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DOE OSTI2019

Syntgen: a system to generate temporal networks with user-specified topology

Abstract In the last few years, the study of temporal networks has progressed markedly. The evolution of clusters of nodes (or communities) is one of the major focus of these studies. However, the time dimension increases complexity, introducing new constructs and requiring novel and enhanced algorithms. In spite of recent improvements, the relative scarcity of timestamped representations of empiric networks, with known ground truth, hinders algorithm validation. A few approaches have been proposed to generate synthetic temporal networks that conform to static topological specifications while in general adopting an ad hoc approach to temporal evolution. We believe there is still a need for a principled synthetic network generator that conforms to problem domain topological specifications from a static as well as temporal perspective. Here, we present such a system. The unique attributes of our system include accepting arbitrary node degree and cluster size distributions and temporal evolution under user control, while supporting tunable joint distribution and temporal correlation of node degrees. Theoretical contributions include the analysis of conditions for graphic sequences of inter- and intracluster node degrees and cluster sizes and the development of a heuristic to search for the cluster membership of nodes that minimizes the shared information distance between clusterings. Our work shows that this system is capable of generating networks under user controlled topology with up to thousands of nodes and hundreds of clusters with strong topology adherence. Much larger networks are possible with relaxed requirements. The generated networks support algorithm validation as well as problem domain analysis.

Pereira, Luis Ramada↗

DOE OSTI2024

Abiotic Stress Reorganizes Rhizosphere and Endosphere Network Structure of Sorghum bicolor

Sorghum bicolor is a promising bioenergy feedstock with high biomass production and unusual tolerance for stresses, such as water and nutrient limitation. Although the membership of the sorghum microbiome in response to stress has been explored, relatively little is known about how microbe–microbe networks change under water- or nutrient-limited conditions. This is important because network changes can indicate impacts on the functionality and stability of microbial communities. We performed network-based analysis on the core bacterial and archaeal community of an agronomically promising high biomass bioenergy genotype, Grassl, grown under nitrogen and water stress. Stress caused relatively minor changes in bacterial abundances within soil, rhizosphere, and endosphere communities but led to significant changes in bacterial network structure and modularity. We found a complete reorganization of network roles in all plant compartments, as well as an increase in the modularity and proportion of positive associations, which potentially could represent coexistence and cooperation in the sorghum bacterial/archaeal community under stress. Although stressors are often believed to be destabilizing, we found stressed networks were as or more stable than non-stressed networks, likely due to their redundancy and compartmentalization. Together, these findings support the idea that both sorghum and its bacterial/archaeal community can be resilient to future environmental stressors.

09 BIOMASS FUELS↗

DOE OSTI2022

Galaxy deblending using residual dense neural networks

We present a new neural network approach for deblending galaxy images in astronomical data using Residual Dense Neural network (RDN) architecture. We train the network on synthetic galaxy images similar to the typical arrangements of field galaxies with a finite point spread function (PSF) and realistic noise levels. The main novelty of our approach is the usage of two distinct neural networks: i) a deblending network which isolates a single galaxy postage stamp from the composite and, ii) a classifier network which counts the remaining number of galaxies. The deblending proceeds by iteratively peeling one galaxy at a time from the composite until the image contains no further objects as determined by the classifier, or by other stopping criteria. By looking at the consistency in the outputs of the two networks, we can assess the quality of the deblending. Further, we characterize the flux and shape reconstructions in different quality bins and compare our deblender with the industry standard, SExtractor. We also discuss possible future extensions for the project with variable PSFs and noise levels.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Characterizing the impact of particle behavior at fracture intersections in three-dimensional discrete fracture networks

We characterize the influence of different intersection mixing rules for particle tracking simulations on transport properties through three-dimensional discrete fracture networks. It is too computationally burdensome to explicitly resolve all fluid dynamics within a large three-dimensional fracture network. In discrete fracture network (DFN) models, mass transport at fracture intersections is modeled as a subgrid scale process based on a local Péclet number. The two most common mass transfer mixing rules are (1) complete mixing, where diffusion dominates mass transfer, and (2) streamline routing, where mass follows pathlines through an intersection. Although it is accepted that mixing rules impact local mass transfer through single intersections, the effect of the mixing rule on transport at the fracture network scale is still unresolved. Through the use of explicit particle tracking simulations, we study transport through a quasi-two-dimensional lattice network and a three-dimensional network whose fracture radii follow a truncated power-law distribution. We find that the impact of the mixing rule is a function of the initial particle injection condition, the heterogeneity of the velocity field, and the geometry of the network. Furthermore, our particle tracking simulations show that the mixing rule can particularly impact concentrations on secondary flow pathways. As a result, we relate these local differences in concentration to reactive transport and show that streamline routing increases the average mixing rate in DFN simulations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

