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DOE OSTI2017

Spatial–spectral Schroedinger embedding for target detection in hyperspectral imagery

In this work, the Schroedinger eigenmaps (SE) algorithm using spatial and spectral information has been applied to supervised classification of hyperspectral imagery (HSI). We have previously introduced the use of SE in spectral target detection problems. The original SE-based target detector was built on the spectral information encoded in the Laplacian and Schroedinger operators. The original SE-based detector is extended such that spatial connectivity of target-like pixels is explored and encoded into the Schroedinger operator using a “knowledge propagation” scheme. The modified SE-based detector is applied to two HSI data sets that share similar target materials. Receiver operating characteristic curves and rates of detection and false alarm at object level are used as quantitative metrics to assess the detector. In addition, the Schroedinger embedding performance in target detection is compared against the performances of principal component embedding and the Laplacian embedding. Finally, results show that the SE-based detector with spatial–spectral features outperforms the other considered approaches.

36 MATERIALS SCIENCE↗

NASA NTRSDate not supplied

Modeling Atmospheric Science Knowledge from Research Publications

NASA Earth Science Data Centers contain enormous amounts of remote sensing digital data. It is often a significant challenge for users to find data suitable for their research topic in these vast archives. One of the approaches is the usage-driven dataset discovery, where users seek publications on projects similar to their intended study. For this approach to be effective, users need a clear connection between the underlying data in the publications and the study objectives; this is not often apparent to non-expert users. Tools and methodologies that can help facilitate and organize these connections are therefore valuable for creating improved knowledge mappings, which can be further used by search engines to suggest data or publications best tailored to a user’s specific research goal. As an illustration of these challenges, in this work we focus on the atmospheric chemistry processes related to Earth environmental impacts such as ozone depletion, aerosols, smog formation, acid rain, and radiative forcing. We further limit our study to publications that use data from the Microwave Limb Sounder (MLS) instrument flown on the Aura Earth Observing System. To create knowledge representations of science carried out in these publications, we use existing ontologies such as the Global Change Master Directory (GCMD) and Semantic Web for Earth and Environmental Terminology (SWEET). These ontologies together encompass term dictionaries that include measured variables, names of molecules or radicals, mission and instrument names, locations, action words, among many others. Based on these terms acknowledge graph database was populated with the terms retrieved from scientific publications that study atmospheric chemistry. These databases can be used to further enhance the automation of knowledge discovery and facilitate machine learning and artificial intelligence algorithms or applications. These tools and methods can also be extended to apply to content from other related Earth science domains.

Irina Gerasimov↗

NASA NTRS1988

Presentation planning using an integrated knowledge base

A description is given of user interface research aimed at bringing together multiple input and output modes in a way that handles mixed mode input (commands, menus, forms, natural language), interacts with a diverse collection of underlying software utilities in a uniform way, and presents the results through a combination of output modes including natural language text, maps, charts and graphs. The system, Integrated Interfaces, derives much of its ability to interact uniformly with the user and the underlying services and to build its presentations, from the information present in a central knowledge base. This knowledge base integrates models of the application domain (Navy ships in the Pacific region, in the current demonstration version); the structure of visual displays and their graphical features; the underlying services (data bases and expert systems); and interface functions. The emphasis is on a presentation planner that uses the knowledge base to produce multi-modal output. There has been a flurry of recent work in user interface management systems. (Several recent examples are listed in the references). Existing work is characterized by an attempt to relieve the software designer of the burden of handcrafting an interface for each application. The work has generally focused on intelligently handling input. This paper deals with the other end of the pipeline - presentations.

