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All sources NASA NTRS DOE OSTI

DOE OSTI2021

Understanding Discrete Fracture Networks Through Spectral Graph Theory

Discrete Fracture Network models (DFNs) are used to simulate fluid flow and particle transport through fracture networks in low permeability rock. Understanding these processes are essential in many subsurface applications, such as environmental restoration of contaminated fractured media, CO 2 sequestration, detection of low-level nuclear tests, and hydrocarbon extraction. Compared with other models, DFNs allow for incorporation of a wider range of network characteristics but have substantially greater computation cost. These networks can be represented with graphs, allowing the use of graph theory tools to study the networks. I used Python to simulate flow and transport on a range of DFNs and analyzed these networks using methods from network analysis and spectral graph theory. My purpose was to find ways to gain insight about flow and transport on DFNs using these graph representations, bypassing the computationally intensive meshing typically required. My work is still in progress, but I have discovered several interesting trends and patterns that I believe could be useful towards my goal. If I am able to bring these results to fruition, they will aid subsurface geologists in extracting flow and transport information about fracture networks more efficiently.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2002

Applying Strategic Visualization(Registered Trademark) to Lunar and Planetary Mission Design

NASA teams, such as the NASA Exploration Team (NEXT), utilize advanced computational visualization processes to develop mission designs and architectures for lunar and planetary missions. One such process, Strategic Visualization (trademark), is a tool used extensively to help mission designers visualize various design alternatives and present them to other participants of their team. The participants, which may include NASA, industry, and the academic community, are distributed within a virtual network. Consequently, computer animation and other digital techniques provide an efficient means to communicate top-level technical information among team members. Today,Strategic Visualization(trademark) is used extensively both in the mission design process within the technical community, and to communicate the value of space exploration to the general public. Movies and digital images have been generated and shown on nationally broadcast television and the Internet, as well as in magazines and digital media. In our presentation will show excerpts of a computer-generated animation depicting the reference Earth/Moon L1 Libration Point Gateway architecture. The Gateway serves as a staging corridor for human expeditions to the lunar poles and other surface locations. Also shown are crew transfer systems and current reference lunar excursion vehicles as well as the Human and robotic construction of an inflatable telescope array for deployment to the Sun/Earth Libration Point.

Frassanito, John R.↗

DOE OSTI2022

Validation and parameterization of a novel physics-constrained neural dynamics model applied to turbulent fluid flow

We report, in fluid physics, data-driven models to enhance or accelerate time to solution are becoming increasingly popular for many application domains, such as alternatives to turbulence closures, system surrogates, or for new physics discovery. In the context of reduced order models of high-dimensional time-dependent fluid systems, machine learning methods grant the benefit of automated learning from data, but the burden of a model lies on its reduced-order representation of both the fluid state and physical dynamics. In this work, we build a physics-constrained, data-driven reduced order model for Navier–Stokes equations to approximate spatiotemporal fluid dynamics in the canonical case of isotropic turbulence in a triply periodic box. The model design choices mimic numerical and physical constraints by, for example, implicitly enforcing the incompressibility constraint and utilizing continuous neural ordinary differential equations for tracking the evolution of the governing differential equation. We demonstrate this technique on a three-dimensional, moderate Reynolds number turbulent fluid flow. In assessing the statistical quality and characteristics of the machine-learned model through rigorous diagnostic tests, we find that our model is capable of reconstructing the dynamics of the flow over large integral timescales, favoring accuracy at the larger length scales. More significantly, comprehensive diagnostics suggest that physically interpretable model parameters, corresponding to the representations of the fluid state and dynamics, have attributable and quantifiable impact on the quality of the model predictions and computational complexity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Oscillatory Spreading and Inertia in Power Grids

