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At least 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

ARCH: Large-scale knowledge graph via aggregated narrative codified health records analysis

Objective: Electronic health record (EHR) systems contain a wealth of clinical data stored as both codified data and free-text narrative notes (NLP). The complexity of EHR presents challenges in feature representation, information extraction, and uncertainty quantification. Here, to address these challenges, we proposed an efficient Aggregated naRrative Codified Health (ARCH) records analysis to generate a large-scale knowledge graph (KG) for a comprehensive set of EHR codified and narrative features. Methods: Using data from 12.5 million Veterans Affairs patients, ARCH first derives embedding vectors and generates similarities along with associated p-values to measure the strength of relatedness between clinical features with statistical certainty quantification. Next, ARCH performs a sparse embedding regression to remove indirect linkage between features to build a sparse KG. Finally, ARCH was validated on various clinical tasks, including detecting known relationships between entity pairs, predicting drug side effects, disease phenotyping, as well as sub-typing Alzheimer’s disease patients. Results: ARCH produces high-quality clinical embeddings and KG for over 60,000 codified and narrative EHR concepts. The KG and embeddings are visualized in the R-shiny powered web-API.3 ARCH achieved high accuracy in detecting EHR concept relationships, with AUCs of 0.926 (codified) and 0.861 (NLP) for similar EHR concepts, and 0.810 (codified) and 0.843 (NLP) for related pairs. It detected drug side effects with a 0.723 AUC, which improved to 0.826 after fine-tuning. Using both codified and NLP features, the detection power increased significantly. Compared to other methods, ARCH has superior accuracy and enhances weakly supervised phenotyping algorithms’ performance. Notably, it successfully categorized Alzheimer’s patients into two subgroups with varying mortality rates. Conclusion: The proposed ARCH algorithm generates large-scale high-quality semantic representations and knowledge graph for both codified and NLP EHR features, useful for a wide range of predictive modeling tasks.

Electronic health records↗
DOE OSTI2022

Ionic Liquid Sheath Stabilizes Atomically Dispersed Reduced Graphene Aerogel‐Supported Iridium Complexes during Ethylene Hydrogenation Catalysis

Abstract An atomically dispersed reduced graphene aerogel (rGA)‐supported iridium catalyst having reactive ethylene ligands was synthesized at an iridium loading of 9.9 wt % and coated with an ionic liquid, 1‐ethyl‐3‐methylimidazolium acetate ([EMIM][OAc]). Continuous‐scan X‐ray absorption spectra demonstrated that the iridium remained site‐isolated in flowing equimolar C 2 H 4 and H 2 during a temperature ramp to 100 °C. The data further showed the lack of detectable iridium aggregation when the feed was H 2 ‐rich or even pure H 2 at 100 °C. An Arrhenius plot determined for ethylene hydrogenation catalysis with the sample in flowing equimolar ethylene and hydrogen showed no variation in the apparent activation energy at temperatures up to 100 °C, confirming that the active sites remained intact at the higher temperatures. The results point to opportunities for overcoming the stability limitations of atomically dispersed supported noble metal catalysts by choice of electron‐donor supports and ionic liquid sheaths.

Kurtoğlu‐Öztulum, Samira F.↗
DOE OSTI2017

Generating short-term probabilistic wind power scenarios via nonparametric forecast error density estimators: Generating short-term probabilistic wind power scenarios via nonparametric forecast error density estimators

Forecasts of available wind power are critical in key electric power systems operations planning problems, including economic dispatch and unit commitment. Such forecasts are necessarily uncertain, limiting the reliability and cost effectiveness of operations planning models based on a single deterministic or “point” forecast. A common approach to address this limitation involves the use of a number of probabilistic scenarios, each specifying a possible trajectory of wind power production, with associated probability. We present and analyze a novel method for generating probabilistic wind power scenarios, leveraging available historical information in the form of forecasted and corresponding observed wind power time series. We estimate non-parametric forecast error densities, specifically using epi-spline basis functions, allowing us to capture the skewed and non-parametric nature of error densities observed in real-world data. We then describe a method to generate probabilistic scenarios from these basis functions that allows users to control for the degree to which extreme errors are captured.We compare the performance of our approach to the current state-of-the-art considering publicly available data associated with the Bonneville Power Administration, analyzing aggregate production of a number of wind farms over a large geographic region. Finally, we discuss the advantages of our approach in the context of specific power systems operations planning problems: stochastic unit commitment and economic dispatch. Here, our methodology is embodied in the joint Sandia – University of California Davis Prescient software package for assessing and analyzing stochastic operations strategies.