Arens, Yigal↗

DOE OSTI2012

A new, analytic, non-perturbative, gauge-invariant formulation of realistic QCD

This Formulation [1], [2], [3] is New, in the sense that it is less than 3 years old. But it could have been done decades ago, since the input information existed, but was overlooked. It is Analytic in the sense that physically-reasonable approximations can be estimated with paper and pencil; and exact amplitudes can be calculated as Meijer G-functions of various orders. It is Non-Perturbative in the sense that sums over all possible gluon exchanges between any pair of quarks and/or antiquarks, including cubic and quartic gluon interactions, are exactly performed. These multiple gluon exchanges combine into 'Gluon Bundles' (GBs), as sums over Feynman graphs with finite numbers of exchanged gluons are replaced by {sup B}undle Graphs{sup .} In effect, gluons disappear from the formalism, and GBs remain as the effective carrier of all interactions between quark lines. A simple re-arrangement of the Schwinger/Symanzik functional solution for the Generating Functional of QCD - a rearrangement possible in QCD but not in QED - produces a formal statement of Gauge-Invariance, even though the formulation contains gauge-dependent gluon propagators. After the non-perturbative sums produce GBs, one sees explicit cancelation of all gauge-dependent gluon propagators; gauge-invariance is achieved as gauge-independence. A new insight into Realistic QCD appears in the non-perturbative domain, because quarks do not have individual asymptotic states; they are always asymptotically bound, and their transverse coordinates cannot, in principle, be measured exactly. 'Transverse Imprecision' is introduced into the basic Lagrangian, and quark-binding potentials for the construction of mesons and nucleons can then be defined and evaluated. And the greatest surprise of all: A new, non-perturbative property appears, called Effective Locality, with the result that all functional integrals reduce to (a few) sets of ordinary integrals, easy to estimate approximately, or calculate on a desk-top computer. A fantastic simplification{exclamation_point} With the aid of the above techniques, this presentation will describe each of the above paragraphs, with explicit descriptions of gauge-invariance, of the summation of all relevant Feynman graphs, of quark-binding into hadrons, and of nucleon-nucleon binding to form a deuteron. To our knowledge, the latter calculation is the first analytic example of Nuclear Physics obtained directly from basic QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2014

An Adaptive Memory Interface Controller for Improving Bandwidth Utilization of Hybrid and Reconfigurable Systems

Emerging applications such as data mining, bioinformatics, knowledge discovery, social network analysis are irregular. They use data structures based on pointers or linked lists, such as graphs, unbalanced trees or unstructures grids, which generates unpredictable memory accesses. These data structures usually are large, but difficult to partition. These applications mostly are memory bandwidth bounded and have high synchronization intensity. However, they also have large amounts of inherent dynamic parallelism, because they potentially perform a task for each one of the element they are exploring. Several efforts are looking at accelerating these applications on hybrid architectures, which integrate general purpose processors with reconfigurable devices. Some solutions, which demonstrated significant speedups, include custom-hand tuned accelerators or even full processor architectures on the reconfigurable logic. In this paper we present an approach for the automatic synthesis of accelerators from C, targeted at irregular applications. In contrast to typical High Level Synthesis paradigms, which construct a centralized Finite State Machine, our approach generates dynamically scheduled hardware components. While parallelism exploitation in typical HLS-generated accelerators is usually bound within a single execution flow, our solution allows concurrently running multiple execution flow, thus also exploiting the coarser grain task parallelism of irregular applications. Our approach supports multiple, multi-ported and distributed memories, and atomic memory operations. Its main objective is parallelizing as many memory operations as possible, independently from their execution time, to maximize the memory bandwidth utilization. This significantly differs from current HLS flows, which usually consider a single memory port and require precise scheduling of memory operations. A key innovation of our approach is the generation of a memory interface controller, which dynamically maps concurrent memory accesses to multiple ports. We present a case study on a typical irregular kernel, Graph Breadth First search (BFS), exploring different tradeoffs in terms of parallelism and number of memories.

BFS↗

DOE OSTI2020

A Scalable Parallel Hypergraph Generator (HyGen)

Graphs are extensively used to model real-world complex systems. An edge in a graph can model pairwise relationships. However, multiway relationships (connections between three or more vertices) are common in many complex systems such as cellular process, image segmentation, and circuit design. A graph edge cannot model multiway relationships. A hypergraph, which can connect more than two vertices, is thus a better option to model multiway relationships. A large-scale hypergraph analysis has the potential to find useful insights from a complex system and assist in knowledge discovery. Currently a limited number of hypergraphs exists that are representative of real-world datasets. Moreover, real-world hypergraph datasets are small in size and inadequate to incorporate future needs. A graph generator that can produce large-scale synthetic hypergraphs can solve the above mentioned problems. In this paper, we present a scalable parallel hypergraph generator (HyGen) based on the Message Passing Interface (MPI) standard. To generate hypergraphs, HyGen takes the following parameter values as inputs: i) number of vertices, ii) number of hyperedges, iii) number of clusters, iv) vertex distribution, v) hyperedge distribution, vi) local cluster cardinality, and vii) global cluster cardinality. We have demonstrated that HyGen can generate hypergraphs of various sizes in a scalable fashion. HyGen takes approximately four minutes to generate a hypergraph with 4.8 million vertices, 1.6 million hyperedges, and 800 clusters using 1,024 processes on a leadership class computing platform. Our strong and weak scaling experiments on supercomputers demonstrate that HyGen can quickly create large-scale hypergraphs in a parallel manner, thus providing a useful capability for hypergraph analysis.