How does your gyroid grow? A mesoatomic perspective on supramolecular, soft matter network crystals

We propose and describe a framework to understand the structure of supramolecular network crystals formed in soft matter in terms of mesoatomic building blocks, collective groupings of amphiphilic molecules that play a role analogous to atomic or molecular subunits of hard matter crystals. While the concept of mesoatoms is intuitive and widely invoked in crystalline arrangements of spherelike or cylinderlike (micellelike) domains, analogous notions of natural and physically meaningful building blocks of triply periodic network (TPN) crystals, like the double-gyroid or double-diamond structures are obscured by the complex, bicontinuous domain shapes and intercatenated topologies of the double networks. Focusing on the specific example of diblock copolymer melts, we propose generic rules for decomposing TPN crystals into a unique set of mesoatomic building blocks. Based on physically motivated principles, the combination of symmetries and topologies of these structures point to mesoatomic elements associated with the nodal connections, leading to mesoatomic volumes that are nonconvex and bound by smoothly curved faces, unlike the more familiar Voronoi polyhedral shapes associated with spherelike and cylinderlike mesoatoms. We analyze the shapes of these mesoatoms, their internal structure, and importantly, their local packing with neighbor mesoatomic units. Importantly, we hypothesize that mesoatoms are kinetically favored intermediate structures whose local shapes and packing template network crystal assembly on long time scales. We propose and study a minimal energetic model of mesoatom assembly for three different cubic double-network crystals, based on local shape packing, which predicts a detailed picture for kinetics of intercatenation and surface growth. Based on these analyses, we discuss several possible extensions and elaborations of the mesoatomic description of supramolecular soft matter network crystals, most notably the implications of mesoatomic malleability, a feature that distinguishes soft matter from hard matter crystals. We describe experimental observations of malleable mesoatomic units in the precursor sponge phase as well as in ordered cubic networks and suggest possibilities for observing mesoatoms in primordial, precrystalline states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Throughput Analytics of Cloud Networks

A network of virtual machines at cloud server sites connected over virtual IO connections is a flexible, easily deployable, and cost-effective alternative to a physical network infrastructure with dedicated servers connected over leased fiber lines. We study the throughput performance of such a cloud network by collecting measurements over Google Cloud infrastructure spanning multiple continents. To study its ideal performance and impact of packet losses, we utilize its emulation using dedicated servers and connection hardware emulation devices. We compare the measurements over the cloud network to those over its emulation on a testbed. We examine the throughput profiles of both networks as a function of the round trip time and their utilization-concavity coefficients, estimated using measurements for common TCP versions. The throughput profile's concave-convex shape and its coefficient are critical indicators of the network performance, qualitatively and quantitatively, respectively. The results indicate their overall agreement between the production cloud network and its emulation using dedicated connections, and a near optimal throughput performance of the former except for a few under-performing connections. Also, the number of parallel flows is found to be a dominant factor in optimizing the throughput across various conditions and TCP versions.

Phanekham, Derek↗

DOE OSTI2025

Real-World Cyber Security Demonstration for Networked Electric Drives

In this article, we present the design and implementation of a cyber-physical security testbed for networked electric drive systems, aimed at conducting real-world security demonstrations. To our knowledge, this is one of the first security testbeds for networked electric drives, seamlessly integrating the domains of power electronics and computer science, and cybersecurity. By doing so, the testbed offers a comprehensive platform to explore and understand the intricate and often complex interactions between cyber and physical systems. The core of our testbed consists of four electric machine drives, meticulously configured to emulate small-scale but realistic information technology (IT) and operational technology (OT) networks. This setup both provides a controlled environment for simulating a wide array of cyber-attacks, and mirrors potential real-world attack scenarios with a high degree of fidelity. The testbed serves as an invaluable resource for the study of cyber-physical security, offering a practical and dynamic platform for testing and validating cybersecurity measures in the context of networked electric drive systems. As a concrete example of the testbed's capabilities, we have developed and implemented a Python-based script designed to execute step-stone attacks over a wireless local area network (WLAN). This script leverages a sequence of target IP addresses, simulating a real-world attack vector that could be exploited by adversaries. To counteract such threats, we demonstrate the efficacy of our developed cyber-attack detection algorithms, which are integral to our testbed's security framework. Furthermore, the testbed incorporates a real-time visualization system using InfluxDB and Grafana, providing a dynamic and interactive representation of networked electric drives and their associated security monitoring mechanisms. This visualization component not only enhances the testbed's usability but also offers insightful, real-time data for researchers and practitioners, thereby facilitating a deeper understanding of cyber-physical security dynamics in networked electric drive systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2016