The increase in variable renewable generators (VRGs) in power systems has altered the dynamics from a historical experience. VRGs introduce new sources of power oscillations, and the stabilizing response provided by synchronous generators (SGs, e.g., natural gas, coal, etc.), which help avoid some power fluctuations, will lessen as VRGs replace SGs. These changes have led to the need for new methods and metrics to quickly assess the likely oscillatory behavior for a particular network without performing computationally expensive simulations. This work studies the impact of a critical dynamical parameter - the inertia value - on the rest of a power system's oscillatory response to representative VRG perturbations. We use a known localization metric in a novel way to quantify the number of nodes responding to a perturbation and the magnitude of those responses. This metric allows us to relate the spread and severity of a system's power oscillations with inertia. We find that as inertia increases, the system response to node perturbations transitions from localized (only a few close nodes respond) to delocalized (many nodes across the network respond). We introduce a heuristic computed from the network Laplacian to relate this oscillatory transition to the network structure. We show that our heuristic accurately describes the spread of oscillations for a realistic power-system test case. Using a heuristic to determine the likely oscillatory behavior of a system given a set of parameters has wide applicability in power systems, and it could decrease the computational workload of planning and operation.

dynamical systems↗

NASA NTRS1998

RIACS

The Research Institute for Advanced Computer Science (RIACS) was established by the Universities Space Research Association (USRA) at the NASA Ames Research Center (ARC) on June 6, 1983. RIACS is privately operated by USRA, a consortium of universities that serves as a bridge between NASA and the academic community. Under a five-year co-operative agreement with NASA, research at RIACS is focused on areas that are strategically enabling to the Ames Research Center's role as NASA's Center of Excellence for Information Technology. The primary mission of RIACS is charted to carry out research and development in computer science. This work is devoted in the main to tasks that are strategically enabling with respect to NASA's bold mission in space exploration and aeronautics. There are three foci for this work: (1) Automated Reasoning. (2) Human-Centered Computing. and (3) High Performance Computing and Networking. RIACS has the additional goal of broadening the base of researcher in these areas of importance to the nation's space and aeronautics enterprises. Through its visiting scientist program, RIACS facilitates the participation of university-based researchers, including both faculty and students, in the research activities of NASA and RIACS. RIACS researchers work in close collaboration with NASA computer scientists on projects such as the Remote Agent Experiment on Deep Space One mission, and Super-Resolution Surface Modeling.

Moore, Robert C.↗

NASA NTRS1998

RIACS

The Research Institute for Advanced Computer Science (RIACS) was established by the Universities Space Research Association (USRA) at the NASA Ames Research Center (ARC) on June 6, 1983. RIACS is privately operated by USRA, a consortium of universities that serves as a bridge between NASA and the academic community. Under a five-year co-operative agreement with NASA, research at RIACS is focused on areas that are strategically enabling to the Ames Research Center's role as NASA's Center of Excellence for Information Technology. Research is carried out by a staff of full-time scientist,augmented by visitors, students, post doctoral candidates and visiting university faculty. The primary mission of RIACS is charted to carry out research and development in computer science. This work is devoted in the main to tasks that are strategically enabling with respect to NASA's bold mission in space exploration and aeronautics. There are three foci for this work: Automated Reasoning. Human-Centered Computing. and High Performance Computing and Networking. RIACS has the additional goal of broadening the base of researcher in these areas of importance to the nation's space and aeronautics enterprises. Through its visiting scientist program, RIACS facilitates the participation of university-based researchers, including both faculty and students, in the research activities of NASA and RIACS. RIACS researchers work in close collaboration with NASA computer scientists on projects such as the Remote Agent Experiment on Deep Space One mission, and Super-Resolution Surface Modeling.