Hasan, S M Shamimul↗

DOE OSTI2025

Graph reinforcement learning for exploring model spaces beyond the standard model

We present a methodology for performing scans of beyond the standard model (BSM) parameter spaces with reinforcement learning. We identify a novel procedure using graph neural networks that is capable of exploring spaces of models without the user specifying a fixed particle content, allowing broad classes of BSM models to be explored—in theory, the technique is applicable to nearly any model space with a prespecified gauge group. We provide a generic procedure by which a suitable graph grammar can be developed for any BSM model that features user-specified symmetry groups and a finite number of different possible particle species, the use of which is applicable to a variety of machine learning tasks over the actions of BSM theories beyond our particular reinforcement learning use case. As a proof of concept, we construct the graph grammar for theories with vectorlike leptons that may or may not be charged under a dark U ( 1 ) group, inspired by portal matter extensions of the sub-GeV vector portal/kinetic mixing simplified dark matter models. We then use this graph grammar to create a reinforcement learning environment tasked with creating models with these vectorlike leptons that are consistent with a list of a variety of precision observables. The reinforcement learning agent succeeds in developing models that can address the observed muon anomalous magnetic moment discrepancy while remaining consistent with flavor violation and electroweak precision observables, including both constructions that have previously been studied as well as new models that have not, to our knowledge, previously been identified. By inspecting the resulting ensembles of models that the agent produces and experimenting with different configurations for our reinforcement learning environment and graph grammar, we also infer various lessons about the development of these environments that can be transferable to reinforcement learning scans of more complicated model spaces and comment on future directions for the development of this technique into a more mature tool. Published by the American Physical Society 2025

Wojcik, George N.↗

DOE OSTI2019

Continuous-time quantum walks on dynamic graphs

Continuous-time quantum walks (CTQWs) on static graphs provide efficient methods for search and sampling as well as a model for universal quantum computation. We consider an extension of CTQWs to the case of dynamic graphs, in which an ordered sequence of graphs governs free evolution of the quantum walk. We then consider how perfect state transfer during the quantum walk can be used to design dynamic graphs that implement a universal set of quantum logic gates. We give explicit examples for a complete logical basis, and we validate implementations using numerical simulations for quantum teleportation and addition circuits. Lastly, we discuss the potential for realizing CTQWs on dynamic graphs using actively controlled quantum optical waveguides.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2015

Multiresolution persistent homology for excessively large biomolecular datasets

Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

MCS+: An Efficient Algorithm for Crawling the Community Structure in Multiplex Networks

In this article, we consider the problem of crawling a multiplex network to identify the community structure of a layer-of-interest. A multiplex network is one where there are multiple types of relationships between the nodes. In many multiplex networks, some layers might be easier to explore (in terms of time, money etc.). We propose MCS+, an algorithm that can use the information from the easier to explore layers to help in the exploration of a layer-of-interest that is expensive to explore. We consider the goal of exploration to be generating a sample that is representative of the communities in the complete layer-of-interest. This work has practical applications in areas such as exploration of dark (e.g., criminal) networks, online social networks, biological networks, and so on. For example, in a terrorist network, relationships such as phone records, e-mail records, and so on are easier to collect; in contrast, data on the face-to-face communications are much harder to collect, but also potentially more valuable. We perform extensive experimental evaluations on real-world networks, and we observe that MCS+ consistently outperforms the best baseline—the similarity of the sample that MCS+ generates to the real network is up to three times that of the best baseline in some networks. We also perform theoretical and experimental evaluations on the scalability of MCS+ to network properties, and find that it scales well with the budget, number of layers in the multiplex network, and the average degree in the original network.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

NASA NTRS2004

Plan-graph Based Heuristics for Conformant Probabilistic Planning

In this paper, we introduce plan-graph based heuristics to solve a variation of the conformant probabilistic planning (CPP) problem. In many real-world problems, it is the case that the sensors are unreliable or take too many resources to provide knowledge about the environment. These domains are better modeled as conformant planning problems. POMDP based techniques are currently the most successful approach for solving CPP but have the limitation of state- space explosion. Recent advances in deterministic and conformant planning have shown that plan-graphs can be used to enhance the performance significantly. We show that this enhancement can also be translated to CPP. We describe our process for developing the plan-graph heuristics and estimating the probability of a partial plan. We compare the performance of our planner PVHPOP when used with different heuristics. We also perform a comparison with a POMDP solver to show over a order of magnitude improvement in performance.