A Study of Complex Deep Learning Networks on High Performance, Neuromorphic, and Quantum Computers

Current Deep Learning models use highly optimized convolutional neural networks (CNN) trained on large graphical processing units (GPU)-based computers with a fairly simple layered network topology, i.e., highly connected layers, without intra-layer connections. Complex topologies have been proposed, but are intractable to train on current systems. Building the topologies of the deep learning network requires hand tuning, and implementing the network in hardware is expensive in both cost and power.In this paper, we evaluate deep learning models using three different computing architectures to address these problems: quantum computing to train complex topologies, high performance computing (HPC) to automatically determine network topology, and neuromorphic computing for a low-power hardware implementation. Due to input size limitations of current quantum computers we use the MNIST dataset for our evaluation.The results show the possibility of using the three architectures in tandem to explore complex deep learning networks that are untrainable using a von Neumann architecture. We show that a quantum computer can find high quality values of intra-layer connections and weights, while yielding a tractable time result as the complexity of the network increases; a high performance computer can find optimal layer-based topologies; and a neuromorphic computer can represent the complex topology and weights derived from the other architectures in low power memristive hardware.This represents a new capability that is not feasible with current von Neumann architecture. It potentially enables the ability to solve very complicated problems unsolvable with current computing technologies.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Quantitative Assessment of Transportation Network Vulnerability with Dynamic Traffic Simulation Methods

Transportation networks are critical to the social and economic function of nations. Given the continuing increase in the populations of cities throughout the world, the criticality of transportation infrastructure is expected to increase. Thus, it is ever more important to mitigate congestion as well as to assess the impact disruptions would have on individuals who depend on transportation for their work and livelihood. Moreover, several government organizations are responsible for ensuring transportation networks are available despite the constant threat of natural disasters and terrorist activities. Most of the previous transportation network vulnerability research has been performed in the context of static traffic models, many of which are formulated as traditional optimization problems. However, transportation networks are dynamic because their usage varies over time. Thus, more appropriate methods to characterize the vulnerability of transportation networks should consider their dynamic properties. This paper presents a quantitative approach to assess the vulnerability of a transportation network to disruptions with methods from traffic simulation. Our approach can prioritize the critical links over time and is generalizable to the case where both link and node disruptions are of concern. We illustrate the approach through a series of examples. Our results demonstrate that the approach provides quantitative insight into the time varying criticality of links. Such an approach could be used as the objective function of less traditional optimization methods that use simulation and other techniques to evaluate the relative utility of a particular network defense to reduce vulnerability and increase resilience.

Shekar, Venkateswaran↗

DOE OSTI2024

Multi-Edge Graph Convolutional Networks for Power Systems

The exponential electrification of transportation has contributed to highly intermittent load variations in the distribution grid. This uncertainty has raised challenges for distribution system operation and control. Accurate nodal voltage estimation is highly essential for the safe and reliable operation of the grid. Graph convolutional networks have been used in machine-learning-based models for power grid applications like voltage estimation for their ability to capture the network topology of the grid. This paper presents a novel multi-edge graph convolutional layer that considers resistance and reactance as edge attributes. This layer is created by modifying the message-passing function within the graph convolutional network. The novel layer is then used to create a multi-edge graph convolutional network-based surrogate model for estimating voltage in the distribution network with highly uncertain electric vehicle loads. Results indicate improved performance of the multi-edge graph convolutional network model when compared to a standard graph convolutional network model.

