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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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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Equation-free and variable free modeling for complex/multiscale systems. Coarse-grained computation in science and engineering using fine-grained models

The work explored the linking of modern developing machine learning techniques (manifold learning and in particular diffusion maps) with traditional PDE modeling/discretization/scientific computation techniques via the equation-free methodology developed by the PI. The result (in addition to several PhD degrees, two of them by CSGF Fellows) was a sequence of strong developments - in part on the algorithmic side, linking data mining with scientific computing, and in part on applications, ranging from PDE discretizations to molecular dynamics and complex network dynamics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

A survey of techniques for optimizing transformer inference

Recent years have seen a phenomenal rise in the performance and applications of transformer neural networks. The family of transformer networks, including Bidirectional Encoder Representations from Transformer (BERT), Generative Pretrained Transformer (GPT) and Vision Transformer (ViT), have shown their effectiveness across Natural Language Processing (NLP) and Computer Vision (CV) domains. Transformer-based networks such as ChatGPT have impacted the lives of common men. However, the quest for high predictive performance has led to an exponential increase in transformers' memory and compute footprint. Researchers have proposed techniques to optimize transformer inference at all levels of abstraction. Further, this paper presents a comprehensive survey of techniques for optimizing the inference phase of transformer networks. We survey techniques such as knowledge distillation, pruning, quantization, neural architecture search and lightweight network design at the algorithmic level. We further review hardware-level optimization techniques and the design of novel hardware accelerators for transformers. We summarize the quantitative results on the number of parameters/FLOPs and the accuracy of several models/techniques to showcase the tradeoff exercised by them. We also outline future directions in this rapidly evolving field of research. We believe that this survey will educate both novice and seasoned researchers and also spark a plethora of research efforts in this field.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

ISAP-MATLAB Package for Sensitivity Analysis of High-Dimensional Stochastic Chemical Networks

Stochastic simulation and modeling play an important role to elucidate the fundamental mechanisms in complex biochemical networks. The parametric sensitivity analysis of reaction networks becomes a powerful mathematical and computational tool, yielding information regarding the robustness and the identifiability of model parameters. However, due to overwhelming computational cost, parametric sensitivity analysis is a extremely challenging problem for stochastic models with a high-dimensional parameter space and for which existing approaches are very slow. Here we present an information-theoretic sensitivity analysis in path-space (ISAP) MATLAB package that simulates stochastic processes with various algorithms and most importantly implements a gradient-free approach to quantify the parameter sensitivities of stochastic chemical reaction network dynamics using the pathwise Fisher information matrix (PFIM; Pantazis, Katsoulakis, and Vlachos 2013). The sparse, block-diagonal structure of the PFIM makes its computational complexity scale linearly with the number of model parameters. As a result of the gradientfree and the sparse nature of the PFIM, it is highly suitable for the sensitivity analysis of stochastic reaction networks with a very large number of model parameters, which are typical in the modeling and simulation of complex biochemical phenomena. Finally, the PFIM provides a fast sensitivity screening method (Arampatzis, Katsoulakis, and Pantazis 2015) which allows it to be combined with any existing sensitivity analysis software.

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

Detecting hidden layers from spreading dynamics on complex networks

When dealing with spreading processes on networks it can be of the utmost importance to test the reliability of data and identify potential unobserved spreading paths. In this paper we address these problems and propose methods for hidden layer identification and reconstruction. We also explore the interplay between difficulty of the task and the structure of the multilayer network describing the whole system where the spreading process occurs. Our methods stem from an exact expression for the likelihood of a cascade in the susceptible-infected model on an arbitrary graph. We then show that by imploring statistical properties of unimodal distributions and simple heuristics describing joint likelihood of a series of cascades one can obtain an estimate of both existence of a hidden layer and its content with success rates far exceeding those of a null model. Furthermore, we conduct our analyses on both synthetic and real-world networks providing evidence for the viability of the approach presented.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Deep Nonparametric Estimation of Operators between Infinite Dimensional Spaces

Learning operators between infinitely dimensional spaces is an important learning task arising in machine learning, imaging science, mathematical modeling and simulations, etc. This paper studies the nonparametric estimation of Lipschitz operators using deep neural networks. Non-asymptotic upper bounds are derived for the generalization error of the empirical risk minimizer over a properly chosen network class. Under the assumption that the target operator exhibits a low dimensional structure, our error bounds decay as the training sample size increases, with an attractive fast rate depending on the intrinsic dimension in our estimation. Our assumptions cover most scenarios in real applications and our results give rise to fast rates by exploiting low dimensional structures of data in operator estimation. We also investigate the influence of network structures (e.g., network width, depth, and sparsity) on the generalization error of the neural network estimator and propose a general suggestion on the choice of network structures to maximize the learning efficiency quantitatively.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Computational approaches to detect allosteric pathways in transmembrane molecular machines

