Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Graph mining”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS2012

Provenance Representation in the Global Change Information System (GCIS)

Global climate change is a topic that has become very controversial despite strong support within the scientific community. It is common for agencies releasing information about climate change to be served with Freedom of Information Act (FOIA) requests for everything that led to that conclusion. Capturing and presenting the provenance, linking to the research papers, data sets, models, analyses, observation instruments and satellites, etc. supporting key findings has the potential to mitigate skepticism in this domain. The U.S. Global Change Research Program (USGCRP) is now coordinating the production of a National Climate Assessment (NCA) that presents our best understanding of global change. We are now developing a Global Change Information System (GCIS) that will present the content of that report and its provenance, including the scientific support for the findings of the assessment. We are using an approach that will present this information both through a human accessible web site as well as a machine readable interface for automated mining of the provenance graph. We plan to use the developing W3C PROV Data Model and Ontology for this system.

Tilmes, Curt↗
DOE OSTI2021

Scalable Pattern Matching in Metadata Graphs via Constraint Checking

Pattern matching is a fundamental tool for answering complex graph queries. Unfortunately, existing solutions have limited capabilities: They do not scale to process large graphs and/or support only a restricted set of search templates or usage scenarios. Moreover, the algorithms at the core of the existing techniques are not suitable for today’s graph processing infrastructures relying on horizontal scalability and shared-nothing clusters, as most of these algorithms are inherently sequential and difficult to parallelize. In this article we present an algorithmic pipeline that bases pattern matching on constraint checking. The key intuition is that each vertex and edge participating in a match has to meet a set of constraints implicitly specified by the search template. These constraints can be verified independently and typically are less expensive to compute than searching the full template. The pipeline we propose generates these constraints and iterates over them to eliminate all the vertices and edges that do not participate in any match, thus reducing the background graph to a subgraph that is the union of all template matches—the complete set of all vertices and edges that participate in at least one match. Additional analysis can be performed on this annotated, reduced graph, such as full match enumeration, match counting, or computing vertex/edge centrality. Furthermore, a vertex-centric formulation for constraint checking algorithms exists, and this makes it possible to harness existing high-performance, vertex-centric graph processing frameworks. This technique (i) enables highly scalable pattern matching in metadata (labeled) graphs; (ii) supports arbitrary patterns with 100% precision; (iii) enables tradeoffs between precision and time-to-solution, while always selects all vertices and edges that participate in matches, thus offering 100% recall; and (iv) supports a set of popular data analytics scenarios. We implement our approach on top of HavoqGT, an open-source asynchronous graph processing framework, and demonstrate its advantages through strong and weak scaling experiments on massive scale real-world (up to 257 billion edges) and synthetic (up to 4.4 trillion edges) labeled graphs, respectively, and at scales (1,024 nodes / 36,864 cores), orders of magnitude larger than used in the past for similar problems. This article serves two purposes: First, it synthesises the knowledge accumulated during a long-term project. Second, it presents new system features, usage scenarios, optimizations, and comparisons with related work that strengthen the confidence that pattern matching based on iterative pruning via constraint checking is an effective and scalable approach in practice. The new contributions include the following: (i) We demonstrate the ability of the constraint checking approach to efficiently support two additional search scenarios that often emerge in practice, interactive incremental search and exploratory search. (ii) We empirically compare our solution with two additional state-of-the-art systems, Arabsque and TriAD. (iii) We show the ability of our solution to accommodate a more diverse range of datasets with varying properties, e.g., scale, skewness, label distribution, and match frequency. (iv) We introduce or extend a number of system features (e.g., work aggregation, load balancing, and the ability to cap the generated traffic) and design optimizations and demonstrate their advantages with respect to improving performance and scalability. (v) We present bottleneck analysis and insights into artifacts that influence performance. (vi) We present a theoretical complexity argument that motivates the performance gains we observe.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Exaflops Biomedical Knowledge Graph Analytics

We are motivated by newly proposed methods for mining large-scale corpora of scholarly publications (e.g., full biomedical literature), which consists of tens of millions of papers spanning decades of research. In this setting, analysts seek to discover relationships among concepts. They construct graph representations from annotated text databases and then formulate the relationship-mining problem as an all-pairs shortest paths (APSP) and validate connective paths against curated biomedical knowledge graphs (e.g., Spoke). In this context, we present Coast (Exascale Communication-Optimized All-Pairs Shortest Path) and demonstrate 1.004 EF/s on 9,200 Frontier nodes (73,600 GCDs). We develop hyperbolic performance models (HYPERMOD), which guide optimizations and parametric tuning. The proposed Coast algorithm achieved the memory constant parallel efficiency of 99% in the single-precision tropical semiring. Looking forward, Coast will enable the integration of scholarly corpora like PubMed into the Spoke biomedical knowledge graph.

