Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “graph clustering”

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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Measuring and Modeling Bipartite Graphs with Community Structure

Network science is a powerful tool for analyzing complex systems in fields ranging from sociology to engineering to biology. This paper is focused on generative models of bipartite graphs, also known as two-way graphs. We propose two generative models that can be easily tuned to reproduce the characteristics of real-world networks, not just qualitatively, but quantitatively. The measurements we consider are the degree distributions and the bipartite clustering coefficient, which we refer to as the metamorphosis coefficient. We define edge, node, and degreewise metamorphosis coefficients, enabling a more detailed understand of the bipartite community structure. Our proposed bipartite Chung-Lu model is able to reproduce real-world degree distributions, and our proposed bipartite “BTER” model reproduces both the degree distributions as well as the degreewise metamorphosis coefficients. We demonstrate the effectiveness of these models on several real-world data sets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Investigating Anomalies in Compute Clusters: An Unsupervised Learning Approach

As compute clusters continue to grow in scale and complexity, the frequency of detected anomalies in their operation significantly increases. Timely detection of anomalous events is vital to maintain system efficiency and availability. This study presents an attentionbased graph neural network (GNN) for detecting anomalies in clusters at the compute node level and for providing detailed root cause analysis. We show the effectiveness of attention-based GNNs to accurately detect and localize anomalies on real-world datasets.

Lu, Yiyang↗
DOE OSTI2024

Streaming Matching and Edge Cover in Practice

Graph algorithms with polynomial space and time requirements often become infeasible for massive graphs with billions of edges or more. State-of-the-art approaches therefore employ approximate serial, parallel, and distributed algorithms to tackle these challenges. However, such approaches require storing the entire graph in memory and thus need access to costly computing resources such as clusters and supercomputers. In this paper, we present practical streaming approaches for solving massive graph problems using limited memory for two prototypical graph problems: maximum weighted matching and minimum weighted edge cover. For matching, we conduct a thorough computational study on two of the semi-streaming algorithms including a recent breakthrough result that achieves a $1/(2+\varepsilon)$-approximation of the weight while using $O( n \log W /\epsilon)$ memory (here $n$ is the number of vertices and $W$ is the maximum edge weight), designed by Paz and Schwartzman [SODA, 2017]. Empirically, we show that the semi-streaming algorithms produce matchings whose weight is close to the best $1/2$-approximate offline algorithm while requiring less time and an order-of-magnitude less memory. For minimum weighted edge cover, we develop three novel semi-streaming algorithms. Two of these algorithms require a single pass through the input graph, require $O(n \log n)$ memory, and provide a 2-approximation guarantee on the objective. We also leverage a relationship between approximate maximum weighted matching and approximate minimum weighted edge cover to develop a two-pass $3/2+\epsilon$-approximate algorithm with the memory requirement of Paz and Schwartzman's semi-streaming matching algorithm. These streaming approaches are compared against the state-of-the-art 3/2-approximate offline algorithm. The semi-streaming matching and the novel edge cover algorithms proposed in this paper can process graphs with several billions of edges in under 30 minutes using 6 GB of memory, which is at least an order of magnitude improvement from the offline (non-streaming) algorithms. For the largest graph, the best alternative offline parallel approximation algorithm (GPA+ROMA) could not finish in three hours even while employing hundreds of processors and 1 TB of memory. We also demonstrate an application of the semi-streaming algorithm by computing a matching using linearly bounded memory on item intersection graphs derived from three machine learning datasets, whereas the existing offline algorithms could not complete on one of these datasets since their memory requirements exceeded 1TB.

Ferdous, S M.↗
DOE OSTI2026

Cluster bootstrap for cosmological correlators

We show that cosmological wavefunction coefficients associated with n-site chain and loop graphs for a cubic scalar theory in de Sitter spacetime have symbol alphabets given by subsets of A 2n−2 and B 2n−1 cluster variables, respectively, and satisfy the associated cluster adjacency properties. The key step in proving this is identifying a precise connection between graph “tubings” that appear in the kinematic flow equation and polygon “triangulations” that encode the combinatorics of cluster compatibility. Our results imply that cosmological wavefunction coefficients in a general power-law FRW cosmology satisfy cluster adjacency to all orders in the ϵ expansion around the de Sitter limit. We use this information as bootstrap input to show that de Sitter symbols for n ≤ 4 are uniquely determined by simple physical constraints.

