematic quantities derivable a posteriori from the flow solution obtained on the graph representation of the DFN to perform system reduction and predict the later stages of the breakthrough curve with high fidelity. We also propose and demonstrate the use of an adaptive pruning algorithm with error control that produces a pruned DFN sub-network whose predicted mass breakthrough agrees with the original DFN within a user-specified tolerance. Lastly, the method allows for the level of accuracy to be a user-controlled parameter.

58 GEOSCIENCES↗
DOE OSTI2019

Near-Optimal and Practical Algorithms for Graph Scan Statistics with Connectivity Constraints

One fundamental task in network analysis is detecting “hotspots” or “anomalies” in the network; that is, detecting subgraphs where there is significantly more activity than one would expect given historical data or some baseline process. Scan statistics is one popular approach used for anomalous subgraph detection. This methodology involves maximizing a score function over all connected subgraphs, which is a challenging computational problem. A number of heuristics have been proposed for these problems, but they do not provide any quality guarantees. Here, we propose a framework for designing algorithms for optimizing a large class of scan statistics for networks, subject to connectivity constraints. Our algorithms run in time that scales linearly on the size of the graph and depends on a parameter we call the “effective solution size,” while providing rigorous approximation guarantees. In contrast, most prior methods have super-linear running times in terms of graph size. Extensive empirical evidence demonstrates the effectiveness and efficiency of our proposed algorithms in comparison with state-of-the-art methods. Our approach improves on the performance relative to all prior methods, giving up to over 25% increase in the score. Further, our algorithms scale to networks with up to a million nodes, which is 1–2 orders of magnitude larger than all prior applications.

97 MATHEMATICS AND COMPUTING↗
NASA NTRSDate not supplied

Graph Convolutional Network-Strengthened Topic Modeling for Scientific Papers

Machine learning has been woven into statistics to modernize topic modeling over textual documents written in natural language, and scientific paper search and recommendation can consequently offer higher accuracy instead of counting on traditional keyword-based search. However, topic distribution of a paper resulted from existing topic modeling techniques only relies on the statistics of words contained in the paper itself. We argue that community users’ views of a paper may also provide insights at the time of recommendation. For example, if a paper on fake image detection has been cited heavily by machine learning papers, such a feature should be absorbed in the embedding of this paper, so that it can be recommended for future query on machine learning. In this paper, we present a Graph Convolutional Network-strengthened Topic Modeling (GCN-TM) method, which employs GCN technique to refine topic modeling of scientific papers. A citation-oriented knowledge graph is constructed, and topic modeling is mapped to feature embedding of the comprising papers. On top of its own topics carried in its content, each paper learns topics from its neighbors and revise its embedding accordingly. Our empirical studies over real-life scientific literature has proved the necessity and effectiveness of our proposed approach.

Jia Zhang↗
DOE OSTI2024

Feature Pathway Graphs using Random Forest Regressors

SAND2025-04671O Feature Pathway Graphs using Random Forest Regressors is a software tool that uses machine learning to determine pathways of influence between features in data sets. It can be used as a surrogate method for casual discovery. The output creates pathway graphs between features of interest. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Peterson, Matthew↗
DOE OSTI2018

Reduced-order modeling through machine learning and graph-theoretic approaches for brittle fracture applications

Typically, thousands of computationally expensive micro-scale simulations of brittle crack propagation are needed to upscale lower length scale phenomena to the macro-continuum scale. Running such a large number of crack propagation simulations presents a significant computational challenge, making reduced-order models (ROMs) attractive for this task. Here, the ultimate goal of this research is to develop ROMs that have sufficient accuracy and low computational cost so that these upscaling simulations can be readily performed. However, constructing ROMs for these complex simulations presents its own challenge. Here, we present and compare four different approaches for reduced-order modeling of brittle crack propagation in geomaterials. These methods rely on machine learning (ML) and graph-theoretic algorithms to approximate key aspects of the brittle crack problem. These methods also incorporate different physics-based assumptions in order to reduce the training requirements while maintaining accurate physics as much as possible. Results from the ROMs are directly compared against a high-fidelity model of brittle crack propagation. Further, the strengths and weaknesses of the ROMs are discussed, and we conclude that combining smart physics-informed feature engineering with highly trainable ML models provides the best performance. The ROMs considered here have computational costs that are orders-of-magnitude less than the cost associated with high-fidelity physical models while maintaining good accuracy.