17 WIND ENERGY↗
DOE OSTI2024

A practical approach to using the Genomic Standards Consortium MIxS reporting standard for comparative genomics and metagenomics

Comparative analysis of (meta)genomes necessitates aggregation, integration, and synthesis of well-annotated data using standards. The Genomic Standards Consortium (GSC) collaborates with the research community to develop and maintain the Minimal Information about any (x) Sequence (MIxS) reporting standard for genomic data. To facilitate use of the GSC’s MIxS reporting standard, we provide a description of the structure and terminology, how to navigate ontologies for required terms in MIxS, and demonstrate practical usage through a soil metagenome example.

standards, metadata, genome, metagenome, schema, v↗
DOE OSTI2020

Scalable line and plane relaxation in a parallel structured multigrid solver

The efficient solution of sparse, linear systems that arise through the discretization of partial differential equations remains a key challenge for a range of high performance scientific simulations. One approach for reducing data movement and improving performance is by exposing and exploiting structure in a problem through the use of robust structured multilevel solvers. By choosing coarsening that preserves the structure of the problem, these methods maintain efficient structured computation and communication throughout the multigrid hierarchy. However, when coarsening is not permitted to be dependent on the operator, anisotropy must be addressed by the smoother — producing error compatible for coarse-grid correction with structured coarsening. Here, the components required in a scalable parallel structured solver are described with a focus on memory and communication efficiency of robust smoothers. While the implementation of communication and memory reduction techniques in smoothers integrated in a complete 3D solver present a significant engineering challenge, a novel approach is proposed that addresses these challenges systematically through a change to the solver’s execution model. Enabled by user-level threading paired with a set of data and communication abstractions, this approach permits seamless aggregation of communication in plane smoothers — directly reusing code for a 2D distributed multilevel cycle. Results show an effective reduction in communication costs for coarse-grid problems, and result in a speedup of 8.7x in smoothing routines shown in Fig. 12 using this approach. This produces a significant improvement to strong scalability while maintaining favorable weak scaling behavior. Finally, a parallel scaling study using a series of refined meshes is included that demonstrates the effectiveness of this approach in an application of interest.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Light absorption and plasmon – exciton interaction in three-layer nanorods with a gold core and outer shell composed of molecular J- and H-aggregates of dyes

Optical properties of hybrid rod-like nanoparticles, consisting of a gold core, an intermediate passive organic layer (spacer) and outer layer of ordered molecular cyanine dye aggregates, are experimentally and theoretically investigated. It is shown that these dyes can form not only ordered J-aggregates but also H-aggregates (differing by the packing angle of dye molecules in an aggregate and having other spectral characteristics) in the outer shell of the hybrid nanostructure. Absorption spectra of synthesised three-layer nanorods are recorded, and their sizes are determined. The optical properties of the composite nanostructures under study are found to differ significantly, depending on the type of the molecular aggregate formed in the outer shell. The experimental data are quantitatively explained based on computer simulation using the finite-difference time-domain (FDTD) method, and characteristic features of the plasmon – exciton interaction in the systems under study are revealed. (nanophotonics)

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Optimizing the Four-Index Integral Transform Using Data Movement Lower Bounds Analysis

The four-index integral transform is a fundamental and computationally demanding calculation used in many computational chemistry suites such as NWChem. It transforms a four-dimensional tensor from an atomic basis to a molecular basis. This transformation is most efficiently implemented as a sequence of four tensor contractions that each contract a four-dimensional tensor with a two-dimensional transformation matrix. Differing degrees of permutation symmetry in the intermediate and final tensors in the sequence of contractions cause intermediate tensors to be much larger than the final tensor and limit the number of electronic states in the modeled systems. Loop fusion, in conjunction with tiling, can be very effective in reducing the total space requirement, as well as data movement. However, the large number of possible choices for loop fusion and tiling, and data/computation distribution across a parallel system, make it challenging to develop an optimized parallel implementation for the four-index integral transform. We develop a novel approach to address this problem, using lower bounds modeling of data movement complexity. We establish relationships between available aggregate physical memory in a parallel computer system and ineffective fusion configurations, enabling their pruning and consequent identification of effective choices and a characterization of optimality criteria. This work has resulted in the development of a significantly improved implementation of the four-index transform that enables higher performance and the ability to model larger electronic systems than the current implementation in the NWChem quantum chemistry software suite.