differential and algebraic geometry↗
DOE OSTI2016

OpenMP Parallelization and Optimization of Graph-Based Machine Learning Algorithms

In this paper, we investigate the OpenMP parallelization and optimization of two novel data classification algorithms. The new algorithms are based on graph and PDE solution techniques and provide significant accuracy and performance advantages over traditional data classification algorithms in serial mode. The methods leverage the Nystrom extension to calculate eigenvalue/eigenvectors of the graph Laplacian and this is a self-contained module that can be used in conjunction with other graph-Laplacian based methods such as spectral clustering. We use performance tools to collect the hotspots and memory access of the serial codes and use OpenMP as the parallelization language to parallelize the most time-consuming parts. Where possible, we also use library routines. We then optimize the OpenMP implementations and detail the performance on traditional supercomputer nodes (in our case a Cray XC30), and test the optimization steps on emerging testbed systems based on Intel’s Knights Corner and Landing processors. We show both performance improvement and strong scaling behavior. Finally, a large number of optimization techniques and analyses are necessary before the algorithm reaches almost ideal scaling.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Deep learning for characterizing the self-assembly of three-dimensional colloidal systems

Creating a systematic framework to characterize the structural states of colloidal self-assembly systems is crucial for unraveling the fundamental understanding of these systems’ stochastic and non-linear behavior. The most accurate characterization methods create high-dimensional neighborhood graphs that may not provide useful information about structures unless these are well-defined reference crystalline structures. Dimensionality reduction methods are thus required to translate the neighborhood graphs into a low-dimensional space that can be easily interpreted and used to characterize non-reference structures. We investigate a framework for colloidal system state characterization that employs deep learning methods to reduce the dimensionality of neighborhood graphs. The framework next uses agglomerative hierarchical clustering techniques to partition the low-dimensional space and assign physically meaningful classifications to the resulting partitions. In this work, we first demonstrate the proposed colloidal self-assembly state characterization framework on a three-dimensional in silico system of 500 multi-flavored colloids that self-assemble under isothermal conditions. We next investigate the generalizability of the characterization framework by applying the framework to several independent self-assembly trajectories, including a three-dimensional in silico system of 2052 colloidal particles that undergo evaporation-induced self-assembly.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Toward a Data Scalable Solution for Facilitating Discovery of Scientific Data Resources

Science is increasingly motivated by the need to process larger quantities of data. It is facing severe challenges in data collection, management, and processing, so much so that the computational demands of "data scaling" are competing with, and in many fields surpassing, the traditional objective of decreasing processing time. Example domains with large datasets include astronomy, biology, genomic, climate and weather, and material sciences. This paper presents a real-world use case in which we wish to answer queries provided by domain scientists in order to facilitate discovery of relevant science resources. The problem is that the metadata for these science resources is very large and is growing quickly, rapidly increasing the need for a data scaling solution. We propose the use of our SGEM stack -- a system designed for answering graph-based queries over large datasets on cluster architectures -- for answering complex queries over the metadata, and we report early results for our current capability.

Chappell, Alan R.↗
DOE OSTI2018

A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions

Abstract Metabolism has been a major field of study in the last years, mainly due to its importance in understanding cell physiology and certain disease phenotypes due to its deregulation. Genome-scale metabolic models (GSMMs) have been established as important tools to help achieve a better understanding of human metabolism. Towards this aim, advances in systems biology and bioinformatics have allowed the reconstruction of several human GSMMs, although some limitations and challenges remain, such as the lack of external identifiers for both metabolites and reactions. A pipeline was developed to integrate multiple GSMMs, starting by retrieving information from the main human GSMMs and evaluating the presence of external database identifiers and annotations for both metabolites and reactions. Information from metabolites was included into a graph database with omics data repositories, allowing clustering of metabolites through their similarity regarding database cross-referencing. Metabolite annotation of several older GSMMs was enriched, allowing the identification and integration of common entities. Using this information, as well as other metrics, we successfully integrated reactions from these models. These methods can be leveraged towards the creation of a unified consensus model of human metabolism.

