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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.

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DOE OSTI2017

Social Network Analysis in R: A Software Review

In education research, social network analysis is being widely used to study different interactions and their overall implications. Recently, there has also been a surge in the development of software tools to implement social network analysis. In this article, we review two popular R packages, igraph and statnet suite, in the context of network summarization and modeling. We discuss different aspects of these packages and demonstrate some of their functionalities by analyzing a friendship network of lawyers. Finally, we end with recommendations for using these packages along with pointers to additional resources for network analysis in R.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Femtojoule optical nonlinearity for deep learning with incoherent illumination

Optical neural networks (ONNs) are a promising computational alternative for deep learning due to their inherent massive parallelism for linear operations. However, the development of energy-efficient and highly parallel optical nonlinearities, a critical component in ONNs, remains an outstanding challenge. Here, we introduce a nonlinear optical microdevice array (NOMA) compatible with incoherent illumination by integrating the liquid crystal cell with silicon photodiodes at the single-pixel level. We fabricate NOMA with more than half a million pixels, each functioning as an optical analog of the rectified linear unit at ultralow switching energy down to 100 femtojoules per pixel. With NOMA, we demonstrate an optical multilayer neural network. Our work holds promise for large-scale and low-power deep ONNs, computer vision, and real-time optical image processing.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Virtual Neuron: A Neuromorphic Approach for Encoding Numbers

Neuromorphic computers perform computations by emulating the human brain and are expected to be indispensable for energy-efficient computing in the future. They are primarily used in spiking neural network-based machine learning applications. However, neuromorphic computers are unable to preprocess data for these applications. Currently, data is preprocessed on a CPU or a GPU-this incurs a significant cost of transferring data from the CPU/GPU to the neuromorphic processor and vice versa. This cost can be avoided if preprocessing is done on the neuromorphic processor. To efficiently preprocess data on a neuromorphic processor, we first need an efficient mechanism for encoding data that can lend itself to all general-purpose preprocessing operations. Current encoding approaches have limited applicability and may not be suitable for all preprocessing operations. In this paper, we present the virtual neuron as a mechanism for encoding integers and rational numbers on neuromorphic processors. We evaluate the performance of the virtual neuron on physical and simulated neuromorphic hardware and show that it can perform an addition operation using 23 nJ of energy on average using a mixed-signal, memristor-based neuromorphic processor. The virtual neuron encoding approach is the first step in preprocessing data on a neuromorphic processor.

Date, Prasanna↗
DOE OSTI2018

Analysis Report for Exascale Storage Requirements for Scientific Data.

Over the next 10 years, the Department of Energy will be transitioning from Petascale to Exascale Computing resulting in data storage, networking, and infrastructure requirements to increase by three orders of magnitude. The technologies and best practices used today are the result of a relatively slow evolution of ancestral technologies developed in the 1950s and 1960s. These include magnetic tape, magnetic disk, networking, databases, file systems, and operating systems. These technologies will continue to evolve over the next 10 to 15 years on a reasonably predictable path. Experience with the challenges involved in transitioning these fundamental technologies from Terascale to Petascale computing systems has raised questions about how these will scale another 3 or 4 orders of magnitude to meet the requirements imposed by Exascale computing systems. This report is focused on the most concerning scaling issues with data storage systems as they relate to High Performance Computing- and presents options for a path forward. Given the ability to store exponentially increasing amounts of data, far more advanced concepts and use of metadata will be critical to managing data in Exascale computing systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

The water retention curve and relative permeability for gas production from hydrate-bearing sediments: pore-network model simulation