Rajbhandari, Samyam↗
NASA NTRS1979

The crop assessment subsystem: System implementation and approaches used for the generation of crop production reports

The primary responsibility of the crop assessment subsystem (CAS) during the three phases of LACIE was to produce crop reports that included estimates of wheat area, yield, and production, as well as a specified set of associated statistical descriptors. The operations of CAS are described with emphasis on sampling strategy, input/output data, evolution of aggregation/reporting system capabilities, and CAS aggregation procedures.

Mcallum, W. E.↗
NASA NTRS2001

A Boundary Condition for Simulation of Flow Over Porous Surfaces

A new boundary condition is presented.for simulating the flow over passively porous surfaces. The model builds on the prior work of R.H. Bush to eliminate the need for constructing grid within an underlying plenum, thereby simplifying the numerical modeling of passively porous flow control systems and reducing computation cost. Code experts.for two structured-grid.flow solvers, TLNS3D and CFL3D. and one unstructured solver, USM3Dns, collaborated with an experimental porosity expert to develop the model and implement it into their respective codes. Results presented,for the three codes on a slender forebody with circumferential porosity and a wing with leading-edge porosity demonstrate a good agreement with experimental data and a remarkable ability to predict the aggregate aerodynamic effects of surface porosity with a simple boundary condition.

Frink, Neal T.↗
NASA NTRS2010

Processing AIRS Scientific Data Through Level 3

The Atmospheric Infra-Red Sounder (AIRS) Science Processing System (SPS) is a collection of computer programs, known as product generation executives (PGEs). The AIRS SPS PGEs are used for processing measurements received from the AIRS suite of infrared and microwave instruments orbiting the Earth onboard NASA's Aqua spacecraft. Early stages of the AIRS SPS development were described in a prior NASA Tech Briefs article: Initial Processing of Infrared Spectral Data (NPO-35243), Vol. 28, No. 11 (November 2004), page 39. In summary: Starting from Level 0 (representing raw AIRS data), the AIRS SPS PGEs and the data products they produce are identified by alphanumeric labels (1A, 1B, 2, and 3) representing successive stages or levels of processing. The previous NASA Tech Briefs article described processing through Level 2, the output of which comprises geo-located atmospheric data products such as temperature and humidity profiles among others. The AIRS Level 3 PGE samples selected information from the Level 2 standard products to produce a single global gridded product. One Level 3 product is generated for each day s collection of Level 2 data. In addition, daily Level 3 products are aggregated into two multiday products: an eight-day (half the orbital repeat cycle) product and monthly (calendar month) product.

Granger, Stephanie↗
DOE OSTI2022

Stream Temperature Predictions for River Basin Management in the Pacific Northwest and Mid-Atlantic Regions Using Machine Learning