Kannan, Ramakrishnan {ramki}↗
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}↗
DOE OSTI2024

Multi-kernel Edge Attention Graph Autoencoder

MEAGraph (Multi-kernel Edge Attention Graph Autoencoder) is a graph-based autoencoder model designed for unsupervised data mining for datasets used in machine learning potentials. It provides accurate clustering for atomic environment identification, unsupervised and unlabeled data pruning for dataset construction.

Sun, Hong↗
DOE OSTI2024

Structure-aware graph neural network based deep transfer learning framework for enhanced predictive analytics on diverse materials datasets

Abstract Modern data mining methods have demonstrated effectiveness in comprehending and predicting materials properties. An essential component in the process of materials discovery is to know which material(s) will possess desirable properties. For many materials properties, performing experiments and density functional theory computations are costly and time-consuming. Hence, it is challenging to build accurate predictive models for such properties using conventional data mining methods due to the small amount of available data. Here we present a framework for materials property prediction tasks using structure information that leverages graph neural network-based architecture along with deep-transfer-learning techniques to drastically improve the model’s predictive ability on diverse materials (3D/2D, inorganic/organic, computational/experimental) data. We evaluated the proposed framework in cross-property and cross-materials class scenarios using 115 datasets to find that transfer learning models outperform the models trained from scratch in 104 cases, i.e., ≈90%, with additional benefits in performance for extrapolation problems. We believe the proposed framework can be widely useful in accelerating materials discovery in materials science.

Chemistry↗
DOE OSTI2022

Graph identification of proteins in tomograms ( GRIP‐Tomo )

Abstract In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases for refinement. We hypothesized that the topological connectivity of protein structures is invariant, and they are distinctive for the purpose of protein identification from distorted data presented in volume densities. Three‐dimensional densities of a protein or a complex from simulated tomographic volumes were transformed into mathematical graphs as observables. We systematically introduced data distortion or defects such as missing fullness of data, the tumbling effect, and the missing wedge effect into the simulated volumes, and varied the distance cutoffs in pixels to capture the varying connectivity between the density cluster centroids in the presence of defects. A similarity score between the graphs from the simulated volumes and the graphs transformed from the physical protein structures in point data was calculated by comparing their network theory order parameters including node degrees, betweenness centrality, and graph densities. By capturing the essential topological features defining the heterogeneous morphologies of a network, we were able to accurately identify proteins and homo‐multimeric complexes from 10 topologically distinctive samples without realistic noise added. Our approach empowers future developments of tomogram processing by providing pattern mining with interpretability, to enable the classification of single‐domain protein native topologies as well as distinct single‐domain proteins from multimeric complexes within noisy volumes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2018

Using a Knowledge Graph to Discover Earth Science Information

Knowledge graphs link key entities within a specific domain to other entities via relationships. Researchers are able to mine these relationships from numerous sources to infer new knowledge. Text extraction from peer-reviewed papers and scientific reports are untapped resources that can be leveraged by knowledge graphs to accelerate scientific discovery.

Freitag, Brian↗
DOE OSTI2018

Anomaly analysis and visualization for dynamic networks through spatiotemporal graph segmentations

With recent technology advance in Internet of Things (IoT) that involves human, sensors, and mobile devices, networks are not only growing much larger but more complex and dynamic in nature. The spatiotemporal dynamics of networks are represented by both topological changes and temporal shifts of attribute information associated with network components. Understanding the pattern and trend of dynamic networks is increasingly important. While data mining approaches are generally useful in analyzing the statistical properties of networks, there has been recent trend to consider bringing human into the loop, and to examine how feedback from visualizations of large-scale dynamic networks can further improve data mining and machine learning. Traditional visualization methods based on animation and sequences of snapshot graphs are also limited by human cognitive capability. Here, we present a dynamic network analysis and visualization (DNAV) tool which explores the spatiotemporal dimensions of graph components. In particular, nodes and edges are augmented with spatiotemporal segmentation based on both topological and attribute dynamics (e.g., time and locations of connectivity). To further facilitate analysis of large dynamic networks, DNAV includes statistical dynamic overviews alongside graph views, as well as data filtering modules for scalable analysis. Using case studies on public datasets, we demonstrate the effectiveness of DNAV in understanding and analyzing anomalies in dynamic networks such as computer communication networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

