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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 sources NASA NTRS DOE OSTI

DOE OSTI2022

NASMDR: a framework for miRNA-drug resistance prediction using efficient neural architecture search and graph isomorphism networks

Abstract As a frontier field of individualized therapy, microRNA (miRNA) pharmacogenomics facilitates the understanding of different individual responses to certain drugs and provides a reasonable reference for clinical treatment. However, the known drug resistance-associated miRNAs are not yet sufficient to support precision medicine. Although existing methods are effective, they all focus on modelling miRNA-drug resistance interaction graphs, making their performance bounded by the interaction density. In this study, we propose a framework for miRNA-drug resistance prediction through efficient neural architecture search and graph isomorphism networks (NASMDR). NASMDR uses attribute information instead of the commonly used interactive graph information. In the cross-validation experiment, the proposed framework can achieve an AUC of 0.9468 on the ncDR dataset, which is 2.29% higher than the state-of-the-art method. In addition, we propose a novel sequence characterization approach, k-mer Sparse Nonnegative Matrix Factorization (KSNMF). The results show that NASMDR provides novel insights for integrating efficient neural architecture search and graph isomorphic networks into a unified framework to predict drug resistance-related miRNAs. The codes for NASMDR are available at https://github.com/kaizheng-academic/NASMDR.

Zheng, Kai↗

DOE OSTI2023

KG-Hub—building and exchanging biological knowledge graphs

Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking. Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract–transform–load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial–environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

CSGL: chemical synthesis graph learning for molecule representation

Abstract Motivation Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. Results Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation https://github.com/li-2023/CSGL.

Biochemistry & Molecular Biology↗

DOE OSTI2014

Omega: an Overlap-graph de novo Assembler for Meta-genomics

Motivation: Metagenomic sequencing allows reconstruction of mi-crobial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed here for assembling and scaffolding Illumina sequencing data of microbial communities. Results: Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming small branches. Unitigs were generat-ed based on minimum cost flow analysis of the overlap graph. Obtained unitigs were merged to contigs and scaffolds using mate-pair information. Omega was compared with two de Bruijn graph assemblers, SOAPdenovo and IDBA-UD, using a publically-available Illumina sequencing dataset of a 64-genome mock com-munity. The assembly results were verified by their alignment with reference genomes. The overall performances of the three assem-blers were comparable and each assembler provided best results for a subset of genomes.

Haider, Bahlul↗

DOE OSTI2026

Community detection robustness of graph neural networks

Graph neural networks (GNNs) are increasingly widely used for community detection in attributed networks. They combine structural topology with node attributes through message passing and pooling. However, their robustness or lack thereof with respect to different perturbations and targeted attacks in conjunction with community detection tasks is not well understood. To shed light on latent mechanisms behind GNN sensitivity on community detection tasks, we conduct a systematic computational evaluation of six widely adopted GNN architectures graph convolutional network, graph attention network, graph sample and aggregate (GraphSAGE), differentiable pooling (DiffPool), minimum cut pooling (MinCUT), and deep modularity networks (DMoN). The analysis covers three perturbation categories: node attribute manipulations, edge topology distortions, and adversarial attacks. We use element-centric similarity as the evaluation metric on synthetic benchmarks and real-world citation networks. Our findings indicate that supervised GNNs tend to achieve higher baseline accuracy, while unsupervised methods, particularly DMoN, maintain stronger resilience under targeted and adversarial perturbations. Furthermore, robustness appears to be strongly influenced by community strength, with well-defined communities reducing performance loss. Across all models, node attribute perturbations associated with targeted edge deletions and shifts in attribute distributions tend to cause the largest degradation in community recovery. These findings highlight important trade-offs between accuracy and robustness in GNN-based community detection and offer insights into selecting architectures resilient to noise and adversarial attacks.