Many of the functions of transmembrane proteins involved in signal processing and transduction across the cell membrane are determined by allosteric couplings that propagate the functional effects well beyond the original site of activation. Data gathered from breakthroughs in biochemistry, crystallography, and single molecule fluorescence have established a rich basis of information for the study of molecular mechanisms in the allosteric couplings of such transmembrane proteins. The mechanistic details of these couplings, many of which have therapeutic implications, however, have only become accessible in synergy with molecular modeling and simulations. Here, we review some recent computational approaches that analyze allosteric coupling networks (ACNs) in transmembrane proteins, and in particular the recently developed Protein Interaction Analyzer (PIA) designed to study ACNs in the structural ensembles sampled by molecular dynamics simulations. The power of these computational approaches in interrogating the functional mechanisms of transmembrane proteins is illustrated with selected examples of recent experimental and computational studies pursued synergistically in the investigation of secondary active transporters and GPCRs. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

Biochemistry & Molecular Biology↗
DOE OSTI2019

Enhancing Network Visibility and Security through Tensor Analysis

The increasing size, variety, rate of growth and change, and complexity of network data has warranted advanced network analysis and services. Tools that provide automated analysis through traditional or advanced signature-based systems or machine learning classifiers suffer from practical difficulties. These tools fail to provide comprehensive and contextual insights into the network when put to practical use in operational cyber security. In this paper, we present an effective tool for network security and traffic analysis that uses high-performance data analytics based on a class of unsupervised learning algorithms called tensor decompositions. The tool aims to provide a scalable analysis of the network traffic data and also reduce the cognitive load of network analysts and be network-expert-friendly by presenting clear and actionable insights into the network. With this being said, In this paper, we demonstrate the successful use of the tool in two completely diverse operational cyber security environments, namely, (1) security operations center (SOC) for the SCinet network at the SuperComputing (SC) Conference in 2016 and 2017 and (2) Reservoir Labs’ Local Area Network (LAN). In each of these environments, we produce actionable results for cyber security specialists including (but not limited to) (1) finding malicious network traffic involving internal and external attackers using port scans, SSH brute forcing, and NTP amplification attacks, (2) uncovering obfuscated network threats such as data exfiltration using DNS port and using ICMP traffic, and (3) finding network misconfiguration and performance degradation patterns.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

GraphCH: A Deep Framework for Assessing Cyber-Human Aspects in Insider Threat Detection

Insider threat is one of the most damaging cyber attacks that could cause the loss of intellectual property and enterprise data security breaches. Action sequence data such as host logs are used to investigate such threats and develop anomaly-based AI detectors. However, insider threat actions are similar to legitimate user activities, causing AI detectors to fail and suffer from high false alarm rates. Therefore, user cyber activity logs are inadequate to fully unfold insider threats. In this study, we adopt human psychological principles of risk-taking and impulsiveness along with host data to assess the influence and usefulness of human behavioral aspects in insider threat detection. Here, we hypothesize that individuals' impulsive and risk-taking behavior correlates with cyberspace activities. To validate our hypothesis, we conducted an IRB-approved study recruiting 35 participants who work in a large U.S. university and collected their cyber and psychological data for 90 days. Host and human-behavioral data analysis and mapping indicate that impulsive and risk-taking users trigger more system errors causing (un)intentional insider threats and are susceptible to attackers' social engineering and cognitive hacking. Utilizing cyber-human aspects, we introduce a Cyber-Human Graph Neural Network (GNN) based framework GraphCH to identify abnormal user behaviors and detect insider threats.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Machine learning-based analysis of COVID-19 pandemic impact on US research networks

Here in this study we explore how fallout from the changing public health policy around COVID-19 has changed how researchers access and process their science experiments. Using a combination of techniques from statistical analysis and machine learning, we conduct a retrospective analysis of historical network data for a period around the stay-at-home orders that took place in March 2020. Our analysis takes data from the entire ESnet infrastructure to explore DOE high-performance computing (HPC) resources at OLCF, ALCF, and NERSC, as well as User sites such as PNNL and JLAB. We look at detecting and quantifying changes in site activity using a combination of t-Distributed Stochastic Neighbor Embedding (t-SNE) and decision tree analysis. Our findings bring insights into the working patterns and impact on data volume movements, particularly during late-night hours and weekends.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Energy Material Network Data Hubs