Ramakrishnan, Salesh↗

NASA NTRS2019

NASA Earthdata Knowledge Base

Prototype work for connecting together the main elements of Earth Observation knowledge and context in a way that is: machine-readable, human-usable and curatable. Using the latest in graph technologies and cloud managed services.

earth data↗

DOE OSTI2022

Towards scaling community detection on distributed-memory heterogeneous systems

Distributed multi-GPU systems pose significant challenges and opportunities for efficient execution of parallel applications. Graph algorithms are generally characterized by irregular memory accesses, low computation to communication ratios, and load balancing problems that are especially hard to address on multi-GPU systems. Graph community detection is an important problem in the emerging domain of graph analytics with numerous applications. In this paper, we present our ongoing work on distributed-memory multi-GPU implementation for graph community detection. Our work parallelizes the widely used (albeit serial) Louvain method on distributed multi-GPU platforms. Supported by an extensive set of experiments on a multi-GPU enabled supercomputer (OLCF Summit) and a single compute node (Nvidia DGX-2®), we demonstrate competitive performance to existing distributed-memory CPU-based implementation, and up to 6.5 better results than Nvidia RAPIDS® CUGRAPH. To the best of our knowledge, this work represents the first effort for community detection on distributed multi-GPU systems. Our approach and related findings can be extended to numerous other iterative graph algorithms on multi-GPU systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Evaluating single-scale and/or non-planar diagrams by differential equations

We apply a recently suggested new strategy to solve differential equations for Feynman integrals. We develop this method further by analyzing asymptotic expansions of the integrals. We argue that this allows the systematic application of the differential equations to single-scale Feynman integrals. Moreover, the information about singular limits significantly simplifies finding boundary constants for the differential equations. To illustrate these points we consider two families of three-loop integrals. The first are form-factor integrals with two external legs on the light cone. We introduce one more scale by taking one more leg off-shell, $p_2^2\neq 0$. We analytically solve the differential equations for the master integrals in a Laurent expansion in dimensional regularization with $\epsilon=(4-D)/2$. Then we show how to obtain analytic results for the corresponding one-scale integrals in an algebraic way. An essential ingredient of our method is to match solutions of the differential equations in the limit of small $p_2^2$ to our results at $p_2^2\neq 0$ and to identify various terms in these solutions according to expansion by regions. The second family consists of four-point non-planar integrals with all four legs on the light cone. We evaluate, by differential equations, all the master integrals for the so-called $K_4$ graph consisting of four external vertices which are connected with each other by six lines. We show how the boundary constants can be fixed with the help of the knowledge of the singular limits. We present results in terms of harmonic polylogarithms for the corresponding seven master integrals with six propagators in a Laurent expansion in $\epsilon$ up to weight six.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2011

Scenario driven data modelling: a method for integrating diverse sources of data and data streams

Background: Biology is rapidly becoming a data intensive, data-driven science. It is essential that data is represented and connected in ways that best represent its full conceptual content and allows both automated integration and data driven decision-making. Recent advancements in distributed multi-relational directed graphs, implemented in the form of the Semantic Web make it possible to deal with complicated heterogeneous data in new and interesting ways. Results: This paper presents a new approach, scenario driven data modelling (SDDM), that integrates multirelational directed graphs with data streams. SDDM can be applied to virtually any data integration challenge with widely divergent types of data and data streams. In this work, we explored integrating genetics data with reports from traditional media. SDDM was applied to the New Delhi metallo-beta-lactamase gene (NDM-1), an emerging global health threat. The SDDM process constructed a scenario, created a RDF multi-relational directed graph that linked diverse types of data to the Semantic Web, implemented RDF conversion tools (RDFizers) to bring content into the Sematic Web, identified data streams and analytical routines to analyse those streams, and identified user requirements and graph traversals to meet end-user requirements. Conclusions: We provided an example where SDDM was applied to a complex data integration challenge. The process created a model of the emerging NDM-1 health threat, identified and filled gaps in that model, and constructed reliable software that monitored data streams based on the scenario derived multi-relational directed graph. The SDDM process significantly reduced the software requirements phase by letting the scenario and resulting multi-relational directed graph define what is possible and then set the scope of the user requirements. Approaches like SDDM will be critical to the future of data intensive, data-driven science because they automate the process of converting massive data streams into usable knowledge.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Cooperative Clustering Techniques Applied to Contact Graph Routing