End-to-end optimization for battery materials and molecules by combining graph neural networks and reinforcement learning

The National Renewable Energy Laboratory (NREL), together with the Colorado School of Mines (CSM) and Colorado State University (CSU), has developed a machine learning-enhanced approach to design new battery materials. Currently, such materials are designed in part via numerous expensive high-fidelity computational simulations that predict the performance of a given composition. Even with computational screening tools, the vast landscape of possible molecular or crystal structures exceeds current and future computational capacity. Improving the efficiency by which new materials can be optimized will therefore disrupt the cost, risk, and time required to bring new energy solutions to the marketplace. Predicting the properties of an organic molecule or periodic crystalline material given its structure has grown increasingly common. These approaches leverage large-scale computational and experimental databases and ML approaches such as graph neural networks. The inverse design problem of finding a material that possesses desired properties is substantially more challenging, since enumerating all valid material structures is not feasible. In this project, we leveraged recent success in reinforcement learning to efficiently navigate this high-dimensional search space. Just as algorithms can find the optimal chess moves from nearly limitless options, we train an approach to evolve a simple starting structure into a complex structure that possess the desired properties. Our solution has been demonstrated by applying it to two related design application tasks for short- and long-term energy storage, respectively: (1) the design of solid-state ion conductors and (2) the design of organic redox-active materials. The project has resulted an open-source software library for material design, documented examples of applying the library to both organic and inorganic material optimization, and peer-reviewed publications detailing the data, computational models, and resulting candidate materials.

25 ENERGY STORAGE↗
DOE OSTI2022

End-to-End Optimization for Battery Materials and Molecules by Combining Graph Neural Networks and Reinforcement Learning

The National Renewable Energy Laboratory (NREL), together with the Colorado School of Mines (CSM) and Colorado State University (CSU), has developed a machine learning-enhanced approach to the design of new battery materials. Currently, such materials are designed in part via numerous expensive high-fidelity computational simulations that predict the performance of a given composition. Even with computational screening tools, the vast landscape of possible molecular or crystal structures exceeds current and future computational capacity. Improving the efficiency by which new materials can be optimized will therefore disrupt the cost, risk, and time required to bring new energy solutions to the marketplace. Predicting the properties of an organic molecule or periodic crystalline material given its structure has grown increasingly common. These approaches leverage large-scale computational and experimental databases and ML approaches such as graph neural networks. The inverse design problem of finding a material that possesses desired properties is substantially more challenging, since enumerating all valid material structures is not feasible. In this project, we leveraged recent success in reinforcement learning to efficiently navigate this high-dimensional search space. Just as algorithms can find the optimal chess moves from nearly limitless options, we train an approach to evolve a simple starting structure into a complex structure that possess the desired properties. Our solution has been demonstrated by applying it to two related design application tasks for short- and long-term energy storage, respectively: (1) the design of solid-state ion conductors and (2) the design of organic redox-active materials. The project has resulted an open-source software library for material design, documented examples of applying the library to both organic and inorganic material optimization, and peer-reviewed publications detailing the data, computational models, and resulting candidate materials.

25 ENERGY STORAGE↗
NASA NTRS2005

Online Tools for Astronomy and Cosmochemistry

Over the past year, the Webnucleo Group at Clemson University has been developing a web site with a number of interactive online tools for astronomy and cosmochemistry applications. The site uses SHP (Simplified Hypertext Preprocessor), which, because of its flexibility, allows us to embed almost any computer language into our web pages. For a description of SHP, please see http://www.joeldenny.com/ At our web site, an internet user may mine large and complex data sets, such as our stellar evolution models, and make graphs or tables of the results. The user may also run some of our detailed nuclear physics and astrophysics codes, such as our nuclear statistical equilibrium code, which is written in fortran and C. Again, the user may make graphs and tables and download the results.