36 MATERIALS SCIENCE↗
DOE OSTI2023

An Incremental Gradient Method for Optimization Problems With Variational Inequality Constraints

We consider minimizing a sum of agent-specific nondifferentiable merely convex functions over the solution set of a variational inequality (VI) problem in that each agent is associated with a local monotone mapping. This problem finds an application in computation of the best equilibrium in nonlinear complementarity problems arising in transportation networks. We develop an iteratively regularized incremental gradient method where at each iteration, agents communicate over a directed cycle graph to update their solution iterates using their local information about the objective and the mapping. The proposed method is single-timescale in the sense that it does not involve any excessive hard-to-project computation per iteration. We derive nonasymptotic agent-wise convergence rates for the suboptimality of the global objective function and infeasibility of the VI constraints measured by a suitably defined dual gap function. Finally, the proposed method appears to be the first fully iterative scheme equipped with iteration complexity that can address distributed optimization problems with VI constraints over cycle graphs.

convergence↗
DOE OSTI2019

Prediction of atomization energy using graph kernel and active learning

Data-driven prediction of molecular properties presents unique challenges to the design of machine learning methods concerning data structure/dimensionality, symmetry adaption, and confidence management. In this paper, we present a kernel-based pipeline that can learn and predict the atomization energy of molecules with high accuracy. The framework employs Gaussian process regression to perform predictions based on the similarity between molecules, which is computed using the marginalized graph kernel. To apply the marginalized graph kernel, a spatial adjacency rule is first employed to convert molecules into graphs whose vertices and edges are labeled by elements and interatomic distances, respectively. We then derive formulas for the efficient evaluation of the kernel. Specific functional components for the marginalized graph kernel are proposed, while the effects of the associated hyperparameters on accuracy and predictive confidence are examined. We show that the graph kernel is particularly suitable for predicting extensive properties because its convolutional structure coincides with that of the covariance formula between sums of random variables. Using an active learning procedure, we demonstrate that the proposed method can achieve a mean absolute error of 0.62 ± 0.01 kcal/mol using as few as 2000 training samples on the QM7 dataset.

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

Solving MaxCut with quantum imaginary time evolution

We introduce a method to solve the MaxCut problem efficiently based on quantum imaginary time evolution (QITE). We employ a linear Ansatz for unitary updates and an initial state involving no entanglement, as well as an imaginary-time-dependent Hamiltonian interpolating between a given graph and a subgraph with two edges excised. We apply the method to thousands of randomly selected graphs with up to fifty vertices. We show that our algorithm exhibits a 93% and above performance converging to the maximum solution of the MaxCut problem for all considered graphs. Our results compare favorably with the performance of classical algorithms, such as the greedy and Goemans–Williamson algorithms. We also discuss the overlap of the final state of the QITE algorithm with the ground state as a performance metric, which is a quantum feature not shared by other classical algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Individualized Selection of Beam Angles and Treatment Isocenter in Tangential Breast Intensity Modulated Radiation Therapy

Purpose and Objective: Propose a novel method for individualized selection of beam angles and treatment isocenter in tangential breast intensity modulated radiation therapy (IMRT). Methods and Materials: For each patient, beam and isocenter selection starts with the fully automatic generation of a large database of IMRT plans (up to 847 in this study); each of these plans belongs to a unique combination of isocenter position, lateral beam angle, and medial beam angle. The imposed hard planning constraint on patient maximum dose may result in plans with unacceptable target dose delivery. Such plans are excluded from further analyses. Owing to differences in beam setup, database plans differ in mean doses to organs at risk (OARs). These mean doses are used to construct 2-dimensional graphs, showing relationships between: (1) contralateral breast dose and ipsilateral lung dose; and (2) contralateral breast dose and heart dose (analyzed only for left-sided). The graphs can be used for selection of the isocenter and beam angles with the optimal, patient-specific tradeoffs between the mean OAR doses. For 30 previously treated patients (15 left-sided and 15 right-sided tumors), graphs were generated considering only the clinically applied isocenter with 121 tangential beam angle pairs. For 20 of the 30 patients, 6 alternative isocenters were also investigated. Results: Computation time for automatic generation of 121 IMRT plans took on average 30 minutes. The generated graphs demonstrated large variations in tradeoffs between conflicting OAR objectives, depending on beam angles and patient anatomy. For patients with isocenter optimization, 847 IMRT plans were considered. Adding isocenter position optimization next to beam angle optimization had a small impact on the final plan quality. Conclusion: A method is proposed for individualized selection of beam angles in tangential breast IMRT. This may be especially important for patients with cardiac risk factors or an enhanced risk for the development of contralateral breast cancer.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
NASA NTRS1961