Routing in the space internet has to face many unique challenges - from unplanned disconnections and interruptions to predictable intermittent connectivity due to high network mobility and long propagation delays. NASA’s current approach to such routing is Contact Graph Routing (CGR), using a graph formed of prescheduled communication contacts to compute routes through the network. While this approach manages to tackle issues of connectivity and propagation delays, it is a global approach that requires continuous knowledge of the entire network. In a potential future Solar Space Internet (SSI) such an approach on its own cannot scale to large networks with thousands of members. In this presentation we propose clustering as a solution to CGR scalability. Clustering has been used in many networking problems as a way to subdivide the network and allow for localized routing and better scalability. Using techniques from graph theory and game theory, we explore various existing clustering algorithms and adapt them to the Contact Graph Routing setting. Finally, we propose a way to combine multiple algorithms to create a Delay Tolerant Clustering Protocol.

Yael Kirkpatrick↗

NASA NTRSDate not supplied

Cooperative Clustering Techniques For Space Network Scalability

Routing in the space internet must face many unique challenges - from unplanned disconnections and interruptions to predictable intermittent connectivity due to high network mobility and long propagation delays. NASA’s current approach to such routing is Contact Graph Routing (CGR), using a graph formed of prescheduled communication contacts to compute routes through the network. While this approach manages to tackle issues of connectivity and propagation delays, it is a global approach that requires continuous knowledge of the entire network. In a potential future Solar Space Internet (SSI) such an approach on its own cannot scale to large networks with thousands of members. In this paper we propose clustering as a solution to CGR scalability. Clustering has been used in many networking problems as a way to subdivide the network and allow for localized routing and better scalability. Using techniques from graph theory and game theory, we explore various existing clustering algorithms and adapt them to the Contact Graph Routing setting. We propose a way to combine multiple algorithms to create a Delay Tolerant Clustering Protocol (DTCP). In addition, we explore the underlying networking mechanisms such as multicast, neighbor discovery, and software defined networking that may be used to enable DTCP.

Delay Tolerant Networking↗

DOE OSTI2012

The maximum clique enumeration problem: algorithms, applications, and implementations

Background: The maximum clique enumeration (MCE) problem asks that we identify all maximum cliques in a finite, simple graph. MCE is closely related to two other well-known and widely-studied problems: the maximum clique optimization problem, which asks us to determine the size of a largest clique, and the maximal clique enumeration problem, which asks that we compile a listing of all maximal cliques. Naturally, these three problems are N P -hard, given that they subsume the classic version of the N P -complete clique decision problem. MCE can be solved in principle with standard enumeration methods due to Bron, Kerbosch, Kose and others. Unfortunately, these techniques are ill-suited to graphs encountered in our applications. We must solve MCE on instances deeply seeded in data mining and computational biology, where high-throughput data capture often creates graphs of extreme size and density. MCE can also be solved in principle using more modern algorithms based in part on vertex cover and the theory of fixed-parameter tractability (FPT). While FPT is an improvement, these algorithms too can fail to scale sufficiently well as the sizes and densities of our datasets grow. Results: An extensive testbed of benchmark graphs are created using publicly available transcriptomic datasets from the Gene Expression Omnibus (GEO). Empirical testing reveals crucial but latent features of such high-throughput biological data. In turn, it is shown that these features distinguish real data from random data intended to reproduce salient topological features. In particular, with real data there tends to be an unusually high degree of maximum clique overlap. Armed with this knowledge, novel decomposition strategies are tuned to the data and coupled with the best FPT MCE implementations. Conclusions: Several algorithmic improvements to MCE are made which progressively decrease the run time on graphs in the testbed. Frequently the final runtime improvement is several orders of magnitude. As a result, instances which were once prohibitively time-consuming to solve are brought into the domain of realistic feasibility.

59 BASIC BIOLOGICAL SCIENCES↗