Here, the water retention curve and relative permeability are critical to predict gas and water production from hydrate–bearing sediments. However, values for key parameters that characterize gas and water flows during hydrate dissociation have not been identified due to experimental challenges. This study utilizes the combined techniques of micro–focus X–ray computed tomography (CT) and pore–network model simulation to identify proper values for those key parameters, such as gas entry pressure, residual water saturation, and curve fitting values. Hydrates with various saturation and morphology are realized in the pore–network that was extracted from micron–resolution CT images of sediments recovered from the hydrate deposit at the Mallik site, and then the processes of gas invasion, hydrate dissociation, gas expansion, and gas and water permeability are simulated. Results show that greater hydrate saturation in sediments lead to higher gas entry pressure, higher residual water saturation, and steeper water retention curve. An increase in hydrate saturation decreases gas permeability but has marginal effects on water permeability in sediments with uniformly distributed hydrate. Hydrate morphology has more significant impacts than hydrate saturation on relative permeability. Sediments with heterogeneously distributed hydrate tend to result in lower residual water saturation and higher gas and water permeability. In this sense, the Brooks–Corey model that uses two fitting parameters individually for gas and water permeability properly capture the effect of hydrate saturation and morphology on gas and water flows in hydrate–bearing sediments.

58 GEOSCIENCES↗
DOE OSTI2025

Dendritic Computing with Multigate Ferroelectric Field-Effect Transistors

Although inspired by neuronal systems in the brain, artificial neural networks generally employ point-neurons, which offer computational complexity far less than that of their biological counterparts. Neurons have dendritic arbors that connect to different sets of synapses and offer local nonlinear accumulation – playing a pivotal role in processing and learning. Inspired by this, we propose a novel neuron design based on a multigate ferroelectric field-effect transistor that mimics dendrites. It leverages ferroelectric nonlinearity for local computations within dendritic branches while utilizing the transistor action to generate the neuronal output. The branched architecture enables smaller crossbar arrays in hardware integration, improving efficiency. Using an experimentally calibrated device-circuit-algorithm cosimulation framework, we demonstrate that networks incorporating our dendritic neurons achieve superior performance compared to much larger networks without dendrites (∼ 17× fewer trainable weight parameters). These findings suggest that dendritic hardware can significantly improve computational efficiency and learning capacity of neuromorphic systems optimized for edge applications.

36 MATERIALS SCIENCE↗
DOE OSTI2018

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times and memory demands. In this paper, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ~70 million nodes with ~68 billion edges in ~2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. Finally, HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Evaluating Quality of Service Traffic Classes on the Megafly Network

An emerging trend in High Performance Computing (HPC) systems that use hierarchical topologies (such as dragonfly) is that the applications are increasingly exhibiting high run-to-run performance variability. This poses a significant challenge for application developers, job schedulers, and system maintainers. One approach to address the performance variability is to use newly proposed network topologies such as megafly (or dragonfly+) that offer increased path diversity compared to a traditional fully connected dragonfly. Yet another approach is to use quality of service (QoS) traffic classes that ensure bandwidth guarantees. In this work, we select HPC application workloads that have exhibited performance variability on current 2-D dragonfly systems. We evaluate the baseline performance expectations of these workloads on megafly and 1-D dragonfly network models with comparably similar network configurations. Our results show that the megafly network, despite using fewer virtual channels (VCs) for deadlock avoidance than a dragonfly, performs as well as a fully connected 1-D dragonfly network. We then exploit the fact that megafly networks require fewer VCs to incorporate QoS traffic classes. We use bandwidth capping and traffic differentiation techniques to introduce multiple traffic classes in megafly networks. In some cases, our results show that QoS can completely mitigate application performance variability while causing minimal slowdown to the background network traffic.

Mubarak, Misbah↗
DOE OSTI2021

Measurement of hybrid rocket solid fuel regression rate for a slab burner using deep learning

This study presents an imaging-based deep learning tool to measure the fuel regression rate in a 2D slab burner experiment for hybrid rocket fuels. The slab burner experiment is designed to verify mechanistic models of reacting boundary layer combustion in hybrid rockets by the measurement of fuel regression rates. A DSLR camera with a high intensity flash is used to capture images throughout the burn and the images are then used to find the fuel boundary to calculate the regression rate. A U-net convolutional neural network architecture is explored to segment the fuel from the experimental images. Here, a Monte-Carlo Dropout process is used to quantify the regression rate uncertainty produced from the network. The U-net computed regression rates are compared with values from other techniques from literature and show error less than 10%. An oxidizer flux dependency study is performed and shows the U-net predictions of regression rates are accurate and independent of the oxidizer flux, when the images in the training set are not over-saturated. Training with monochrome images is explored and is not successful at predicting the fuel regression rate from images with high noise. The network is superior at filtering out noise introduced by soot, pitting, and wax deposition on the chamber glass as well as the flame when compared to traditional image processing techniques, such as threshold binary conversion and spatial filtering. U-net consistently provides low error image segmentations to allow accurate computation of the regression rate of the fuel.

