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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Clinical Natural Language Processing for Radiation Oncology: A Review and Practical Primer

Natural language processing (NLP), which aims to convert human language into expressions that can be analyzed by computers, is one of the most rapidly developing and widely used technologies in the field of artificial intelligence. Natural language processing algorithms convert unstructured free text data into structured data that can be extracted and analyzed at scale. In medicine, this unlocking of the rich, expressive data within clinical free text in electronic medical records will help untap the full potential of big data for research and clinical purposes. Recent major NLP algorithmic advances have significantly improved the performance of these algorithms, leading to a surge in academic and industry interest in developing tools to automate information extraction and phenotyping from clinical texts. Thus, these technologies are poised to transform medical research and alter clinical practices in the future. Radiation oncology stands to benefit from NLP algorithms if they are appropriately developed and deployed, as they may enable advances such as automated inclusion of radiation therapy details into cancer registries, discovery of novel insights about cancer care, and improved patient data curation and presentation at the point of care. However, challenges remain before the full value of NLP is realized, such as the plethora of jargon specific to radiation oncology, nonstandard nomenclature, a lack of publicly available labeled data for model development, and interoperability limitations between radiation oncology data silos. Successful development and implementation of high quality and high value NLP models for radiation oncology will require close collaboration between computer scientists and the radiation oncology community. Here, we present a primer on artificial intelligence algorithms in general and NLP algorithms in particular; provide guidance on how to assess the performance of such algorithms; review prior research on NLP algorithms for oncology; and describe future avenues for NLP in radiation oncology research and clinics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

Data for Post-Access Report: Tidal Energy Resource Characterization and Model Validation via the Assessment of Cost-effective Spatially Distributed Current Measurements from microFloat Swarms

This project evaluated how high-resolution, spatially distributed field data can be used to refine and validate site-scale hydrodynamic simulations of tidal channels. Use of such spatially-distributed field observations or site-scale hydrodynamic simulations will be needed for producing accurate predictions of tidal energy production over larger arrays of tidal turbines. The data contained in this archive includes field observations of water velocity from a series of short surveys in Agate Pass taken on August 20th, 2020 using station-keeping ADCP (acoustic doppler current profiler) measurements, drifting downward-looking ADCPs, and microFloats, gathered by researchers at APL-UW under a previous project. It also includes high-resolution hydrodynamic model runs for the site during that time generated under TEAMER support. An explanatory file (.pdf format) describes the survey and field data structure. Processed data is stored in .mat format. Survey summary: start time, number of floats, water level. microFloat data: - Cleaned data for each float in survey, - Time series of position (lat., lon.), depth (relative to surface), and horizontal velocity (u, v) Drifting ADCP data: - Cleaned data for each drifting ADCP in survey - Time series of position (lat., lon.), sample depth (relative to surface), and observed water velocity (u,v,w) Stationary ADCP data: - Cleaned data for each station-keeping data set in survey - Time series of position (lat., lon.), sample depth (relative to surface), and observed water velocity (u,v,w) FVCOM (Finite Volume Coastal Ocean Model) model outputs: Water level and velocity, as well as derived variables (e.g., power density) from the final refined model simulations for the Agate Pass subdomain. Contained in NetCDF and ASCII files for the duration of August 18th and 20th 2020 field surveys. Additional scripts for processing the data and generating the figures in the report are included.

16 TIDAL AND WAVE POWER↗
DOE OSTI2022

The LLNL nuclear data infrastructure for the GNDS data format

The next generation of nuclear data infrastructure tools at the Livermore National Laboratory (LLNL) consists of pipeline of codes that read and process nuclear data from evaluated files saved in the new GNDS (Generalised Nuclear Data Structure) nuclear data format. The processing code FUDGE (For Updating Data and Generating Evaluations) is at the front-end of this pipeline as it reads and process the evaluated data for use in downstream transport codes. FUDGE is Python based with C and C++ extensions for computationally intensive tasks. As is the case for the evaluated data, the processed output is also saved in the GNDS format and the GIDI+ API is provided as the interface between the processed data and the transport codes. GIDI+ is a C++ based suite of codes and it includes GIDI (General Interaction Data Interface), a library for reading and writing GNDS data, and MCGIDI which is the cross section lookup, and reaction and product distribution sampling interface between Monte Carlo transport codes and the GNDS data. GIDI provides methods for easy access to the multi-group processed GNDS data and this is demonstrated through its implementation in ARDRA, the LLNL deterministic transport code. The evaluation and sampling methods in MCGIDI are available as both CPU and GPU methods which facilitates the use of MCGIDI in both traditional CPU-based as well as the next generation mixed model computational architectures. This is demonstrated through the GIDI+ implementation in MERCURY, the LLNL Monte Carlo transport code. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2018

pnnl/SHAD

Scalable High-performance Algorithms and Data-structures. Scalable High-performance Algorithms and Data-structures (SHAD) is an application programming interface based on a generic software library. It has a modular design that enables reuse of modules. The core of this software tool set is built on an Abstract Runtime interface and it's library includes the common data structures such as array, vector, map and set. It is designed to accommodate significant amount of data which can be accessed in massively parallel environments, and used as building blocks for SHAD extensions, i.e. higher level software libraries.

