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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 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Networks (DGAPNs), a curiosity-driven reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. Here, the framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention Network (sGAT) that leverages self-attention over both node and edge attributes as well as encoding spatial structure -- this capability is of considerable interest in areas such as molecular and synthetic biology and drug discovery. An attentional policy network is then introduced to learn decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with enhanced stability. Exploration is efficiently encouraged by incorporating innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while increasing the diversity of proposed molecules and reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗
DOE OSTI2022

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure --- this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗
DOE OSTI2022

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Networks (DGAPNs), a curiosity-driven reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention Network (sGAT) that leverages self-attention over both node and edge attributes as well as encoding spatial structure -- this capability is of considerable interest in areas such as molecular and synthetic biology and drug discovery. An attentional policy network is then introduced to learn decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with enhanced stability. Exploration is efficiently encouraged by incorporating innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while increasing the diversity of proposed molecules and reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗
DOE OSTI2022

SPATIAL GRAPH ATTENTION AND CURIOSITY-DRIVEN POLICY FOR ANTIVIRAL DRUG DISCOVERY

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure - this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.

Wu, Y↗
DOE OSTI2023

Methods and apparatus to detect and annotate backedges in a dataflow graph

Disclosed examples to detect and annotate backedges in data-flow graphs include: a characteristic detector to store a node characteristic identifier in memory in association with a first node of a dataflow graph; a characteristic comparator to compare the node characteristic identifier with a reference criterion; and a backedge identifier generator to generate a backedge identifier indicative of a backedge between the first node and a second node of the dataflow graph based on the comparison, the memory to store the backedge identifier in association with a connection arc between the first and second nodes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Scalable Graph Analytics and HPC Operational Enhancement: Parallel Computing and ML/DL Innovations

Parallel computing plays a pivotal role in the efficient processing of large-scale graphs. Complex network analysis stands as a capti- vating research frontier, holding promise across diverse scientific domains such as sociology, biology, online media, and recommenda- tion systems. In this era, Machine Learning (ML) and Deep Learning (DL) have emerged as indispensable tools, underpinning remarkable technological achievements. Within this dynamic landscape, my research revolves around advancing parallel algorithms tailored for large-scale graph operations. To achieve this, I harness the power of cutting-edge technologies including OpenMP, MPI, HIP, and CUDA, on the High-Performance Computing (HPC) platforms to unlock optimal performance. I also apply ML/DL techniques to HPC operational data, to streamline the monitoring and maintenance of supercomputers, alleviating the complexities associated with their upkeep and enhancing user support. My research echoes the syn- ergy between parallel computing, large-scale graph analysis, and ML/DL, improving computational efficiency and user experience.

Sattar, Naw Safrin↗
DOE OSTI2024

Extending Power of Nature from Binary Problems to Real-Valued Graph Learning in Real World

Nature performs complex computations constantly at clearly lower cost and higher performance than digital computers. It is crucial to understand how to harness the unique computational power of nature in Machine Learning (ML). In the past decade, besides the development of Neural Networks (NNs), the community has also relentlessly explored nature-powered ML paradigms. Although most of them are still predominantly theoretical, a new practical paradigm enabled by the recent advent of CMOS-compatible room-temperature nature-based computers has emerged. By harnessing the nature's power of entropy increase, this paradigm can solve binary learning problems delivering immense speedup and energy savings compared with NNs, while maintaining comparable accuracy. Regrettably, its values to the real world are highly constrained by its binary nature. A clear pathway to its extension to real-valued problems remains elusive. This paper aims to unleash this pathway by proposing a novel end-to-end Nature-Powered Graph Learning (NP-GL) framework. Specifically, through a three-dimensional co-design, NP-GL can leverage the nature's power of entropy increase to efficiently solve real-valued graph learning problems. Experimental results across 4 real-world applications with 6 datasets demonstrate that NP-GL delivers, on average, 6970X speedup and 10^5x energy consumption reduction with comparable or even higher accuracy than Graph Neural Networks (GNNs).

artificial intelligence↗
DOE OSTI2023

Graph-based Compact Modeling (GCM) of CMOS transistors for efficient parameter extraction: A machine learning approach

Parameter extraction of compact transistor models is an expensive process, heavily relying on engineering knowledge and experience. To automate such a process, we propose a novel approach, Graph-based Compact Model (GCM), that integrates physical modeling and data-driven learning. GCM utilizes Graph Neural Networks (GNNs) to establish the model structure, while retaining the physicality in compact models. Here, we implement our GCM in Verilog-A to support circuit simulations. As demonstrated with an academic 7 nm FinFET PDK, the new approach automatically generates a GCM model within a minute, and achieves excellent accuracy and efficiency in SPICE.