42 ENGINEERING↗
DOE OSTI2016

A survey on software methods to improve the energy efficiency of parallel computing

Energy consumption is one of the top challenges for achieving the next generation of supercomputing. Codesign of hardware and software is critical for improving energy efficiency (EE) for future large-scale systems. Many architectural power-saving techniques have been developed, and most hardware components are approaching physical limits. Accordingly, parallel computing software, including both applications and systems, should exploit power-saving hardware innovations and manage efficient energy use. In addition, new power-aware parallel computing methods are essential to decrease energy usage further. This article surveys software-based methods that aim to improve EE for parallel computing. It reviews the methods that exploit the characteristics of parallel scientific applications, including load imbalance and mixed precision of floating-point (FP) calculations, to improve EE. In addition, this article summarizes widely used methods to improve power usage at different granularities, such as the whole system and per application. In particular, it describes the most important techniques to measure and to achieve energy-efficient usage of various parallel computing facilities, including processors, memories, and networks. Overall, this article reviews the state-of-the-art of energy-efficient methods for parallel computing to motivate researchers to achieve optimal parallel computing under a power budget constraint.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

DL-TODA: A Deep Learning Tool for Omics Data Analysis

Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Joint Optimization of Multimodal Transit Frequency and Shared Autonomous Vehicle Fleet Size with Hybrid Metaheuristic and Nonlinear Programming

Shared autonomous vehicles (SAVs) bring competition to traditional transit services but redesigning multimodal transit network can utilize SAVs as feeders to enhance service efficiency and coverage. This paper presents an optimization framework for the joint multimodal transit frequency and SAV fleet size problem, a variant of the transit network frequency setting problem. The objective is to maximize total transit ridership (including SAV-fed trips and subtracting boarding rejections) across multiple time periods under budget constraints, considering endogenous mode choice (transit, point-to-point SAVs, driving) and route selection, while allowing for strategic route removal by setting frequencies to zero. Due to the problem’s non-linear, non-convex nature and the computational challenges of large-scale networks, we develop a hybrid solution approach that combines a metaheuristic approach (particle swarm optimization) with nonlinear programming for local solution refinement. To ensure computational tractability, the framework integrates analytical approximation models for SAV waiting times based on fleet utilization, multimodal network assignment for route choice, and multinomial logit mode choice behavior, bypassing the need for computationally intensive simulations within the main optimization loop. Applied to the Chicago metropolitan area’s multimodal network, our method illustrates a 33.3% increase in transit ridership through optimized transit route frequencies and SAV integration, particularly enhancing off-peak service accessibility and strategically reallocating resources.

Ng, Max↗
DOE OSTI2016

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

SGD-Net: Efficient Model-Based Deep Learning with Theoretical Guarantees

Deep unfolding networks have recently gained popularity for solving imaging inverse problems. However, the computational and memory complexity of data-consistency layers within traditional deep unfolding networks scales with the number of measurements, limiting their applicability to large-scale imaging inverse problems. We propose SGD-Net as a new methodology for improving the efficiency of deep unfolding through stochastic approximations of the data-consistency layers. Our theoretical analysis shows that SGD-Net can be trained to approximate batch deep unfolding networks to an arbitrary precision. Our simulations on intensity diffraction tomography and sparse-view computed tomography show that SGD-Net can match the performance of the traditional batch network at a fraction of training and testing complexity.Deep unfolding networks have recently gained popularity for solving imaging inverse problems. However, the computational and memory complexity of data-consistency layers within traditional deep unfolding networks scales with the number of measurements, limiting their applicability to large-scale imaging inverse problems. We propose SGD-Net as a new methodology for improving the efficiency of deep unfolding through stochastic approximations of the data-consistency layers. Our theoretical analysis shows that SGD-Net can be trained to approximate batch deep unfolding networks to an arbitrary precision. Our simulations on intensity diffraction tomography and sparse-view computed tomography show that SGD-Net can match the performance of the traditional batch network at a fraction of training and testing complexity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Resource Aware Intelligent Network Services (RAINS) Final Technical Report