Meyer, B. S.↗
DOE OSTI2022

Computational Estimation by Scientific Data Mining with Classical Methods to Automate Learning Strategies of Scientists

Experimental results are often plotted as 2-dimensional graphical plots (aka graphs) in scientific domains depicting dependent versus independent variables to aid visual analysis of processes. Repeatedly performing laboratory experiments consumes significant time and resources, motivating the need for computational estimation. The goals are to estimate the graph obtained in an experiment given its input conditions, and to estimate the conditions that would lead to a desired graph. Existing estimation approaches often do not meet accuracy and efficiency needs of targeted applications. We develop a computational estimation approach called AutoDomainMine that integrates clustering and classification over complex scientific data in a framework so as to automate classical learning methods of scientists. Knowledge discovered thereby from a database of existing experiments serves as the basis for estimation. Challenges include preserving domain semantics in clustering, finding matching strategies in classification, striking a good balance between elaboration and conciseness while displaying estimation results based on needs of targeted users, and deriving objective measures to capture subjective user interests. These and other challenges are addressed in this work. The AutoDomainMine approach is used to build a computational estimation system, rigorously evaluated with real data in Materials Science. Our evaluation confirms that AutoDomainMine provides desired accuracy and efficiency in computational estimation. It is extendable to other science and engineering domains as proved by adaptation of its sub-processes within fields such as Bioinformatics and Nanotechnology.

Computer Science↗
NASA NTRS2008

RHSEG and Subdue: Background and Preliminary Approach for Combining these Technologies for Enhanced Image Data Analysis, Mining and Knowledge Discovery

Under a project recently selected for funding by NASA's Science Mission Directorate under the Applied Information Systems Research (AISR) program, Tilton and Cook will design and implement the integration of the Subdue graph based knowledge discovery system, developed at the University of Texas Arlington and Washington State University, with image segmentation hierarchies produced by the RHSEG software, developed at NASA GSFC, and perform pilot demonstration studies of data analysis, mining and knowledge discovery on NASA data. Subdue represents a method for discovering substructures in structural databases. Subdue is devised for general-purpose automated discovery, concept learning, and hierarchical clustering, with or without domain knowledge. Subdue was developed by Cook and her colleague, Lawrence B. Holder. For Subdue to be effective in finding patterns in imagery data, the data must be abstracted up from the pixel domain. An appropriate abstraction of imagery data is a segmentation hierarchy: a set of several segmentations of the same image at different levels of detail in which the segmentations at coarser levels of detail can be produced from simple merges of regions at finer levels of detail. The RHSEG program, a recursive approximation to a Hierarchical Segmentation approach (HSEG), can produce segmentation hierarchies quickly and effectively for a wide variety of images. RHSEG and HSEG were developed at NASA GSFC by Tilton. In this presentation we provide background on the RHSEG and Subdue technologies and present a preliminary analysis on how RHSEG and Subdue may be combined to enhance image data analysis, mining and knowledge discovery.

Tilton, James C.↗
NASA NTRSDate not supplied

Open Science for Life in Space: Data Sharing and Tools for Knowledge Discovery

The fast-growing array of space biological data, which in the past was simply archived after minimal analysis, holds great potential if it can be reorganized and formatted for Open Science. Organizing the data for such analysis is a challenge because of its diverse nature (molecular, cellular, tissue, whole organism, behavior; tabular, imagery). Open Science is the concept that the more people have access to scientifically curated data, the more knowledge will be gained. This led NASA to start the development of GeneLab in 2015. GeneLab houses spaceflight and space-analog multi-omics datasets from plant, rodent, small animal, and microbial experiments. The success and knowledge gained from GeneLab led to a new alliance of NASA “Open Science Data Repositories” (OSDR), which include the Ames Life Sciences Data Archive (ALSDA) and the NASA Biological Institutional Scientific Collection (NBISC). Both are adopting the GeneLab data system, so data are more findable, accessible, interoperable, and reusable (FAIR). OSDR systems provide users the ability to upload, download, search, share, analyze, and visualize. Open Science also needs strong confidence in the data, which is gained through building science communities. With ~400 current members, GeneLab and ALSDA formed Analysis Working Groups (AWGs) to provide feedback on processing pipelines, metadata curation standards (for ‘omics and phenotypic-physiological-behavioral assays), and to collaborate in effectively reusing data. The AWG also led to the development of the Radiation Biology Ontology (RBO), ensuring radiation metadata are efficiently captured, connected, and interoperable. Feedback from the AWG provided design input toward the new single point-of-entry data submission portal for all investigators to submit, curate, and share their research data. Space biological data is now maximally open access, collected-curated with rich metadata, and formatted for interoperability to enable systems biology, meta-analysis, knowledge graphs, machine learning, modeling, and other reuse approaches. With potential for further federation of OSDR for data mining with traditional biological and medical databases (NIH, NCI, EBI, etc.), a new era for space biology has begun to support the knowledge discovery necessary for Lunar and Martian missions.