42 ENGINEERING↗
DOE OSTI2024

Leveraging graph clustering techniques for cyber‐physical system analysis to enhance disturbance characterisation

Abstract Cyber‐physical systems have behaviour that crosses domain boundaries during events such as planned operational changes and malicious disturbances. Traditionally, the cyber and physical systems are monitored separately and use very different toolsets and analysis paradigms. The security and privacy of these cyber‐physical systems requires improved understanding of the combined cyber‐physical system behaviour and methods for holistic analysis. Therefore, the authors propose leveraging clustering techniques on cyber‐physical data from smart grid systems to analyse differences and similarities in behaviour during cyber‐, physical‐, and cyber‐physical disturbances. Since clustering methods are commonly used in data science to examine statistical similarities in order to sort large datasets, these algorithms can assist in identifying useful relationships in cyber‐physical systems. Through this analysis, deeper insights can be shared with decision‐makers on what cyber and physical components are strongly or weakly linked, what cyber‐physical pathways are most traversed, and the criticality of certain cyber‐physical nodes or edges. This paper presents several types of clustering methods for cyber‐physical graphs of smart grid systems and their application in assessing different types of disturbances for informing cyber‐physical situational awareness. The collection of these clustering techniques provide a foundational basis for cyber‐physical graph interdependency analysis.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Graph learning for particle accelerator operations

Particle accelerators play a crucial role in scientific research, enabling the study of fundamental physics and materials science, as well as having important medical applications. This study proposes a novel graph learning approach to classify operational beamline configurations as good or bad. By considering the relationships among beamline elements, we transform data from components into a heterogeneous graph. We propose to learn from historical, unlabeled data via our self-supervised training strategy along with fine-tuning on a smaller, labeled dataset. Additionally, we extract a low-dimensional representation from each configuration that can be visualized in two dimensions. Leveraging our ability for classification, we map out regions of the low-dimensional latent space characterized by good and bad configurations, which in turn can provide valuable feedback to operators. This research demonstrates a paradigm shift in how complex, many-dimensional data from beamlines can be analyzed and leveraged for accelerator operations.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Trigger Detection for the sPHENIX Experiment via Bipartite Graph Networks with Set Transformer

Trigger (interesting events) detection is crucial to high-energy and nuclear physics experiments because it improves data acquisition efficiency. It also plays a vital role in facilitating the downstream offline data analysis process. The sPHENIX detector, located at the Relativistic Heavy Ion Collider in Brookhaven National Laboratory, is one of the largest nuclear physics experiments on a world scale and is optimized to detect physics processes involving charm and beauty quarks. Furthermore, these particles are produced in collisions involving two proton beams, two gold nuclei beams, or a combination of the two and give critical insights into the formation of the early universe. This paper presents a model architecture for trigger detection with geometric information from two fast silicon detectors. Transverse momentum is introduced as an intermediate feature from physics heuristics. We also prove its importance through our training experiments. Each event consists of tracks and can be viewed as a graph. A bipartite graph neural network is integrated with the attention mechanism to design a binary classification model. Compared with the state-of-the-art algorithm for trigger detection, our model is parsimonious and increases the accuracy and the AUC score by more than 15%.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

ORCA: Outlier detection and Robust Clustering for Attributed graphs

Here, a framework is proposed to simultaneously cluster objects and detect anomalies in attributed graph data. Our objective function along with the carefully constructed constraints promotes interpretability of both the clustering and anomaly detection components, as well as scalability of our method. In addition, we developed an algorithm called Outlier detection and Robust Clustering for Attributed graphs (ORCA) within this framework. ORCA is fast and convergent under mild conditions, produces high quality clustering results, and discovers anomalies that can be mapped back naturally to the features of the input data. The efficacy and efficiency of ORCA is demonstrated on real world datasets against multiple state-of-the-art techniques.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Quantifying the atomistic free-volume morphology of materials with graph theory

Here, we introduce a new computational methodology for the identification and characterization of free volume within/around atomistic configurations. This scheme employs a three-stage workflow, by which spheres are iteratively grown inside of voxels, and ultimately converted to planar graphs, which are then characterized via a graph-based order parameter. Our approach is computationally efficient, physically intuitive, and universally transferable to any material system. Validation of our methodology is performed on several sets of materials problems: (1) classification of unique free volumes in various crystal phases, (2) autonomous detection and classification of complex surface defects during epitaxial growth simulations, (3) characterization of free volume defects in metals/alloys, and (4) quantification of the spatio-temporal behavior of nano-scale free volume morphologies as a function of both temperature and free-volume size. Our method accurately identifies and characterizes unique free volumes over a multitude of systems and length scales, indicating its potential for future use in understanding the relationship between free volume morphology and material properties under both static and dynamic conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Phenomena-based graph representations and applications to chemical process simulation

Rapid and robust simulation of chemical processes is critical to conduct process design, optimization, techno-economic analysis, and sustainability analysis. Yet, efficiently solving simulation models remains a challenge due to the highly coupled and nonlinear nature of the underlying algebraic equations that capture the physical phenomena taking place in the process (e.g., material and energy conservation, phase equilibrium, reactions). In this work, we show that graph-theoretic representations of the physical phenomena within unit operations can help navigate and decompose equations to systematically identify alternative approaches for fast and robust numerical solutions. Specifically, we present a graph-theoretic abstraction that captures the connectivity between the model variables/equations and use this abstraction to group variables/equations into fundamental phenomena. We show that phenomena-based decomposition of the underlying equations can help decouple nonlinearities and enforce material/energy conservation at the process level to accelerate convergence. The proposed decomposition approach differs from the more traditional sequential modular simulation approach, in which equations are grouped and decomposed by unit operations. We implemented the phenomena-based decomposition in BioSTEAM—an open-source process simulation platform in Python—and demonstrated that this approach can converge a variety of separation process models. Compared to sequential modular simulation, the phenomena-based approach can converge idealized systems faster, but it can be slower for (or even fail to converge) highly coupled and nonideal process systems.