Moore, Robert C.↗

DOE OSTI2016

The Livermore Brain: Massive Deep Learning Networks Enabled by High Performance Computing

The proliferation of inexpensive sensor technologies like the ubiquitous digital image sensors has resulted in the collection and sharing of vast amounts of unsorted and unexploited raw data. Companies and governments who are able to collect and make sense of large datasets to help them make better decisions more rapidly will have a competitive advantage in the information era. Machine Learning technologies play a critical role for automating the data understanding process; however, to be maximally effective, useful intermediate representations of the data are required. These representations or “features” are transformations of the raw data into a form where patterns are more easily recognized. Recent breakthroughs in Deep Learning have made it possible to learn these features from large amounts of labeled data. The focus of this project is to develop and extend Deep Learning algorithms for learning features from vast amounts of unlabeled data and to develop the HPC neural network training platform to support the training of massive network models. This LDRD project succeeded in developing new unsupervised feature learning algorithms for images and video and created a scalable neural network training toolkit for HPC. Additionally, this LDRD helped create the world’s largest freely-available image and video dataset supporting open multimedia research and used this dataset for training our deep neural networks. This research helped LLNL capture several work-for-others (WFO) projects, attract new talent, and establish collaborations with leading academic and commercial partners. Finally, this project demonstrated the successful training of the largest unsupervised image neural network using HPC resources and helped establish LLNL leadership at the intersection of Machine Learning and HPC research.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

A review on recent machine learning applications for imaging mass spectrometry studies

Imaging mass spectrometry (IMS) is a powerful analytical technique widely used in biology, chemistry, and materials science fields that continue to expand. IMS provides a qualitative compositional analysis and spatial mapping with high chemical specificity. The spatial mapping information can be 2D or 3D depending on the analysis technique employed. Due to the combination of complex mass spectra coupled with spatial information, large high-dimensional datasets (hyperspectral) are often produced. Therefore, the use of automated computational methods for an exploratory analysis is highly beneficial. The fast-paced development of artificial intelligence (AI) and machine learning (ML) tools has received significant attention in recent years. These tools, in principle, can enable the unification of data collection and analysis into a single pipeline to make sampling and analysis decisions on the go. There are various ML approaches that have been applied to IMS data over the last decade. Here, in this review, we discuss recent examples of the common unsupervised (principal component analysis, non-negative matrix factorization, k-means clustering, uniform manifold approximation and projection), supervised (random forest, logistic regression, XGboost, support vector machine), and other methods applied to various IMS datasets in the past five years. The information from this review will be useful for specialists from both IMS and ML fields since it summarizes current and representative studies of computational ML-based exploratory methods for IMS.

47 OTHER INSTRUMENTATION↗

DOE OSTI2017

Report from the 2016 CrossConnects workshop: improving data mobility & management for bioinformatics

Due to significant declines in the price of genome sequencing technology, the bioinformatics sciences are experiencing a massive upswing in data generation resulting in an increasing need for data distribution and access. The sheer number of biological areas of study, many of which benefit from the scientific breakthroughs of one another, are adding to the increase of shared data usage. The need for effective data management, analysis, and access are becoming more critical. While there are commonalities facing both precision medicine and metagenomics, each area has its own unique challenges and needs. A workshop was held in April 2016 at Lawrence Berkeley National Laboratory that brought together scientists from both fields, along with experts in computing and networking. Presenters and attendees discussed current research and pressing data issues facing the bioinformatics field today and in the near future.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

MINEs: Open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

Metabolomics have proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography–mass spectrometry (LC–MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges require new approaches that consider compounds beyond those available in curated biochemistry databases. Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and common biochemical reactions. We utilize an algorithm called the Biochemical Network Integrated Computational Explorer (BNICE) and expert-curated reaction rules based on the Enzyme Commission classification system to propose the novel chemical structures and reactions that comprise MINE databases. Starting from the Kyoto Encyclopedia of Genes and Genomes (KEGG) COMPOUND database, the MINE contains over 571,000 compounds, of which 93% are not present in the PubChem database. However, these MINE compounds have on average higher structural similarity to natural products than compounds from KEGG or PubChem. MINE databases were able to propose annotations for 98.6% of a set of 667 MassBank spectra, 14% more than KEGG alone and equivalent to PubChem while returning far fewer candidates per spectra than PubChem (46 vs. 1715 median candidates). Application of MINEs to LC–MS accurate mass data enabled the identity of an unknown peak to be confidently predicted. MINE databases are freely accessible for non-commercial use via user-friendly web-tools at http://minedatabase.mcs.anl.gov and developer-friendly APIs. MINEs improve metabolomics peak identification as compared to general chemical databases whose results include irrelevant synthetic compounds. MINEs complement and expand on previous in silico generated compound databases that focus on human metabolism. We are actively developing the database; future versions of this resource will incorporate transformation rules for spontaneous chemical reactions and more advanced filtering and prioritization of candidate structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1987