Castellana, Vito↗
DOE OSTI2018

Multithreaded sparse matrix-matrix multiplication for many-core and GPU architectures

Sparse matrix-matrix multiplication is a key kernel that has applications in several domains such as scientific computing and graph analysis. Several algorithms have been studied in the past for this foundational kernel. In this work, we develop parallel algorithms for sparse matrix-matrix multiplication with a focus on performance portability across different high performance computing architectures. The performance of these algorithms depend on the data structures used in them. We compare different types of accumulators in these algorithms and demonstrate the performance difference between these data structures. Furthermore, we develop a meta-algorithm, kkSpGEMM, to choose the right algorithm and data structure based on the characteristics of the problem. We show performance comparisons on three architectures and demonstrate the need for the community to develop two phase sparse matrix-matrix multiplication implementations for efficient reuse of the data structures involved.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Nuclear Data Sheets for A=170☆

Nuclear structure data pertaining to all nuclei with mass number A=170 have been evaluated, and incorporated into the ENSDF data file. This evaluation supersedes the previous evaluation (Coral M. Baglin), Nuclear Data Sheets 96, 611 (2002), (cutoff date 15 August 2002) and subsequent updates of the ENSDF file for Yb to Dy (cutoff 15 April 2010), Lu (cutoff 8 October 1998), Pt (cutoff 17 February 1999) and Ta, Os (cutoff 7 April 1998). Since the previous evaluation, {sup 170}Gd has been observed and the ground state T{sub 1/2} measured. New excited states have also been observed in the neutron rich {sup 170}Dy. The ground state T{sub 1/2} of {sup 170}Tb has been determined, however, there are currently still no excited states observed in this nucleus. There remains some uncertainty in the ground state and longer-lived isomer in {sup 170}Ir which could warrent further experimental investigation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication

Writing large amounts of data concurrently to stable storage is a typical I/O pattern of many HPC workflows. This pattern introduces high I/O overheads and results in increased storage space utilization especially for workflows that need to capture the evolution of data structures with high frequency as checkpoints. In this context, many applications, such as graph pattern matching, perform sparse updates to large data structures between checkpoints. For these applications, incremental checkpointing techniques that save only the differences from one checkpoint to another can dramatically reduce the checkpoint sizes, I/O bottlenecks, and storage space utilization. However, such techniques are not without challenges: it is non-trivial to transparently determine what data has changed since a previous checkpoint and assemble the differences in a compact fashion that does not result in excessive metadata. State-of-art data reduction techniques (e.g., compression and de-duplication) have significant limitations when applied to modern HPC applications that leverage GPUs: slow at detecting the differences, generate a large amount of metadata to keep track of the differences, and ignore crucial spatiotemporal checkpoint data redundancy. This paper addresses these challenges by proposing a Merkle tree-based incremental checkpointing method to exploit GPUs' high memory bandwidth and massive parallelism. Experimental results at scale show a significant reduction of the I/O overhead and space utilization of checkpointing compared with state-of-the-art incremental checkpointing and compression techniques.

Tan, Nigel↗
DOE OSTI2018

Nuclear Data Sheets for A=164

Experimental nuclear structure data for the known A=164 isobaric nuclides (Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Ta, W, Re, Os, Ir) have been evaluated, and presented together with Adopted properties of level energies, and associated γ rays. The decay data for these nuclides have also been evaluated, providing Adopted values of γ and β radiations, and log ft values. No excited states are known in 164 Eu, 164 Tb, and 164 Ir. Information for 164 Gd, 164 Re and 164 Os is limited due to insufficient experimental data. For radioactive nuclides, decay schemes of 164 Sm, 164 Gd and 164 Re are not known, and those of 164 W, 164 Tb, 164 Lu, 164 Hf, 164 Ta and 164 W are incomplete. The decay schemes of 164 Ho and the two activities of 164 Tm seem fairly complete. The decay scheme of 164 Yb presents a major problem that the Q(ε) value of 887 keV 29 recommended in 2017Wa10 is in disagreement with the population of levels at 928, 952 and 1060 keV in the daughter nucleus. This decay scheme, which so far has been mainly reported in a secondary reference (1982AdZZ) needs further investigation. Also the masses of 164 Yb and 164 Tm need either new measurements or a re-evaluation to resolve discrepancy of about 220 keV in the Q value of 164 Yb decay to 164 Tm. The reactions and decays for which no new experimental information has become available since the 2001 update have undergone revisions to incorporate conversion coefficients from BrIcc code, and evaluated Q values from 2017Wa10, but the essential content of such datasets may have remained the same as in previous evaluations. Finally, in this respect the present work greatly benefited from all the previous NDS evaluations (2001Si27,1992Sh07, 1986Sh03,1974Bu30), but at the same time data presented herein supersede all the previous published evaluations.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2019