Goel, Jaidev [Virginia Polytechnic Inst. and State↗

DOE OSTI2022

Transactional Knowledge Graph Generation To Model Adversarial Activities

A Knowledge Graph (KG) is a formal and structured representation of facts, relationships, and semantic descriptions of a set of entities. Traditionally, KGs are used to describe metadata about entities and to provide additional context to target application results. Many real-world domains also involve temporal interactions between entities in addition to the metadata data. Modeling these attributed transactions is a critical requirement when using KGs in complex real-world applications. Modeling adversarial activities is one such application that develops methodology and tools to produce realistic large-scale background activity graphs that include embedded Weapons of Mass Destruction (WMD) activity patterns. We present a novel platform for constructing a transactional knowledge graph from a diverse set of sources. We present the core components and architecture of the framework, and a use case for generating a background knowledge graph and WMD activity template to evaluate network alignment and subgraph matching algorithms.

Purohit, Sumit↗

DOE OSTI2022

Efficient Hierarchical State Vector Simulation of Quantum Circuits via Acyclic Graph Partitioning

Early but promising results in quantum computing have been enabled by the concurrent development of quantum algorithms, devices, and materials. Classical simulation of quantum programs has enabled the design and analysis of algorithms and implementation strategies targeting current and anticipated quantum device architectures. In this paper, we present a graph-based approach to achieve efficient quantum circuit simulation. Our approach involves partitioning the graph representation of a given quantum circuit into sub-graphs/circuits that exhibit better data locality. Simulation of each sub-circuit is organized hierarchically, with the iterative construction and simulation of smaller state vectors, improving overall performance. Also, this partitioning reduces the number of passes through data, improving the total computation time. We present three partitioning strategies and observe that acyclic graph partitioning typically results in the best time-to-solution. In contrast, other strategies reduce the partitioning time at the expense of potentially increased simulation times. Experimental evaluation demonstrates the effectiveness of our approach.

Fang, Bo↗

DOE OSTI2016

Multilayer spectral graph clustering via convex layer aggregation

Multilayer graphs are commonly used for representing different relations between entities and handling heterogeneous data processing tasks. New challenges arise in multilayer graph clustering for assigning clusters to a common multilayer node set and for combining information from each layer. This paper presents a theoretical framework for multilayer spectral graph clustering of the nodes via convex layer aggregation. Under a novel multilayer signal plus noise model, we provide a phase transition analysis that establishes the existence of a critical value on the noise level that permits reliable cluster separation. The analysis also specifies analytical upper and lower bounds on the critical value, where the bounds become exact when the clusters have identical sizes. Numerical experiments on synthetic multilayer graphs are conducted to validate the phase transition analysis and study the effect of layer weights and noise levels on clustering reliability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Applying Graph Analytics to Understand Compute Core Usage and Publication Trends in a Petascale Supercomputing Facility

The Oak Ridge Leadership Computing Facility (OLCF) runs Titan, the No. 4 supercomputer in the world, to deliver over four billion compute core hours every year to several scientific domains, in their pursuit of leadership science. In this paper, we analyze four years worth of heterogeneous log data sources from the OLCF resource fabric, capturing metadata on entities such as users (2,546), scientific project allocations (674), jobs (1,352,402) and publications (1,146), to derive insights into the trends in core hour usage and publications, across 35 science domains. We have constructed a scalable graph to represent the OLCF entities and apply rich graph analytics for our analysis. Based on this, we have analyzed the metadata across five dimensions, namely (1) quantitative analysis of Titan system usage, (2) quantitative analysis of OLCF publications, (3) correlation analysis between system usage and publications, (4) text analysis to derive OLCF research trends, and (5) utilization of graph mining for association analysis. To the best of our knowledge, our work is the first of its kind to apply graph- based big data techniques to provide comprehensive insights on an HPC center's core hour usage and users' publication trends. Our results provide valuable details into an HPC center's core allocation program, measuring the productivity of scientific domains, the interplay between core usage and research output, accelerating collaboration, and in predicting new connections between resource entities.