Vieira, Vítor↗
NASA NTRS1991

Stellar turbulent convection - A new model and applications

Improvements of the mixing-length theory (MLT) of turbulent convection in stellar atmospheres are developed theoretically. It is pointed out that inaccuracies are introduced into MLT by the approximating assumptions of a single large eddy (rather than many eddies of different sizes) and of incompressibility. In the proposed new model, the full spectrum of turbulent eddies is determined using more recent turbulence models (e.g., the eddy-damped quasi-normal Markovian model of Orszag, 1977), and a new formula for the convective flux is obtained which gives values up to 10 times greater than those of the MLT at high convective efficiencies. The problem of compressibility is addressed by adding one of two new expressions (one with no free parameters) for the mixing length. Numerical results from simulations of a solar-type star and a 0.8-solar-mass globular-cluster star are presented in tables and graphs and discussed in detail; the agreement with observations is found to be better than with the MLT.

Canuto, V. M.↗
DOE OSTI2011

Numerical Methods for Large-Scale Data Factorization (Final Report (Milestone Date 9/30/11) for Subcontract No. B594099)

The following work has been performed by PI Hans De Sterck and graduate student Manda Winlaw for the required tasks 1-5 (as listed in the Statement of Work). Graduate student Manda Winlaw has visited LLNL January 31-March 11, 2011 and May 23-August 19, 2010, working with Van Henson and Mike O'Hara on non-negative matrix factorizations (NMF). She has investigated the dense subgraph clustering algorithm from 'Finding Dense Subgraphs for Sparse Undirected, Directed, and Bipartite Graphs' by Chen and Saad, testing this method on several term-document matrices and adapting it to cluster based on the rank of the subgraphs instead of the density. Manda Winlaw was awarded a first prize in the annual LLNL summer student poster competition for a poster on her NMF research. PI Hans De Sterck has developed a new adaptive algebraic multigrid algorithm for computing a few dominant or minimal singular triplets of sparse rectangular matrices. This work builds on adaptive algebraic multigrid methods that were further developed by the PI and collaborators (including Sanders and Henson) for Markov chains. The method also combines and extends existing multigrid algorithms for the symmetric eigenproblem. The PI has visited LLNL February 22-25, 2011, and has given a CASC seminar 'Algebraic Multigrid for the Singular Value Problem' on this work on February 23, 2011. During his visit, he has discussed this work and related topics with Van Henson, Geoffrey Sanders, Panayot Vassilevski, and others. He has tested the algorithm on PDE matrices and on a term-document matrix, with promising initial results. Manda Winlaw has also started to work, with O'Hara, on estimating probability distributions over undirected graph edges. The goal is to estimate probabilistic models from sets of undirected graph edges for the purpose of prediction, anomaly detection and support to supervised learning. Graduate student Manda Winlaw is writing a paper on the results obtained with O'Hara which will be submitted some time later in 2011 to a data mining conference. PI Hans De Sterck has developed a new optimization algorithm for canonical tensor approximation, formulating an extension of the nonlinear GMRES method to optimization problems. Numerical results for tensors with up to 8 modes show that this new method is efficient for sparse and dense tensors. He has written a paper on this which has been submitted to the SIAM Journal on Scientific Computing. PI Hans De Sterck has further developed his new optimization algorithm for canonical tensor approximation, formulating an extension in terms of steepest-descent preconditioning, which makes the approach generally applicable for nonlinear optimization. He has written a paper on this extension which has been submitted to Numerical Linear Algebra with Applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Community detection and unveiling of hierarchy in networks: a density-based clustering approach

Abstract The unveiling of communities within a network or graph, and the hierarchization of its members that results is of utmost importance in areas ranging from social to biochemical networks, from electronic circuits to cybersecurity. We present a statistical mechanics approach that uses a normalized Gaussian function which captures the impact of a node within its neighborhood and leads to a density-ranking of nodes by considering the distance between nodes as punishment. A hill-climbing procedure is applied to determine the density attractors and identify the unique parent (leader) of each member as well as the group leader. This organization of the nodes results in a tree-like network with multiple clusters, the community tree. The method is tested using synthetic networks generated by the LFR benchmarking algorithm for network sizes between 500 and 30,000 nodes and mixing parameter between 0.1 and 0.9 . Our results show a reasonable agreement with the LFR results for low to medium values of the mixing parameter and indicate a very mild dependence on the size of the network.