Ryan T Scott↗
DOE OSTI2022

Six Machine-Learning Methods for Predicting Hospital-Stay Duration for Patients with Sepsis: A Comparative Study

Sepsis is a life-threatening medical condition that, if not treated promptly, can result in tissue damage, organ failure, and death. According to the Centers for Disease Control, about 270,000 individuals die of sepsis in the US each year. Further, sepsis expenditures accounted for 13% of total US hospital costs in 2013, totaling more than $24 billion. Our project objectives were to determine if Machine Learning algorithms could reliably predict hospital stay duration for patients with sepsis. The data set we used has been de-identified and is freely available through the BupaR package. The data includes 1050 cases, 15214 events, and 16 types of actions related to sepsis patient care. First, we used process mining to determine how long each patient was in the hospital. Using BupaR’s functions, we created several process model graphs. These process models depict the movement of patients at a hospital and provide duration data for each patent case. Second, we identified outlier data and created two dataset versions: one with and one without outliers. We then applied the following analysis methods: Linear Regression, Random Forest, K-Nearest Neighbors, Neural Networks, XGBoost, and lightGBM. We compared the model validations for the six machine learning models using the same data-splitting method. We found that the XGBoost model had the best prediction accuracy of 73.9 percent for cases with outliers, and 79 percent for cases without outliers. We also found that the lightGBM model had the lowest mean absolute error between prediction and actual duration in days with 3.66 days for the case with outliers, and 2.4 days for the case without outliers. These two models outperformed the other four models. This work will be enhanced in the future by exploring new prediction algorithms and comparing them with the results of this study.

Chen, Lingtao↗
DOE OSTI2022

Generative Design for Resilience of Interdependent Network Systems

Abstract Interconnected complex systems usually undergo disruptions due to internal uncertainties and external negative impacts such as those caused by harsh operating environments or regional natural disaster events. To maintain the operation of interconnected network systems under both internal and external challenges, design for resilience research has been conducted from both enhancing the reliability of the system through better designs and improving the failure recovery capabilities. As for enhancing the designs, challenges have arisen for designing a robust system due to the increasing scale of modern systems and the complicated underlying physical constraints. To tackle these challenges and design a resilient system efficiently, this study presents a generative design method that utilizes graph learning algorithms. The generative design framework contains a performance estimator and a candidate design generator. The generator can intelligently mine good properties from existing systems and output new designs that meet predefined performance criteria while the estimator can efficiently predict the performance of the generated design for a fast iterative learning process. Case studies results based on synthetic supply chain networks and power systems from the IEEE dataset have illustrated the applicability of the developed method for designing resilient interdependent network systems.

Engineering↗
DOE OSTI2024

Studying CPU and memory utilization of applications on Fujitsu A64FX and Nvidia Grace Superchip

ARM-based manycore CPU architectures are well-positioned to provide the rising memory throughput requirements of modern data intensive scientific applications in High Performance Computing (HPC). The Fujitsu A64FX CPU platform is based on the ARM v8.2A architecture, and is the processor of the flagship Japanese supercomputer - "Fugaku", which was previously ranked as the #1 supercomputer in the world according to the Top500 list. The Nvidia Grace superchip features 144 Neoverse V2 cores based on the ARMv9 architecture with 4x128b SVE2, providing exceptional computational power. The chip supports up to 480GB of memory, making it ideal for AI, machine learning, and scientific computing workloads. In this paper, we conduct a thorough performance exploration of a variety of parallel bandwidth-sensitive benchmarks and applications compiled with the native Fujitsu compiler on a Fugaku A64FX compute node and ARM (LLVM) Compiler on an NVIDIA Grace superchip compute node, engaging all the computational cores per cluster using OpenMP multithreading (assuming the cores can drive the available bandwidth). Our ultimate goals are to study the resource utilization of scientific applications and benchmarks on A64FX and Grace superchip, considering graph application scenarios ( GAP Benchmark suite) and eleven appli- cation proxies from the Rodinia heterogeneous benchmark suite (considering domains such as Data Mining, Bioinformatics, Fluid Dynamics, Pattern Recognition, etc.). Through exhaustive performance monitoring, we quantify the resource utilization of diverse OpenMP-based HPC applications on both the Fujitsu A64FX and the Nvidia Grace Superchip platforms.

benchmarking, Performance Analysis, High performan↗