Lee, Sangkeun (Matt)↗

DOE OSTI2021

Static Graphs for Coding Productivity in OpenACC

The main contribution of this work is to increase the coding productivity for GPU programming by using the concept of Static Graphs. To do so, we have combined the new CUDA Graph API with the OpenACC programming model. We use as test cases a well-known and widely used problems in HPC and AI: the Particle Swarm Optimization. We complement the OpenACC functionality with the use of CUDA Graph, achieving accelerations of more than one order of magnitude, and a performance very close to a reference and optimized CUDA code. Finally, we propose a new specification to incorporate the concept of Static Graphs into the OpenACC specification.

Toledo, Leonel↗

DOE OSTI2023

Impact-Driven Sampling Strategies for Hybrid Attack Graphs

Cyber-Physical Systems (CPSs) have a large input space, with discrete and continuous elements across multiple layers. Hybrid Attack Graph (HAG) provide a flexible and efficient approach to generate attack sequences for a CPS. Analysis and testing of large-scale HAGs are prohibitively costly. We propose a dimension reduction via property-preserving multi-layer graph sampling algorithms. Existing property-preserving graph sampling approaches generate a representative subgraph of an original large-sized graph while preserving the key properties, such as node and edge distribution, clustering coefficients, and betweenness. On the other hand, we propose impact-driven sampling strategies to transform the input data to a lower-dimensional representation while retaining key properties of the data.

Subasi, Omer↗

DOE OSTI2023

Towards Geospatial Knowledge Graph Infused Neuro-Symbolic AI for Remote Sensing Scene Understanding

Deep learning has proven its effectiveness in numerous tasks for remote sensing scene understanding. However there is an increasing interest to explore fusion of domain-specific background information to the deep neural network to further improve its performance. Remote sensing researchers are also working towards developing models that generalize and adapt to multiple applications. Generalization challenges coupled with the scarcity of large corpora of high-quality noise-free labelled data, have together fueled an interest for leveraging background information. Knowledge graphs serve as excellent choice to represent domain-specific information in a structured, standardized and extensible manner. Integrating symbolic knowledge representations in the form of Knowledge Graph Embedding (KGE) to perform neuro-symbolic reasoning is an emerging research direction promising significant impacts. This vision paper seeks to position ideas and provoke early thoughts toward advancing neuro-symbolic artificial intelligence in the context of geospatial challenges. Specifically, it conceptualizes and elaborates on an architecture for infusing geospatial knowledge from knowledge graph in a deep neural network pipeline. As guiding case studies - land-use land-cover classification, object detection and instance segmentation can benefit from infusing spatio-contextual information with remote sensing imagery. The discussion further reflects on and articulates the challenges and explainable AI opportunities anticipated when scaling and maintaining large-scale geospatial knowledge graphs.

Potnis, Abhishek↗

DOE OSTI2024

Picasso: Memory-Efficient Graph Coloring Using Palettes With Applications in Quantum Computing

A coloring of a graph is an assignment of colors to vertices such that no two neighboring vertices have the same color. The need for memory-efficient coloring algorithms is motivated by their application in computing clique partitions of graphs arising in quantum computations where the objective is to map a large set of Pauli strings into a compact set of unitaries. We present Picasso, a randomized memory-efficient iterative parallel graph coloring algorithm with theoretical sublinear space guarantees under practical assumptions. The parameters of our algorithm provide a trade-off between coloring quality and resource consumption. To assist the user, we also propose a machine learning model to predict the coloring algorithm’s parameters considering these trade-offs. We provide a sequential and a parallel implementation of the proposed algorithm. We perform an experimental evaluation on a 64-core AMD CPU equipped with 512 GB of memory and an Nvidia A100 GPU with 40GB of memory. For a small dataset where existing coloring algorithms can be executed within the 512 GB memory budget, we show up to 68× memory savings. On massive datasets we demonstrate that GPU-accelerated Picasso can process inputs with 49.5× more Pauli strings (vertex set in our graph) and 2,478× more edges than state-of-the-art parallel approaches.

artificial intelligence, quantum computing↗

DOE OSTI2013

Combining Structure and Property Values is Essential for Graph-based Learning

Graph mining algorithms that seek to find interesting structure in a graph are compelling for many reasons but may not lead to useful information learned from the data. This position paper explores the current graph mining approaches and suggests why certain algorithms may provide misleading information whereas others may be just what is needed. In particular, algorithms that ignore the rich set of node and edge properties that are prevalent in many real-world graphs are in danger of finding results based on the wrong information.