Ravi, Abhijith↗

DOE OSTI2022

Deep learning multiphysics network for imaging CO 2 saturation and estimating uncertainty in geological carbon storage

Multiphysics inversion exploits different types of geophysical data that often complement each other and aims to improve overall imaging resolution and reduce uncertainties in geophysical interpretation. Despite the advantages, traditional multiphysics inversion is challenging because it requires a large amount of computational time and intensive human interactions for preprocessing data and finding trade-off parameters. These issues make it nearly impossible for traditional multiphysics inversion to be applied as a real-time monitoring tool for geological carbon storage. In this paper, we present a deep learning (DL) multiphysics network for imaging CO 2 saturation in real time. The multiphysics network consists of three encoders for analysing seismic, electromagnetic and gravity data and shares one decoder for combining imaging capabilities of the different geophysical data for better predicting CO 2 saturation. The network is trained on pairs of CO 2 label models and multiphysics data so that it can directly image CO 2 saturation. Here we use the bootstrap aggregating method to enhance the imaging accuracy and estimate uncertainties associated with CO 2 saturation images. Using realistic CO 2 label models and multiphysics data derived from the Kimberlina CO 2 storage model, we evaluate the performance of the deep learning multiphysics network and compare its imaging results to those from the deep learning single-physics networks. Our modelling experiments show that the deep learning multiphysics network for seismic, electromagnetic, and gravity data not only improves the imaging accuracy but also reduces uncertainties associated with CO 2 saturation images. Our results also suggest that the deep learning multiphysics network for the non-seismic data (i.e., electromagnetic and gravity) can be used as an effective low-cost monitoring tool in between regular seismic monitoring.

58 GEOSCIENCES↗

DOE OSTI2015

Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation: Competition in bioremediation system

When trying to discern network interactions among different species/populations in microbial communities interests have been evoked in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. We modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the network interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140–269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. In particular, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Characterization of River Networks: A GIS Approach and Its Applications

Abstract Fluvial geomorphology provides the basis for characterizing complex river networks and evaluating biophysical processes within watersheds. Understanding the spatial organization of morphological features, their influencing processes, and resultant geomorphic diversity in stream networks are important for efficient restoration, river health assessment, and improving our knowledge of the resilience of riverine landscapes. River characterization is a means to determine the biophysical character of river networks but many methods are fraught with pitfalls, such as the use of incorrect variables and limited acknowledgment of the hierarchical organization of rivers. In this paper, a top‐down geographic information system‐based approach for determining the physical typology of river networks is outlined. A suite of multivariate analyses are used to develop a nomenclature for functional process zones (FPZs) — large tracts of the river network with similar hydro‐geomorphological character. Applied to the Little Miami River, Ohio, six distinct FPZs emerged, which had a nonuniform distribution along the river network. Some FPZs repeated downstream; others were rare in terms of total length and number of FPZ segments. The physical structure of the Little Miami River network was analyzed using a series of community metrics. Application of this approach for river monitoring, establishing reference conditions, as well as management of threatened and endangered species and asset trading is highlighted.

Thoms, Martin↗

DOE OSTI2026

Comprehensive framework for assessing and optimizing existing research networks

Conservation, monitoring, and research networks, or collections of ecological research sites unified under a common mission of data collection or a research mission, are essential infrastructure for understanding large landscapes. However, most networks developed opportunistically over decades rather than through systematic design, creating potential limitations in the ability to address conservation challenges across entire regions. We developed a framework to evaluate how well an existing research network represents the environmental conditions its members study and devised an approach to rank sites of priority for strategic expansion. Our approach measures performance through environmental representativeness, geographic coverage, and adequacy for scientific inference and thus optimizes limited monitoring resources to maximize scientific impact. We demonstrated this approach with the U.S. Department of Agriculture (USDA) Forest Service Experimental Forests and Ranges Network (EFRN), a 79‐site network across the United States that grew opportunistically over a century. At the national scale, the network effectively captured high‐biomass forests important for carbon cycle research; 82% of forest biomass was in well‐represented areas. Some areas in Texas, Florida, the Rocky Mountains, and the West Coast had no relevant EFRN sites, which limits the ability to make regional inferences. A fundamental challenge for the EFRN was that sites improving regional extent coverage sometimes provided minimal national benefits, which can create conflicts between local and global priorities. Adding the highest‐ranked candidate site provided a relevant site for 17% of currently poorly represented 1‐km pixel cells nationally, but regional and national site rankings varied considerably due to nested spatial inference. This framework provides quantitative tools for strategic infrastructure decision‐making, ensures that limited monitoring resources maximize conservation impact, and can be applied broadly to address the widespread challenge of optimizing conservation and monitoring networks worldwide.

