Results for “Graph Processing” — Page 28

DOE OSTI2017

Speleogenesis, geometry, and topology of caves: A quantitative study of 3D karst conduits

Karst systems are hierarchically spatially organized three-dimensional (3D) networks of conduits behaving as drains for groundwater flow. Recently, geostatistical approaches proposed to generate karst networks from data and parameters stemming from analogous observed karst features. Other studies have qualitatively highlighted relationships between speleogenetic processes and cave patterns. However, few studies have been performed to quantitatively define these relationships. This paper reports a quantitative study of cave geometries and topologies that takes the underlying speleogenetic processes into account. In order to study the spatial organization of caves, a 3D numerical database was built from 26 caves, corresponding to 621 km of cumulative cave passages representative of the variety of karst network patterns. The database includes 3D speleological surveys for which the speleogenetic context is known, allowing the polygenic karst networks to be divided into 48 monogenic cave samples and classified into four cave patterns: vadose branchwork (VB), water-table cave (WTC), looping cave (LC), and angular maze (AM). Eight morphometric cave descriptors were calculated, four geometrical parameters (width-height ratio, tortuosity, curvature, and vertical index) and four topological ones (degree of node connectivity, α and γ graph indices, and ramification index) respectively. The results were validated by statistical analyses (Kruskal-Wallis test and PCA). The VB patterns are clearly distinct from AM ones and from a third group including WTC and LC. A quantitative database of cave morphology characteristics is provided, depending on their speleogenetic processes. These characteristics can be used to constrain and/or validate 3D geostatistical simulations. This study shows how important it is to relate the geometry and connectivity of cave networks to recharge and flow processes. Conversely, the approach developed here provides proxies to estimate the evolution of the vadose zone to epiphreatic and phreatic zones in limestones from the quantitative analysis of existing cave patterns.

58 GEOSCIENCES↗

DOE OSTI2023

Optimal Sizing of Movable Energy Resources for Enhanced Resilience in Distribution Systems: A Techno-Economic Analysis

This article introduces a techno-economic analysis aimed at identifying the optimal total size of movable energy resources (MERs) to enhance the resilience of electric power supply. The core focus of this approach is to determine the total size of MERs required within the distribution network to expedite restoration after extreme events. Leveraging distribution line fragility curves, the proposed methodology generates numerous line outage scenarios, with scenario reduction techniques employed to minimize computational burden. For each reduced multiple line outage scenario, a systematic reconfiguration of the distribution network, represented as a graph, is executed using tie-switches within the system. To evaluate each locational combination of MERs for a specific number of these resources, the expected load curtailment (ELC) is calculated by summing the load curtailment within microgrids formed due to multiple line outages. This process is repeated for all possible locational combinations of MERs to determine minimal ELC for each MER total size. For every MER total size, the minimal ELCs are determined. Finally, a techno-economic analysis is performed using power outage cost and investment cost of MERs to pinpoint an optimal total size of MERs for the distribution system. To demonstrate the effectiveness of the proposed approach, case studies are conducted on the 33-node and the modified IEEE 123-node distribution test systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2014

Ligand placement based on prior structures: the guided ligand-replacement method

A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR leverages prior knowledge from earlier structures to facilitate ligand placement in the current structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Quantifying Graph Uncertainty from Communication Data

Graphs are a widely used abstraction for representing a variety of important real-world problems including emulating cyber networks for situational awareness, or studying social networks to understand human interactions or pandemic spread. Communication data is often converted into graphs to help understand social and technical patterns in the underlying communication data. However, prior to this project, little work had been performed analyzing how best to develop graphs from such data. Thus, many critical, national security problems were being performed against graph representations of questionable quality. Herein, we describe our analyses that were precursors to our final statistically grounded technique for creating static graph snapshots from a stream of communication events. The first analyzes the statistical distribution properties of a variety of real-world communication datasets generally fit best by Pareto, log normal, and extreme value distributions. The second derives graph properties that can be estimated given the expected statistical distribution for communication events and the communication interval to be viewed node observability, edge observability, and expected accuracy of node degree. Unfortunately, as that final process is under review for publication, we can't publish it here at this time.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Training courses on neutron detection systems on the ISIS research reactor: on-site and through internet training