Haglin, David J.↗

DOE OSTI2023

DeepGraphONet: A Deep Graph Operator Network to Learn and Zero-Shot Transfer the Dynamic Response of Networked Systems

This article develops a deep graph operator network (DeepGraphONet) framework that learns to approximate the dynamics of a complex system (e.g., the power grid or traffic) with an underlying subgraph structure. Here, we build our DeepGraphONet by fusing the ability of graph neural networks to exploit spatially correlated graph information and deep operator networks to approximate the solution operator of dynamical systems. The resulting DeepGraphONet can then predict the dynamics within a given short/medium-term time horizon by observing a finite history of the graph state information. Furthermore, we design our DeepGraphONet to be resolution independent. That is, we do not require the finite history to be collected at the exact/same resolution. In addition, to disseminate the results from a trained DeepGraphONet, we design a zero-shot learning strategy that enables using it on a different subgraph. Finally, empirical results on the transient stability prediction problem of power grids and traffic flow forecasting problem of a vehicular system illustrate the effectiveness of the proposed DeepGraphONet.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Impedance-Aware Graph Convolutional Networks for Voltage Estimation in Active Distribution Networks

Voltage estimation plays a key role in ensuring the effective control and reliability of distribution networks. However, traditional machine learning methods often fail to capture the details of the distribution network’s topology. To overcome this challenge, graph convolutional networks (GCN) have emerged as an alternative. Graph convolutional networks inherently capture the topology of the grid, utilizing correlations to achieve precise voltage estimation. Other machine learning models and conventional GCNs fail to account for the distribution line characteristics found in the real world, limiting their effectiveness. This paper proposes an advanced variant of GCN called the Impedance-Aware Graph Convolutional Network (IA-GCN). The IA-GCN layer incorporates the magnitude of the impedance into the graph convolution mechanism, allowing it to capture topological nuances and provide valuable insights into node interrelationships by considering impedance as an intrinsic dimension. The performance of the IA-GCN layer is then compared with that of GCN and GraphSAGE layers through a surrogate model for voltage estimation. The performance analysis demonstrates that IA-GCN outperforms GCN by reducing the MAE by 87.55% and improving the R-squared value by 98%.

Ravi, Abhijith↗

DOE OSTI2026

Predicting Band-Gap of Inorganic Materials Using Neuromorphic Graph Learning

Predicting properties of inorganic materials is a heavily researched topic, with several new prediction approaches emerging as competitors. One such competitor is graph neural networks, which leverage the structure of the graph to aid in the prediction process. In this work, we propose integration of neuromorphic computation into the graph neural network pipeline. We call this approach Neuromorphic Graph Learning (NGL). We utilize the NGL approach to leverage evolutionary algorithms and a novel Spike Pipeline for Raster Analysis (SPIRE) for the prediction of band gap in inorganic materials.

Mulet, Ian [University of Tennessee (UT)]↗

DOE OSTI2024

BCSR on GPU: A Way Forward Extreme-scale Graph Processing on Accelerator-enabled Frontier Supercomputer

Handling large graphs in a distributed environment requires effective partitioning across processors and efficient management of local partitions. In 2D partitioning, local graphs often become too sparse, making memory-efficient data structures crucial. Using the Compressed Sparse Row (CSR) format wastes space, especially for > 83% of vertices with empty edges for the sparse graphs. This study explores bit-CSR (BCSR), a modified CSR representation, on GPUs to reduce memory usage in graph computations. We achieved 16.67% memory savings on a sparse rmat dataset with 268 million vertices and 357 million edges, without performance degradation, supported by both theoretical and experimental storage savings of 33%. However, we observed a 1.7× slowdown in degree lookup times due to bitwise operations on AMD CPUs. This analysis highlights the potential of BCSR on GPUs for improving Graph500 benchmark performance on GPU-accelerated systems, such as the Frontier supercomputer.

Sattar, Naw Safrin↗