In early 2015 the United States Department of Energy conceived of a consortium of collaborative bodies based on shared expertise, data, and resources that could be targeted towards the more difficult problems in energy materials research. The concept of virtual laboratories had been envisioned and discussed earlier in the decade in response to the advent of the Materials Genome Initiative and similar scientific thrusts. To be effective, any virtual laboratory needed a robust method for data management, communication, security, data sharing, dissemination, and demonstration to work efficiently and effectively for groups of remote researchers. With the accessibility of new, easily deployed cloud technology and software frameworks, such individual elements could be integrated, and the required collaboration architecture is now possible. The developers have leveraged open-source software frameworks, customized them, and merged them into a platform to enable collaborative energy materials science, regardless of the geographic dispersal of the people and resources. After five years in operations, the systems are demonstratively an effective platform for enabling research within the Energy Material Networks (EMN). This paper will show the design and development of a secured scientific data sharing platform, the ability to customize the system to support diverse workflows, and examples of the enabled research and results connected with some of the Energy Material Networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

How Many Trip Requests Could We Support? An Activity-Travel Based Vehicle Scheduling Approach

In a world of ever-changing travel behavior and ever-increasing modal options, is vital to have integrated models that could capture the interactions between supply and demand layers of travel. Addressing this need, we propose three different versions of network representation and mathematical models for the activity-based vehicle routing problem to connect activity-travel graphs of passengers (demand layer) to spatio-temporal networks of vehicles (supply layer). Versions I and II are arc-based, while version III is path-based. In version I, we introduce the concept of activity-travel graphs for passengers. For vehicles, we construct space–time networks and add a new dimension, called “under-service state”, to track the execution status of trip requests at any location and time. In version II, we reduce the complexity of the network structure by eliminating the state dimension and some other modifications in the structure of the passengers’ and vehicles’ network. Although both versions can capture various behavioral constraints of the activity-based vehicle routing problem (e.g., mandatory and optimal activities, duration of activities, chain of activities, preferred starting and ending times of activities), due to the high level of complexity of the network structure, both versions can only solve small-sized problems. To tackle the computational complexity, we propose a path-based network representation in version III, and to make a balance between the disutility of passengers and vehicles, we present a tolled user equilibrium problem. Mathematical models are coded in C and GAMS and implemented on real-world Phoenix regional transportation network with more than 39 million trip requests, which demonstrate the effectiveness of the proposed solution for the original and restricted master problems.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2024

Neural network based emulation of galaxy power spectrum covariances: A reanalysis of BOSS DR12 data

We train neural networks to quickly generate redshift-space galaxy power spectrum covariances from a given parameter set (cosmology and galaxy bias). This covariance emulator utilizes a combination of traditional fully connected network layers and transformer architecture to accurately predict covariance matrices for the high redshift, north galactic cap sample of the BOSS DR12 galaxy catalog. We run simulated likelihood analyses with emulated and brute-force computed covariances, and we quantify the network’s performance via two different metrics: (1) difference in Χ 2 and (2) likelihood contours for simulated BOSS DR 12 analyses. We find that the emulator returns excellent results over a large parameter range. We then use our emulator to perform a reanalysis of the BOSS HighZ NGC galaxy power spectrum, and find that varying covariance with cosmology along with the model vector produces Ω m = $0.27⁢6$$^{+0.013}_{–0.015}$, H 0 = 70.2 ± 1.9 km/s/Mpc, and σ 8 = $0.67⁢4$$^{+0.058}_{–0.077}$. These constraints represent an average 0.46⁢σ shift in best-fit values and a 5% increase in constraining power compared to fixing the covariance matrix (Ω m = 0.293 ± 0.017, H 0 = 70.3 ± 2.0 km/s/Mpc, σ 8 = $0.70⁢2$$^{+0.063}_{–0.075}$). As a result, this work demonstrates that emulators for more complex cosmological quantities than second-order statistics can be trained over a wide parameter range at sufficiently high accuracy to be implemented in realistic likelihood analyses.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

On Concavity and Utilization Analytics of Wide-Area Network Transport Protocols

Wide-area data transfers in high-performance computing infrastructures and big data applications are increasingly carried over dynamically provisioned dedicated network connections, which provide high capacities with no competing traffic. Throughput of TCP and UDT over wide-area connections depends, often in a complex non-linear way, on the congestion control mechanism, buffer sizes, and the number of parallel streams. In addition, our extensive TCP and UDT throughput measurements and time traces over a suite of physical and emulated 10 Gbps connections with 0-366 ms round-trip times (RTTs) show significant statistical and temporal variations. Consequently, parameter selection and optimization for transport methods require data analytics to complement analytical throughput models. We present analytics based on the concavity-convexity of throughput profiles which provide insights into peak throughput and superior/inferior trend compared to linear interpolations based on RTT. In particular, we propose the utilization-concavity coefficient, a scalar metric that incorporates both utilization and concavity profile to characterize the overall performance of a transport protocol. These measurements-based anaytics enable us to select a transport protocol and its parameters for a given host and connection configuration to achieve high throughput with statistical guarantees.