Today, ISIS research reactor is an essential tool for Education and Training programs organized by the National Institute for Nuclear Science and Technology (INSTN) from CEA. In the field of nuclear instrumentation, the INSTN offers both, theoretical courses and training courses on the use of neutron detection systems taking advantage of the ISIS research reactor for the supply of a wide range of neutron fluxes. This paper describes the content of the training carried out on the use of neutron detectors and detection systems, on-site or remote. The ISIS reactor is a 700 kW open core pool type reactor. The facility is very flexible since neutron detectors can be inserted into the core or its vicinity, and be used at different levels of power according to the needs of the course. Neutron fluxes, typically ranging from 1 to 10{sup 12} n/cm{sup 2}.s, can be obtained for the characterisation of the neutron detectors and detection systems. For the monitoring of the neutron density at low level of power, the Instrumentation and Control (I and C) system of the reactor is equipped with two detection systems, named BN1 and BN2. Each way contains a fission chamber, type CFUL01, connected to an electronic system type SIREX.The system works in pulse mode and exhibits two outputs: the counting rate and the doubling time. For the high level of power, the I and C is equipped with two detection systems HN1 and HN2.Each way contain a boron ionization chamber (type CC52) connected to an electronics system type SIREX. The system works in current mode and has two outputs: the current and the doubling time. For each mode, the trainees can observe and measure the signal at the different stages of the electronic system, with an oscilloscope. They can understand the role of each component of the detection system: detector, cable and each electronic block. The limitation of the detection modes and their operating range can be established from the measured signal. The trainees can also modify the settings of the electronic system, such as the high voltage and the discrimination level in order to obtain all the characteristic curves of the detectors. These curves are used to define the right setting of the electronic system and to discuss the expected degradation of the detector signal resulting from the detector damage under the integrated neutron and gamma fluxes. Moreover, in addition to the study of the neutron detection systems itself, the integration of the measurements made by these detection systems in the logic of the safety system of the nuclear reactor is also addressed. Providing the trainees with an extensive overview of each part of the neutron monitoring instrumentation apply to a nuclear reactor, hands-on measurements on the ISIS reactor play a major role in ensuring a practical and comprehensive understanding of the neutron detection system and their integration in the safety system of nuclear reactors. It also gives a solid background for the follow up and the development of the neutron detection systems. In addition to on-reactor training, Internet Reactor Laboratory capability has been implemented on the ISIS reactor in 2014. For the Internet Reactor Laboratory an extensive video conference system has been implemented on ISIS reactor. The system includes 4 cameras and the transmission of the video signal given by the supervision system of the reactor which records and processes the data of the reactor. According to the pedagogic needs during the training courses, the lecturer on the ISIS reactor chooses to broadcast the relevant information at each stage of the course. For example, graph showing the histogram of the counting and current as a function of the time, or the electrical signal observed on the oscilloscope, can be broadcasted trough internet. By interacting through the video conference, the remote classroom is able to ask for changes in the reactor power or settings of the detection systems. They can also ask for the broadcast of some particular information. At the guest institution, the information is displayed in two parts or screens, as shown in the Figure 3. Concerning the interaction with - and the feedback from - the remote classroom, the camera of the video system in the remote classroom is used to ensure the contact between the trainees and the lecturer and reactor operators. Thus, the Internet Reactor Laboratory is complementary to the on reactor training courses. It allows distant learning, reducing the overall cost of the course when this is necessary. It can efficiently be used for the development of the human resources needed by the nuclear industry and the nuclear programs in countries without research reactors.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2023

A Graph Dynamical neural network approach for decoding dynamical states in ferroelectrics.

Ferroelectric materials such as BaTiO 3 show tremendous potential for emerging advances in memory devices, particular neuromorphic type devices. High density of memory can be obtained by stabilising polar domain walls at the nanoscale, regions of discontinuity between the well-defined polarization order parameter, but little is known about what controls their structure and dynamics in real nanoscale materials. Indeed, chiral polar domain walls have been observed in heterogeneous ferroelectrics, such as oxygen-deficient BaTiO 3 , but very little is known about how such polar-domains walls interact with defects. Indeed, a critical understanding of how dynamics of domain-walls depend on point-defects is crucial to create engineered ferroelectric memory devices. For this work, we perform large-scale simulations of nansocale domain-wall dynamics in pristine and defective BaTiO 3 using reactive force-field developed by us earlier (Phys. Chem. Chem. Phys., 2019, 21, 18240–18249), and capture their dynamical dependence on point defects using a graph dynamical neural-network approach, which we adapted to interrogate solids with well-defined order-parameters, and implemented using Pytorch based libraries. Our machine learning (ML) approach goes beyond the traditional post-processing methods to capture both spatial and temporal heterogeneities of large-scale molecular dynamics simulations of complex defective ferroelectric oxide materials. We crucially find that isolated oxygen vacancies introduce very localized spatial regions (~1–2 unit-cell in length) that show slow dipole relaxation due to formation of defect-dipoles, and that these defect-dipoles in turn slow the intrinsic dynamics of domain walls. Further, the roughness of domain walls, also influenced by vacancies, introduce dynamic heterogeneity along the domain-wall. As such we find a novel mechanism by which quenched disorder due to defects introduce dynamic heterogeneity thereby influencing response to external fields (particularly time varying fields) in a ferroelectric. Our study also emphasizes the need for creating digital twins of dynamical quantities to achieve autonomous in operando control of nanoscale switching.