The Use of Higher-Order Difference Methods in Beam Vibration Analysis

Simple and higher-order difference methods for the solution for the natural frequencies of vibration of a uniform beam are compared. The same basic higher-order method is used throughout for the interior cells, but three different methods of boundary-condition representation are given. Tables and graphs of the error in mode frequencies, as compared with a continuous beam, are given for the various methods as a function of the number of cells. It is concluded that higher-order methods improve accuracy for a given number of cells, with essentially no change in the quantity of computing equipment required.

Greenwood, Donald T.↗
DOE OSTI2015

Noninvasive differential diagnosis of dental periapical lesions in cone-beam CT scans

Purpose: This paper proposes a novel application of computer-aided diagnosis (CAD) to an everyday clinical dental challenge: the noninvasive differential diagnosis of periapical lesions between periapical cysts and granulomas. A histological biopsy is the most reliable method currently available for this differential diagnosis; however, this invasive procedure prevents the lesions from healing noninvasively despite a report that they may heal without surgical treatment. A CAD using cone-beam computed tomography (CBCT) offers an alternative noninvasive diagnostic tool which helps to avoid potentially unnecessary surgery and to investigate the unknown healing process and rate for the lesions. Methods: The proposed semiautomatic solution combines graph-based random walks segmentation with machine learning-based boosted classifiers and offers a robust clinical tool with minimal user interaction. As part of this CAD framework, the authors provide two novel technical contributions: (1) probabilistic extension of the random walks segmentation with likelihood ratio test and (2) LDA-AdaBoost: a new integration of weighted linear discriminant analysis to AdaBoost. Results: A dataset of 28 CBCT scans is used to validate the approach and compare it with other popular segmentation and classification methods. The results show the effectiveness of the proposed method with 94.1% correct classification rate and an improvement of the performance by comparison with the Simon’s state-of-the-art method by 17.6%. The authors also compare classification performances with two independent ground-truth sets from the histopathology and CBCT diagnoses provided by endodontic experts. Conclusions: Experimental results of the authors show that the proposed CAD system behaves in clearer agreement with the CBCT ground-truth than with histopathology, supporting the Simon’s conjecture that CBCT diagnosis can be as accurate as histopathology for differentiating the periapical lesions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Physics-informed graphical neural network for power system state estimation

State estimation is highly critical for accurately observing the dynamic behavior of the power grids and minimizing risks from cyber threats. However, existing state estimation methods encounter challenges in accurately capturing power system dynamics, primarily because of limitations in encoding the grid topology and sparse measurements. Here, this paper proposes a physics-informed graphical learning state estimation method to address these limitations by leveraging both domain physical knowledge and a graph neural network (GNN). We employ a GNN architecture that can handle the graph-structured data of power systems more effectively than traditional data-driven methods. The physics-based knowledge is constructed from the branch current formulation, making the approach adaptable to both transmission and distribution systems. The validation results of three IEEE test systems show that the proposed method can achieve lower mean square error more than 20% than the conventional methods.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Scalable Knowledge Graph Analytics at 136 Petaflop/s

We are motivated by newly proposed methods for data mining large-scale corpora of scholarly publications, such as the full biomedical literature, which may consist of tens of millions of papers spanning decades of research. In this setting, analysts seek to discover how concepts relate to one another. They construct graph representations from annotated text databases and then formulate the relationship-mining problem as one of computing all-pairs shortest paths (APSP), which becomes a significant bottleneck. In this context, we present a new high-performance algorithm and implementation of the Floyd-Warshall algorithm for distributed-memory parallel computers accelerated by GPUs, which we call DSNAPSHOT (Distributed Accelerated Semiring All-Pairs Shortest Path). For our largest experiments, we ran DSNAPSHOT on a connected input graph with millions of vertices using 4, 096nodes (24,576GPUs) of the Oak Ridge National Laboratory's Summit supercomputer system. We find DSNAPSHOT achieves a sustained performance of 136×1015 floating-point operations per second (136petaflop/s) at a parallel efficiency of 90% under weak scaling and, in absolute speed, 70% of the best possible performance given our computation (in the single-precision tropical semiring or “min-plus” algebra). Looking forward, we believe this novel capability will enable the mining of scholarly knowledge corpora when embedded and integrated into artificial intelligence-driven natural language processing workflows at scale.