The Resource Aware Intelligent Network Services (RAINS) project conducted research and developed technologies in the area of cyber infrastructure resource modeling and computation. The goal of this work was to provide a foundation to enable intelligent, software defined services which spanned the network AND the resources which connect to the network. A Multi-Resource Service Plane (MRSP) was defined, which allows resource owners/managers to locate and place themselves from a topology and service availability perspective within the dynamic networked cyberinfrastructure ecosystem. The MRSP enables the presentation of integrated topology views and computation results which can include resources across the spectrum of compute, storage, and networks. The RAINS project developed MSRP includes the following key components: i) Multi-Resource Service (MRS) Ontology/Multi-Resource Markup Language (MRML), ii) Resource Computation Engine (RCE), iii) Modular Driver Framework (to allow integration of a variety of external resources). The MRS/MRML is a general and extensible modeling framework that allows for resource owners to model, or describe, a wide variety of resource types. All resources are described using three categories of elements: Resources, Services, and Relationships between the elements. This modeling framework defines a common method for the transformation of cyber infrastructure resources into data in the form of MRML models. In order to realize this infrastructure datification, the RAINS project developed a model based computation system, i.e. “RAINS Computation Engine (RCE)”. The RCE has the ability to ingest, process, integrate, and compute based on automatically generated MRML models. The RCE interacts with the resources thru system drivers which are specific to the type of external network or resource controller. The RAINS project developed a modular and pluggable driver system which facilities a variety of resource controllers to automatically generate, maintain, and distribute MRML based resource descriptions. Once all of the resource topologies are absorbed by the RCE, a connected graph of the full distributed system topology is constructed, which forms the basis for computation and workflow processing. The RCE includes a Modular Computation Element (MCE) framework which allows for tailoring of the computation process to the specific set of resources under control, and the services desired. The input and output of an MCE are both model data based on MRS/MRML ontology and schema. Some of the RAINS project accomplishments include: Development of general and extensible multi-resource modeling framework; Design of a Resource Computation Engine (RCE) system which includes the following key capabilities; Absorb a variety of multi-resource model types and build integrated models; Novel architecture which uses model based communications across the full stack for all Flexible provision of abstract or intent based user facing interfaces; Workflow processing based on model descriptions; Release of the RCE as an open source software; Deployment of RCE in the University of Maryland/Mid-Atlantic Crossroad ScienceDMZ in prototype mode with a plan under way to transition to production; Deployment at the Argonne National Laboratory DTN Facility in prototype mode; Selection of RCE by the DOE SENSE (SDN for End-to-end Networked Science at the Exascale) project as the basis for their orchestration service.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Exact enforcement of temporal continuity in sequential physics-informed neural networks

The use of deep learning methods in scientific computing represents a potential paradigm shift in engineering problem solving. One of the most prominent developments is Physics-Informed Neural Networks (PINNs), in which neural networks are trained to satisfy partial differential equations (PDEs). While this method shows promise, the standard version has been shown to struggle in accurately predicting the dynamic behavior of time-dependent problems. To address this challenge, methods have been proposed that decompose the time domain into multiple segments, employing a distinct neural network in each segment and directly incorporating continuity between them in the loss function of the minimization problem. In this work we introduce a method to exactly enforce continuity between successive time segments via a solution ansatz. This hard constrained sequential PINN (HCS-PINN) method is simple to implement and eliminates the need for any loss terms associated with temporal continuity. The method is tested for a number of benchmark problems involving both linear and non-linear PDEs. Examples include various first order time dependent problems in which traditional PINNs struggle, namely advection, Allen–Cahn, and Korteweg–de Vries equations. Furthermore, second and third order time-dependent problems are demonstrated via wave and Jerky dynamics examples, respectively. Notably, the Jerky dynamics problem is chaotic, making the problem especially sensitive to temporal accuracy. Finally, the numerical experiments conducted with the proposed method demonstrated superior convergence and accuracy over both traditional PINNs and the soft-constrained counterparts.

42 ENGINEERING↗