Convergence↗
DOE OSTI2025

Harnessing distributed GPU computing for generalizable graph convolutional networks in power grid reliability assessments

Although machine learning (ML) has emerged as a powerful tool for rapidly assessing grid contingencies, prior studies have largely considered a static grid topology in their analyses. This limits their application, since they need to be re-trained for every new topology. Here, this paper explores the development of generalizable graph convolutional network (GCN) models by pre-training them across a range of grid topologies and contingency types. We found that a GCN model with auto-regressive moving average (ARMA) layers with a line graph representation of the grid offered the best predictive performance in predicting voltage magnitudes (VM) and voltage angles (VA). We introduced the concept of phantom nodes to consider disparate grid topologies with a varying number of nodes and lines. For pre-training the GCN ARMA model across a variety of topologies, distributed graphics processing unit (GPU) computing afforded us significant training scalability. The predictive performance of this model on grid topologies that were part of the training data is substantially better than the direct current (DC) approximation. Although direct application of the pre-trained model to topologies that are not part of the grid is not particularly satisfactory, fine-tuning with small amounts of data from a specific topology of interest significantly improves predictive performance. In general, this paper highlights the feasibility of training large-scale GNN models to assess the reliability of power grids by considering a wide variety of grid topologies and contingency types. With the advent of foundational models in ML and the exponential increase in GPU computing clusters, generalizable ML models will significantly enhance how utilities manage power systems and make decisions in real-time or near-real-time.

24 - POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Graph-based design of irregular metamaterials

In the field of metamaterial research, random structures offer a novel and less conventional approach compared to traditional periodic designs. Designing random metamaterials is challenging when it comes to ensuring intercon- nectivity, which is essential for manufacturability. This study introduces an innovative framework for generating random metamaterials using graph al- gorithms, ensuring connectivity and adaptability across various base shapes, including cylinders, triangles, pyramids, and cubes. By employing graph algorithms, our framework enhances the intuitiveness and efficiency of de- sign representation and manipulation, streamlining the design process. The framework generates families of designs that exhibit a wide range of prop- erty magnitudes that can be adjusted intuitively by modifying the input parameters. The rapid design process allows many designs to be generated, offering the user a multitude of solutions around the target property range. The designs can be effectively implemented in various fields and subjected to diverse analytical studies, including static, dynamic, and eigenfrequency assessments. We illustrate computational results for two key properties (stiff- ness and acoustic impedance), showcasing the method’s effectiveness through examples ranging from rod-based to cube-based designs. Here, the framework not only advances metamaterial research but also creates new opportunities for innovation in fields requiring customized material properties.

36 MATERIALS SCIENCE↗
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 OSTI2024

GrainGNN: A dynamic graph neural network for predicting 3D grain microstructure

We propose GrainGNN, a surrogate model for the evolution of polycrystalline grain structure under rapid solidification conditions in metal additive manufacturing. High fidelity simulations of solidification microstructures are typically performed using multicomponent partial differential equations (PDEs) with moving interfaces. The inherent randomness of the PDE initial conditions (grain seeds) necessitates ensemble simulations to predict microstructure statistics, e.g., grain size, aspect ratio, and crystallographic orientation. Here, currently such ensemble simulations are prohibitively expensive and surrogates are necessary.In GrainGNN, we use a dynamic graph to represent interface motion and topological changes due to grain coarsening. We use a reduced representation of the microstructure using hand-crafted features; we combine pattern finding and altering graph algorithms with two neural networks, a classifier (for topological changes) and a regressor (for interface motion). Both networks have an encoder-decoder architecture; the encoder has a multi-layer transformer long-short-term-memory architecture; the decoder is a single layer perceptron.We evaluate GrainGNN by comparing it to high-fidelity phase field simulations for in-distribution and out-of-distribution grain configurations for solidification under laser power bed fusion conditions. GrainGNN results in 80%–90% pointwise accuracy; and nearly identical distributions of scalar quantities of interest (QoI) between phase field and GrainGNN simulations compared using Kolmogorov-Smirnov test. GrainGNN's inference speedup (PyTorch on single x86 CPU) over a high-fidelity phase field simulation (CUDA on a single NVIDIA A100 GPU) is 150×–2000× for 100-initial grain problem. Further, using GrainGNN, we model the formation of 11,600 grains in 220 seconds on a single CPU core.

36 MATERIALS SCIENCE↗