Distributed computer system enhances productivity for SRB joint optimization

Initial calculations of a redesign of the solid rocket booster joint that failed during the shuttle tragedy showed that the design had a weight penalty associated with it. Optimization techniques were to be applied to determine if there was any way to reduce the weight while keeping the joint opening closed and limiting the stresses. To allow engineers to examine as many alternatives as possible, a system was developed consisting of existing software that coupled structural analysis with optimization which would execute on a network of computer workstations. To increase turnaround, this system took advantage of the parallelism offered by the finite difference technique of computing gradients to allow several workstations to contribute to the solution of the problem simultaneously. The resulting system reduced the amount of time to complete one optimization cycle from two hours to one-half hour with a potential of reducing it to 15 minutes. The current distributed system, which contains numerous extensions, requires one hour turnaround per optimization cycle. This would take four hours for the sequential system.

Rogers, James L., Jr.↗

DOE OSTI2018

Detecting anomalous behavior via user authentication graphs

Significant and aggregate user authentication activity may be analyzed across a population of users and computers in one or more networks to differentiate between authorized users and intruders in a network, and/or to detect inappropriate behavior by otherwise authorized users. Dynamic graphs and graph models over user and computer authentication activity, including time-constrained models, may be used for the purposes of profiling and analyzing user behavior in computer networks. More specifically, an edge-based breadth first search of graphs may be used that enforces time-constraints while maintaining traditional breadth first search computational complexity equivalence.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Detecting anomalous behavior via user authentication graphs

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2004

Intelligent Systems Technologies and Utilization of Earth Observation Data

The addition of raw data and derived geophysical parameters from several Earth observing satellites over the last decade to the data held by NASA data centers has created a data rich environment for the Earth science research and applications communities. The data products are being distributed to a large and diverse community of users. Due to advances in computational hardware, networks and communications, information management and software technologies, significant progress has been made in the last decade in archiving and providing data to users. However, to realize the full potential of the growing data archives, further progress is necessary in the transformation of data into information, and information into knowledge that can be used in particular applications. Sponsored by NASA s Intelligent Systems Project within the Computing, Information and Communication Technology (CICT) Program, a conceptual architecture study has been conducted to examine ideas to improve data utilization through the addition of intelligence into the archives in the context of an overall knowledge building system (KBS). Potential Intelligent Archive concepts include: 1) Mining archived data holdings to improve metadata to facilitate data access and usability; 2) Building intelligence about transformations on data, information, knowledge, and accompanying services; 3) Recognizing the value of results, indexing and formatting them for easy access; 4) Interacting as a cooperative node in a web of distributed systems to perform knowledge building; and 5) Being aware of other nodes in the KBS, participating in open systems interfaces and protocols for virtualization, and achieving collaborative interoperability.