additional site↗

DOE OSTI2019

Computer-aided detection using non-convolutional neural network Gaussian processes

Deep convolutional neural networks (CNNs) have in recent years achieved record-breaking performance on many image classification tasks and are therefore well-suited for computer aided detection (CAD). The need for uncertainty quantification for CAD motivates the need for a probabilistic framework for deep learning. The most well-known probabilistic neural network model is the Bayesian neural network (BNN), but BNNs are notoriously difficult to sample for large complex network architectures, and as such their use is restricted to small problems. It is known that the limit of BNNs as their widths increase toward infinity is a Gaussian process (GP), and there has been considerable research interest in these infinitely wide BNNs. Recently, this classic result has been extended to deep architectures in what is termed the neural network Gaussian process (NNGP) model. In this work, we implement an NNGP model and apply it to the ChestXRay14 dataset at the full resolution of 1024x1024 pixels. Even without any convolutional aspects to the network architecture and without any data augmentation, our five layer deep NNGP model outperforms other non-convolutional models and therefore helps to narrow the performance gap between non-convolutional and convolutional models. Our NNGP model is fully Bayesian and therefore offers uncertainty information through its predictive variance that can be used to formulate a predictive confidence measure. We show that the performance of the NNGP model is significantly boosted after low-confidence predictions are rejected, suggesting that convolution is most beneficial only for these low-confidence examples. Finally, our results indicate that an extremely large fully-connected neural network with appropriate regularization could perform as well as the NNGP if not for the computational bottleneck resulting from the large number of model parameters.

Agrawal, Devanshu↗

DOE OSTI2018

SuperNeurons: Dynamic GPU Memory Management for Training Deep Neural Networks

Going deeper and wider in neural architectures improves their accuracy, while the limited GPU DRAM places an undesired restriction on the network design domain. Deep Learning (DL) practitioners either need to change to less de- sired network architectures, or nontrivially dissect a network across multiGPUs. These distract DL practitioners from concentrating on their original machine learning tasks. We present SuperNeurons: a dynamic GPU memory scheduling runtime to enable the network training far beyond the GPU DRAM capacity. SuperNeurons features 3 memory optimizations, Liveness Analysis, Unified Tensor Pool, and Cost-Aware Recomputation; together they effectively reduce the network-wide peak memory usage down to the maximal memory usage among layers. We also address the performance issues in these memory-saving techniques. Given the limited GPU DRAM, SuperNeurons not only provisions the necessary memory for the training, but also dynamically allocates the memory for convolution workspaces to achieve the high performance. Evaluations against Caffe, Torch, MXNet and TensorFlow have demonstrated that SuperNeurons trains at least 3.2432 deeper network than current ones with the leading performance. Particularly, SuperNeurons can train ResNet2500 that has 104 basic network layers on a 12GB K40c.

Wang, Linnan↗

DOE OSTI2019

Situational Awareness of Network System Roles (SANSR)

In a large enterprise it is difficult for cyber security analysts to know what services and roles every machine on the network is performing (e.g. file server, domain name server, email server). Understanding the roles of the systems in the network provides analysts with a situational awareness that will allow them to detect consequential changes in the network, initiate an incident response plan, and optimize their security posture. Using the network flow data, already collected by most enterprises, we developed a tool that enables analysts to automatically detect/classify services and roles of every machine that’s operating on a network (e.g. file server, domain name server, email server) for better situational awareness of potential threats to the network. his tool queries Elasticsearch for network flow data, creates a temporal behavior model of each system, uses unsupervised machine learning to cluster the models with a set of labeled temporal behavior models, and the resulting information can be printed to the console or programmatically accessed. The results include the likelihood that a machine has a labeled role and lists other machines that are most similar in behavior.

Huffer, KellyM.↗

DOE OSTI2020

Optical networking within the Lightwave Energy-Efficient Datacenter project [Invited]

The Lightwave Energy-Efficient Datacenter (LEED) project within the ARPA-e ENLITENED program is developing novel energy-efficient multichannel lightwave networks. These networks are enabled by a new optical “rotor” switch that can reconfigure the network topology in less than 20 µs and a field-programmable-gate-array-based network interface controller called Corundum that can provide precise network-wide synchronization of packets admitted into the lightwave network. Here we review the optical networking research within LEED and discuss future directions.

Mellette, William M.↗