Rao, Nageswara↗
DOE OSTI2021

Training Spiking Neural Networks with Synaptic Plasticity under Integer Representation

Neuromorphic computing is emerging as a promising Beyond Moore computing paradigm that employs event-triggered computation and non-von Neumann hardware. Spike Timing Dependent Plasticity (STDP) is a well-known bio-inspired learning rule that relies on activities of locally connected neurons to adjust the weights of their respective synapses. In this work, we analyze a basic STDP rule and its sensitivity on the different hyperparameters for training spiking neural networks (SNNs) with supervision, customized for a neuromorphic hardware implementation with integer weights. We compare the classification performance on four UCI datasets (iris, wine, breast cancer and digits) that depict varying levels of complexity. We perform a search for optimal set of hyperparameters using both grid search and Bayesian optimization. Through the use of Bayesian optimization, we show the general trends in hyperparameter sensitivity in SNN classification problem. With the best sets of hyperparameters, we achieve accuracies comparable to some of the best performing SNNs on these four datasets. With a highly optimized supervised STDP rule we show that these accuracies can be achieved with just 20 epochs of training.

Kulkarni, Shruti↗
DOE OSTI2016

An efficient and portable SIMD algorithm for charge/current deposition in Particle-In-Cell codes

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (≈20pJ/word on-die to ≈10,000 pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use many-core processors on each compute nodes that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD register length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignment constraints and avoids gather/scat;ter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of ×2 to ×2.5 speed-up in double precision for particle shape factor of orders 1–3. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles). Program summary Program Title: vec_deposition Program Files doi:http://dx.doi.org/10.17632/nh77fv9k8c.1 Licensing provisions: BSD 3-Clause Programming language: Fortran 90 External routines/libraries: OpenMP > 4.0 Nature of problem: Exascale architectures will have many-core processors per node with long vector data registers capable of performing one single instruction on multiple data during one clock cycle. Data register lengths are expected to double every four years and this pushes for new portable solutions for efficiently vectorizing Particle-In-Cell codes on these future many-core architectures. One of the main hotspot routines of the PIC algorithm is the current/charge deposition for which there is no efficient and portable vector algorithm. Solution method: Here we provide an efficient and portable vector algorithm of current/charge deposition routines that uses a new data structure, which significantly reduces gather/scatter operations. Vectorization is controlled using OpenMP 4.0 compiler directives for vectorization which ensures portability across different architectures. Restrictions: Here we do not provide the full PIC algorithm with an executable but only vector routines for current/charge deposition. These scalar/vector routines can be used as library routines in your 3D Particle-In-Cell code. However, to get the best performances out of vector routines you have to satisfy the two following requirements: (1) Your code should implement particle tiling (as explained in the manuscript) to allow for maximized cache reuse and reduce memory accesses that can hinder vector performances. The routines can be used directly on each particle tile. (2) You should compile your code with a Fortran 90 compiler (e.g Intel, gnu or cray) and provide proper alignment flags and compiler alignment directives (more details in README file).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

deep-taxon v0.1

deep-taxon is a package for training neural networks for classifying genomic sequence data. deep-taxon provides tools for converting genomic sequence data into high performance computing file formats capable of training neural networks at scale.

Tritt, Andrew↗
DOE OSTI2015

Fencing network direct memory access data transfers in a parallel active messaging interface of a parallel computer

Fencing direct memory access (`DMA`) data transfers in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI including data communications endpoints, each endpoint including specifications of a client, a context, and a task, the endpoints coupled for data communications through the PAMI and through DMA controllers operatively coupled to a deterministic data communications network through which the DMA controllers deliver data communications deterministically, including initiating execution through the PAMI of an ordered sequence of active DMA instructions for DMA data transfers between two endpoints, effecting deterministic DMA data transfers through a DMA controller and the deterministic data communications network; and executing through the PAMI, with no FENCE accounting for DMA data transfers, an active FENCE instruction, the FENCE instruction completing execution only after completion of all DMA instructions initiated prior to execution of the FENCE instruction for DMA data transfers between the two endpoints.

97 MATHEMATICS AND COMPUTING↗