Nuclear Data Sheets for A=73☆

Experimental nuclear structure data for the known A=73 isobaric nuclides (Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Se, Br, Kr, Rb and Sr) have been evaluated, and presented together with Adopted properties of level energies, and associated γ rays. The decay data for these nuclides have also been evaluated, providing Adopted values of γ and β radiations, and log ft values. For {sup 73}Mn, only the isotopic identification has been established, with no knowledge of its g.s. half-life. For {sup 73}Fe, {sup 73}Co and {sup 73}Sr, only the ground states and their half-lives are known with no information about the excited states. For {sup 73}Ni, {sup 73}Cu, {sup 73}Zn and {sup 73}Rb, little data are available for excited states. The half-life and decay modes of possibly proton-unbound {sup 73}Rb need firmly established. {sup 73}Ga structure presents a special challenge in that the 1/2{sup −} ground state and the first 3/2{sup −} state have recently been proposed, in a Coulomb excitation experiment by 2010Di14, to form an almost degenerate doublet with an estimated spacing of 229 Th with its first excited state at 7.8 eV, and {sup 235}U with its first excited state at 76 eV. Ultra-high resolution gamma-ray spectroscopic studies are warranted to search for the low-lying (73 Ga, and to determine its half-life. Level structures of {sup 73}Ga, {sup 73}Ge, {sup 73}As, {sup 73}Se, {sup 73}Br and {sup 73}Kr are quite well known, although decay schemes of radioactive ground states of {sup 73}Co, {sup 73}Cu and {sup 73}Br are considered incomplete. The reactions and decays for which no new experimental information has become available since the 2003 update have undergone revisions to incorporate conversion coefficients from BrIcc code, and evaluated Q values from 2017Wa10, but essential content of such datasets may have remained the same as in previous evaluations. In this respect the present work greatly benefited from all the previous NDS evaluations (2004Si08,1993Ki25,1987Ki13, 1980Ek01,1974Al33), but at the same time data presented herein supersede all the previous published evaluations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

The Stellar decomposition: A compact representation for simplicial complexes and beyond

Here, we introduce the Stellar decomposition, a model for efficient topological data structures over a broad range of simplicial and cell complexes. A Stellar decomposition of a complex is a collection of regions indexing the complex’s vertices and cells such that each region has sufficient information to locally reconstruct the star of its vertices, i.e., the cells incident in the region’s vertices. Stellar decompositions are general in that they can compactly represent and efficiently traverse arbitrary complexes with a manifold or non-manifold domain. They are scalable to complexes in high dimension and of large size, and they enable users to easily construct tailored application-dependent data structures using a fraction of the memory required by a corresponding global topological data structure on the complex. As a concrete realization of this model for spatially embedded complexes, we introduce the Stellar tree, which combines a nested spatial tree with a simple tuning parameter to control the number of vertices in a region. Stellar trees exploit the complex’s spatial locality by reordering vertex and cell indices according to the spatial decomposition and by compressing sequential ranges of indices. Stellar trees are competitive with state-of-the-art topological data structures for manifold simplicial complexes and offer significant improvements for cell complexes and non-manifold simplicial complexes. We conclude with a high-level description of several mesh processing and analysis applications that utilize Stellar trees to process large datasets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study

Abstract Atomic-level three-dimensional (3D) structure data for biological macromolecules often prove critical to dissecting and understanding the precise mechanisms of action of cancer-related proteins and their diverse roles in oncogenic transformation, proliferation, and metastasis. They are also used extensively to identify potentially druggable targets and facilitate discovery and development of both small-molecule and biologic drugs that are today benefiting individuals diagnosed with cancer around the world. 3D structures of biomolecules (including proteins, DNA, RNA, and their complexes with one another, drugs, and other small molecules) are freely distributed by the open-access Protein Data Bank (PDB). This global data repository is used by millions of scientists and educators working in the areas of drug discovery, vaccine design, and biomedical and biotechnology research. The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to the PDB archive that streamlines access for millions of worldwide PDB data consumers worldwide. Herein, we review online resources made available free of charge by the RCSB PDB to basic and applied researchers, healthcare providers, educators and their students, patients and their families, and the curious public. We exemplify the value of understanding cancer-related proteins in 3D with a case study focused on human papillomavirus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB

Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A decay database of coincident γ–γ and γ–X -ray branching ratios for in-field spectroscopy applications

Current fieldable spectroscopy techniques often use single detector systems heavily impacted by interferences from intense background radiation fields. These effects result in low-confidence measurements that can lead to misinterpretation of the collected spectrum. To help improve interpretation of the fission products and short-lived radionuclides produced in a composite sample, a coincidence-database is being developed in support of a robust portable and X-ray coincidence detector system concurrently under development at the Pacific Northwest National Laboratory for in-field deployment. Hitherto, no database exists containing coincident γ–γ and γ–X-ray branching-ratio intensities on an absolute scale that will greatly enhance isotopic identification for in-field applications. As part of this project, software has been developed to parse all radioactive-decay data sets from the Evaluated Nuclear Structure Data File (ENSDF) archive to enable translation into a more useful JavaScript Object Notation (JSON) formats that more readily supports query-based data manipulation. The coincident database described in this work is the first of its kind and contains coincidence γ–γ and γ–X-ray intensities and their corresponding uncertainties, together with auxiliary metadata associated with each decay data set. The new JSON format provides a convenient and portable means of data storage that can be imported into analysis frameworks with relatively low overhead allowing for meaningful comparison with measured data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Learning to Predict Material Structure from Neutron Scattering Data

Understanding structural properties of materials and how they relate to its atomic structure, while extremely challenging, is a key scientific quest that has dominated the landscape of materials research for decades. Neutron and X-ray scattering is a state-of-the-art method to investigate material structure on the atomic scale. Traditional methods of processing neutron scattering data to decipher the structure of target materials have relied on computing scattering patterns using physics-based forward models and comparing them with experimentally gathered scattering profiles within a computationally expensive optimization loop. Here, we report an initial design of a data-driven machine learning pipeline for material structure prediction that is computationally faster (once trained) and potentially more accurate. We describe the architecture of the ML pipeline and a preliminary benchmarking study of shallow machine learning models in terms of their prediction accuracy and limitations. We show that material structure prediction from neutron scattering data using shallow learning models is feasible to within 90% prediction accuracy for certain classes of materials but deeper models are required for more general material structure predictions.

Garcia Cardona, Cristina↗
DOE OSTI2018

Portable Data-Parallel Surface Reconstruction on a Uniform Rectilinear Grid

With the increasing heterogeneity and on-node parallelism of high-performance computing hardware, a major challenge is to develop portable and efficient algorithms and software. In this work, we present our implementation of a portable code to perform surface reconstruction using NVIDIA's Thrust library. Surface reconstruction is a technique commonly used in volume tracking methods for simulations of multimaterial flow with interfaces. Here, we have designed a 3D mesh data structure that is easily mapped to the 1D vectors used by Thrust and at the same time is simple to use and uses familiar data structure terminology (such as cells, faces, vertices, and edges). With this new data structure in place, we have implemented a piecewise linear interface reconstruction algorithm in 3 dimensions that effectively exploits the symmetry present in a uniform rectilinear computational cell. Finally, we report performance results, which show that a single implementation of these algorithms can be compiled to multiple backends (specifically, multi-core CPUs, NVIDIA GPUs, and Intel Xeon Phi processors), making efficient use of the available parallelism on each. We also compare performance of our implementation to a legacy FORTRAN implementation in Message Passing Interface (MPI) and show performance parity on single and multi-core CPU and achieved good parallel speed-ups on GPU. In conclusion, our research demonstrates the advantage of performance portability of the underlying data-parallel programming model.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

A view into FleCSI [Slides]

FleCSI is largely based around sharing of memory spaces. FleCSI facilitates parallel execution and sharing of memory across memory spaces. Execute() transforms sender-side data structures into receiver-side data structures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Core Model Proposal #410: Updates to Socioeconomic and Macroeconomic Data, Processing Structure, and Visualization

This Core Model Proposal (CMP) comprehensively restructures and updates the macroeconomic and socioeconomic modules in gcamdata. It includes visualizations of key data inputs, accounting identities, and data flows in the context of GCAM-Macro-KLEM. Major improvements include: (1) updating the Penn World Table (PWT) to version 10 and incorporating a new source, the Global Macro Database (GMD); (2) updating the SSP socioeconomics database from version 3.0.1 to 3.2; (3) introducing SSP-specific differentiation of employment and labor force data; (4) improving data integration between national accounts (from PWT, GMD, and GTAP) and GDP/population data from external sources; and (5) general data cleaning and structural refinements. We document the data sources and key assumptions used throughout the processing. These updates establish the foundation for the forthcoming KLEAM version of GCAM-macro.

97 MATHEMATICS AND COMPUTING↗