Felfli, Zineb (ORCID:0000000275294635)↗
NASA NTRS1988

A radial-velocity survey of the Hyades

Photoelectric radial-velocity measurements, obtained with external error as small as 0.1 km/s using the 200-inch Hale telescope at Palomar Observatory during the period 1971-1986, are reported for over 400 candidate members (with V magnitude between 6 and 14) of the Hyades cluster. The history of Hyades observations is recalled; the Palomar instrumentation and observing program are described; the data-reduction and standardization procedures are discussed in detail; and the data are presented in extensive tables and graphs. About 200 of the stars are classified as cluster members, including 60 spectroscopic binaries.

Griffin, R. F.↗
DOE OSTI2015

In-Memory Graph Databases for Web-Scale Data

RDF databases have emerged as one of the most relevant way for organizing, integrating, and managing expo- nentially growing, often heterogeneous, and not rigidly structured data for a variety of scientific and commercial fields. In this paper we discuss the solutions integrated in GEMS (Graph database Engine for Multithreaded Systems), a software framework for implementing RDF databases on commodity, distributed-memory high-performance clusters. Unlike the majority of current RDF databases, GEMS has been designed from the ground up to primarily employ graph-based methods. This is reflected in all the layers of its stack. The GEMS framework is composed of: a SPARQL-to-C++ compiler, a library of data structures and related methods to access and modify them, and a custom runtime providing lightweight software multithreading, network messages aggregation and a partitioned global address space. We provide an overview of the framework, detailing its component and how they have been closely designed and customized to address issues of graph methods applied to large-scale datasets on clusters. We discuss in details the principles that enable automatic translation of the queries (expressed in SPARQL, the query language of choice for RDF databases) to graph methods, and identify differences with respect to other RDF databases.

GEMS↗
DOE OSTI2023

Evaluating Robust Entanglement on a Trapped Ion Platform

We present proof of principle results for evaluating an entanglement volumetric benchmark [1] on trapped ion platforms. The benchmark quantifies the robustness of multipartite and bipartite entanglement using stabilizer measurements and witness functions. Each n-qubit graph state is prepared and used to evaluate n state-specific stabilizer strings. These stabilizer measurements are used to evaluate entanglement witness functions. The entanglement benchmark defines families of graph states associated with an initial sub-graph of the hardware qubit connectivity - with all-to-all connectivity, trapped ion systems provide a flexibility in the choice of this initial graph, and this will affect the associated family. In this work, we present results targeting several classes of entangled states: 1) 1-D cluster states, 2) n-qubit GHZ states, and 3) cycle graph states. These states have been found in the literature as standard hardware benchmarks, and have connections to many near-term applications.

Hamilton, Kathleen↗
DOE OSTI2020

Symbol alphabets from plabic graphs

Symbol alphabets of n-particle amplitudes in N = 4 super-Yang-Mills theory are known to contain certain cluster variables of Gr(4, n) as well as certain algebraic functions of cluster variables. In this paper we suggest an algorithm for computing these symbol alphabets from plabic graphs by solving matrix equations of the form C ∙ Z = 0 to associate functions on Gr(m, n) to parameterizations of certain cells of Gr(k, n) indexed by plabic graphs. For m = 4 and n = 8 we show that this association precisely reproduces the 18 algebraic symbol letters of the two-loop NMHV eight-particle amplitude from four plabic graphs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

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

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

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1989

Decision net, directed graph, and neural net processing of imaging spectrometer data

A decision-net solution involving a novel hierarchical classifier and a set of multiple directed graphs, as well as a neural-net solution, are respectively presented for large-class problem and mixture problem treatments of imaging spectrometer data. The clustering method for hierarchical classifier design, when used with multiple directed graphs, yields an efficient decision net. New directed-graph rules for reducing local maxima as well as the number of perturbations required, and the new starting-node rules for extending the reachability and reducing the search time of the graphs, are noted to yield superior results, as indicated by an illustrative 500-class imaging spectrometer problem.

Casasent, David↗