Kannan, Ramakrishnan {ramki}↗
NASA NTRS2016

Evaluation of the Effect of Surface Finish on High-Cycle Fatigue of SLM-IN718

The surface finish of parts produced by additive manufacturing processes is much rougher than the surface finish generated by machining processes, and a rougher surface can reduce the fatigue strength of a part. This paper discusses an effort to quantify that reduction of strength in high-cycle fatigue for selective laser melt (SLM) coupons. A high-cycle fatigue (HCF) knockdown factor was estimated for Inconel 718, manufactured with the SLM process. This factor is the percentage reduction from the maximum stress in fatigue for low-stress ground (LSG) specimens to the maximum stress of those left with the original surface condition at the same fatigue life. Specimens were provided by a number of vendors, free to use their "best practice"; only one heat treat condition was considered; and several test temperatures were characterized, including room temperature, 800F, 1000F, and 1200F. The 1000F data had a large variance, and was omitted from consideration in this document. A first method used linear approximations extracted from the graphs, and only where data was available for both. A recommended knockdown factor of the as-built surface condition (average roughness of approximately 245 micro-inches/inch) versus low-stress ground condition (roughness no more than 4 micro-inches/inch) was established at approximately 1/3 or 33%. This is to say that for the as-built surface condition, a maximum stress of 2/3 of the stress for LSG can be expected to produce a similar life in the as-built surface condition. In this first evaluation, the knockdown factor did not appear to be a function of temperature. A second approach, the "KP method", incorporated the surface finish measure into a new parameter termed the pseudo-stress intensity factor, Kp, which was formulated to be similar to the fracture mechanics stress intensity factor. Using Kp, the variance seemed to be reduced across all sources, and knockdown factors were estimated using Kp over the range where data occurred. A plot of the results suggests that the knockdown factor is a function of temperature, and that for low lives the knockdown might be lower than the knockdown observed above about one million cycles, where it tended to stabilize. This was not universal for all temperatures tested. The higher temperature tests are thought to be influenced by the test temperature, which perhaps continued the aging process. Further evaluation of the method is suggested.

Lambert, D. M.↗
NASA NTRS1994

Aligning parallel arrays to reduce communication

Axis and stride alignment is an important optimization in compiling data-parallel programs for distributed-memory machines. We previously developed an optimal algorithm for aligning array expressions. Here, we examine alignment for more general program graphs. We show that optimal alignment is NP-complete in this setting, so we study heuristic methods. This paper makes two contributions. First, we show how local graph transformations can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. Second, we give a heuristic that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. Our algorithms have been implemented; we present experimental results showing their effect on the performance of some example programs running on the CM-5.

Sheffler, Thomas J.↗
DOE OSTI2023

Accelerating discrete dislocation dynamics simulations with graph neural networks

Discrete dislocation dynamics (DDD) is a widely employed computational method to study plasticity at the mesoscale that connects the motion of dislocation lines to the macroscopic response of crystalline materials. However, the computational cost of DDD simulations remains a bottleneck that limits its range of applicability. Here, we introduce a new DDD-GNN framework in which the expensive time-integration of dislocation motion is entirely substituted by a graph neural network (GNN) model trained on DDD trajectories. As a first application, we demonstrate the feasibility and potential of our method on a simple yet relevant model of a dislocation line gliding through an array of obstacles. We show that the DDD-GNN model is stable and reproduces very well unseen ground-truth DDD simulation responses for a range of straining rates and obstacle densities, without the need to explicitly compute nodal forces or dislocation mobilities during time-integration. Our approach opens new promising avenues to accelerate DDD simulations and to incorporate more complex dislocation motion behaviors.

36 MATERIALS SCIENCE↗