42 ENGINEERING↗

DOE OSTI2024

A graph neural network-state predictive information bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics

Molecular dynamics simulations offer detailed insights into atomic motions but face timescale limitations. Enhanced sampling methods have addressed these challenges but even with machine learning, they often rely on pre-selected expert-based features. Here, in this work, we present a Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) framework, which combines graph neural networks and the state predictive information bottleneck to automatically learn low-dimensional representations directly from atomic coordinates. Tested on three benchmark systems, our approach predicts essential structural, thermodynamic and kinetic information for slow processes, demonstrating robustness across diverse systems. The method shows promise for complex systems, enabling effective enhanced sampling without requiring pre-defined reaction coordinates or input features.

Zou, Ziyue↗

DOE OSTI2026

REDI – Readiness Engine for Data Integration

The Readiness Engine for Data Integration (REDI) is an open-source framework for automating, standardizing, and assessing the process of preparing scientific data for AI training. REDI implements a five-stage pipeline (ingest, preprocess, transform, structure, output) with per-stage provenance instrumentation via Flowcept, domain-aware transformation logic (PII anonymization, regridding, graph encoding, and more), and built-in readiness assessment and validation modes. REDI has been evaluated across climate, proteomics, materials science, and nuclear fusion datasets, demonstrating near-ideal parallel scaling to 100 nodes on OLCF's Frontier system. REDI is deployable as an agent-callable skill in coding environments such as Claude Code and OpenAI Codex, and is complemented by SetGo for FAIR compliance and catalog publication.

Brewer, Wesley [Oak Ridge National Laboratory (ORN↗

DOE OSTI2020

UPC++ v1.0 Specification, Revision 2020.10.0

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

UPC++ v1.0 Specification, Revision 2021.9.0

UPC++ is a C++ library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2023

UPC++ v1.0 Specification (Rev. 2023.9.0)

UPC++ is a C++ library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Vulcan-Forge: Architecture and Design of a Multi-Modal Forensic Analysis Plugin for CALDERA

Forge and VULCAN together describe an open-architecture cybersecurity analysis ecosystem that unifies forensic artifact processing, detection engineering, and vulnerability intelligence within integrated platforms. Forge operates as a plugin for MITRE CALDERA, ingesting diverse evidence formats—including EVTX, PCAP/PCAPNG, CSV, JSON, YAML, XML, binaries, and archives—to construct a unified artifact graph enriched with severity scoring, TLP classification, and audit trails. It provides subsystems for artifact parsing, streaming structured-data visualization, NetworkMiner-based packet inspection, PE/.NET binary analysis, and LLM-assisted triage and rule generation, with outputs validated against CCCS-YARA and pySigma schemas. VULCAN complements this by serving as a cybersecurity analyst platform that integrates a Neo4j knowledge graph, Qdrant vector retrieval, SSVC-based triage, and a local LLM to deliver CVE intelligence and forensic analysis through a multi-source ingest pipeline drawing from NVD, CISA KEV, EPSS, MITRE ATT&CK, and CAPEC. Together, they bridge structured threat intelligence with automated forensic analysis and detection workflows.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

UPC++ v1.0 Specification (Revision 2022.3.0)

UPC++ is a C++ library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

UPC++ v1.0 Specification, Revision 2023.3.0

UPC++ is a C++ library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

UPC++ v1.0 Specification (Revision 2021.3.0)

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

UPC++ v1.0 Specification, Revision 2022.9.0

UPC++ is a C++ library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

UPC++ v1.0 Specification, Revision 2020.3.0

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Triangle Counting with Cyclic Distributions

Triangles are the simplest non-trivial subgraphs and triangle counting is used in a number of different applications. The order in which vertices are processed in triangle counting strongly effects the amount of work that needs to be done (and thus the overall performance). Ordering vertices by degree has been shown to be one particularly effective ordering approach. However, for graphs with skewed degree distributions (such as power-law graphs), ordering by degree effects the distribution of work; parallelization must account for this distribution in order to balance work among workers. In this paper we provide an in- depth analysis of the ramifications of degree-based ordering on parallel triangle counting. We present approach for partitioning work in triangle counting, based on cyclic distribution and some surprisingly simple C++ implementations. Experimental results demonstrate the effectiveness of our approach, particularly for power-law (and social network) graphs.

Graph algorithms, parallel algorithms↗