Ramapriyan, H. K.↗

DOE OSTI2020

A Computational Theory for the Emergence of Grammatical Categories in Cortical Dynamics

A general agreement in psycholinguistics claims that syntax and meaning are unified precisely and very quickly during online sentence processing. Although several theories have advanced arguments regarding the neurocomputational bases of this phenomenon, we argue that these theories could potentially benefit by including neurophysiological data concerning cortical dynamics constraints in brain tissue. In addition, some theories promote the integration of complex optimization methods in neural tissue. In this paper we attempt to fill these gaps introducing a computational model inspired in the dynamics of cortical tissue. In our modeling approach, proximal afferent dendrites produce stochastic cellular activations, while distal dendritic branches–on the other hand–contribute independently to somatic depolarization by means of dendritic spikes, and finally, prediction failures produce massive firing events preventing formation of sparse distributed representations. The model presented in this paper combines semantic and coarse-grained syntactic constraints for each word in a sentence context until grammatically related word function discrimination emerges spontaneously by the sole correlation of lexical information from different sources without applying complex optimization methods. By means of support vector machine techniques, we show that the sparse activation features returned by our approach are well suited—bootstrapping from the features returned by Word Embedding mechanisms—to accomplish grammatical function classification of individual words in a sentence. In this way we develop a biologically guided computational explanation for linguistically relevant unification processes in cortex which connects psycholinguistics to neurobiological accounts of language. We also claim that the computational hypotheses established in this research could foster future work on biologically-inspired learning algorithms for natural language processing applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Stochastic Gradient-Based Distributed Bayesian Estimation in Cooperative Sensor Networks

Distributed Bayesian inference provides a full quantification of uncertainty offering numerous advantages over point estimates that autonomous sensor networks are able to exploit. However, fully-decentralized Bayesian inference often requires large communication overheads and low network latency, resources that are not typically available in practical applications. In this paper, we propose a decentralized Bayesian inference approach based on stochastic gradient Langevin dynamics, which produces full posterior distributions at each of the nodes with significantly lower communication overhead. We provide analytical results on convergence of the proposed distributed algorithm to the centralized posterior, under typical network constraints. Finally, we also provide extensive simulation results to demonstrate the validity of the proposed approach.

42 ENGINEERING↗

NASA NTRS1992

MODIS algorithm development and data visualization using ACTS

The study of the Earth as a system will require the merger of scientific and data resources on a much larger scale than has been done in the past. New methods of scientific research, particularly in the development of geographically dispersed, interdisciplinary teams, are necessary if we are to understand the complexity of the Earth system. Even the planned satellite missions themselves, such as the Earth Observing System, will require much more interaction between researchers and engineers if they are to produce scientifically useful data products. A key component in these activities is the development of flexible, high bandwidth data networks that can be used to move large amounts of data as well as allow researchers to communicate in new ways, such as through video. The capabilities of the Advanced Communications Technology Satellite (ACTS) will allow the development of such networks. The Pathfinder global AVHRR data set and the upcoming SeaWiFS Earthprobe mission would serve as a testbed in which to develop the tools to share data and information among geographically distributed researchers. Our goal is to develop a 'Distributed Research Environment' that can be used as a model for scientific collaboration in the EOS era. The challenge is to unite the advances in telecommunications with the parallel advances in computing and networking.

Abbott, Mark R.↗

DOE OSTI2017

High Performance Data Transfer for Distributed Data Intensive Sciences

We report on the development of ZX software providing high performance data transfer and encryption. The design scales in: computation power, network interfaces, and IOPS while carefully balancing the available resources. Two U.S. patent-pending algorithms help tackle data sets containing lots of small files and very large files, and provide insensitivity to network latency. It has a cluster-oriented architecture, using peer-to-peer technologies to ease deployment, operation, usage, and resource discovery. Its unique optimizations enable effective use of flash memory. Using a pair of existing data transfer nodes at SLAC and NERSC, we compared its performance to that of bbcp and GridFTP and determined that they were comparable. With a proof of concept created using two four-node clusters with multiple distributed multi-core CPUs, network interfaces and flash memory, we achieved 155Gbps memory-to-memory over a 2x100Gbps link aggregated channel and 70Gbps file-to-file with encryption over a 5000 mile 100Gbps link.

97 MATHEMATICS AND COMPUTING↗