Stream temperature (Ts) is an important water quality parameter that affects ecosystem health and human water use for beneficial purposes. Accurate Ts predictions at different spatial and temporal scales can inform water management decisions that account for the effects of changing climate and extreme events. In particular, widespread predictions of Ts in unmonitored stream reaches can enable decision makers to be responsive to changes caused by unforeseen disturbances. In this study, we demonstrate the use of classical machine learning (ML) models, support vector regression and gradient boosted trees (XGBoost), for monthly Ts predictions in 78 pristine and human-impacted catchments of the Mid-Atlantic and Pacific Northwest hydrologic regions spanning different geologies, climate, and land use. The ML models were trained using long-term monitoring data from 1980–2020 for three scenarios: (1) temporal predictions at a single site, (2) temporal predictions for multiple sites within a region, and (3) spatiotemporal predictions in unmonitored basins (PUB). In the first two scenarios, the ML models predicted Ts with median root mean squared errors (RMSE) of 0.69–0.84 °C and 0.92–1.02 °C across different model types for the temporal predictions at single and multiple sites respectively. For the PUB scenario, we used a bootstrap aggregation approach using models trained with different subsets of data, for which an ensemble XGBoost implementation outperformed all other modeling configurations (median RMSE 0.62 °C).The ML models improved median monthly Ts estimates compared to baseline statistical multi-linear regression models by 15–48% depending on the site and scenario. Air temperature was found to be the primary driver of monthly Ts for all sites, with secondary influence of month of the year (seasonality) and solar radiation, while discharge was a significant predictor at only 10 sites. The predictive performance of the ML models was robust to configuration changes in model setup and inputs, but was influenced by the distance to the nearest dam with RMSE <1 °C at sites situated greater than 16 and 44 km from a dam for the temporal single site and regional scenarios, and over 1.4 km from a dam for the PUB scenario. Our results show that classical ML models with solely meteorological inputs can be used for spatial and temporal predictions of monthly Ts in pristine and managed basins with reasonable (<1 °C) accuracy for most locations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

FFT-based model for irradiated aggregate microstructures in concrete

The concrete biological shield of light water reactors is exposed to neutron and gamma irradiation throughout its lifetime, which results in the long-term degradation of the concrete’s mechanical properties. Under neutron irradiation, the concrete’s aggregates are subjected to radiation-induced volumetric expansion (RIVE), which strongly depends on the mineral content of the aggregate and exhibits the largest expansion in silicate-bearing minerals. In this work, the authors used the fast Fourier transform-based code Microstructure-Oriented Scientific Analysis of Irradiated Concrete (MOSAIC) in 2D to model the expansion of five different aggregates provided by the Japan Concrete Aging Management Program (JCAMP). Comparable rock specimens were irradiated at the JEEP-II test reactor. The model uses realistic aggregate microstructure reconstruction based on high-resolution characterization images. The model accounts for anisotropic RIVE, thermal expansion, and the associated initiation and propagation of damage. The RIVE models are calibrated based on expansion data in the literature. The authors assume that damage occurs exclusively at interfaces between the particles that compose an aggregate and that these interfaces also exhibit swelling. Using a micromechanical model, the evolution of Young’s modulus with RIVE is calculated for each aggregate and compared with Russian irradiation data. The modeled linear expansion agrees well with the experimentally measured expansion. Furthermore, the model also predicts that anisotropic RIVE and thermal expansion result in an earlier onset of damage with neutron fluence than in the isotropic case.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markov process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.

36 MATERIALS SCIENCE↗
DOE OSTI2019

A Unified Ice Microphysical Parameterization for Numerical Models: Development and Testing with In-situ Data

The primary goal of the project is to develop and test new microphysical parameterizations of ice crystal growth. Over the past 7 years, we have developed a bulk ice microphysical model that evolves a measure of particle shape and density during vapor diffusional growth. The method allows smaller, pristine ice crystals to evolve into larger snow crystals in a more natural fashion than traditional microphysical schemes. In doing so, the new method avoids problems that occur when ice is transferred among pre-defined classes. The new model was developed and tested for vapor grown ice only, and so the goal of this project is to develop bulk parameterizations of the missing physics for the model including the prediction of surface deposition coefficients, riming, and aggregation. The parameterizations are being developed using prior laboratory data as a constraint, and then will be tested in simulations of case studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2012

Constructing a Database from Multiple 2D Images for Camera Pose Estimation and Robot Localization

The LMDB (Landmark Database) Builder software identifies persistent image features (landmarks) in a scene viewed multiple times and precisely estimates the landmarks 3D world positions. The software receives as input multiple 2D images of approximately the same scene, along with an initial guess of the camera poses for each image, and a table of features matched pair-wise in each frame. LMDB Builder aggregates landmarks across an arbitrarily large collection of frames with matched features. Range data from stereo vision processing can also be passed to improve the initial guess of the 3D point estimates. The LMDB Builder aggregates feature lists across all frames, manages the process to promote selected features to landmarks, and iteratively calculates the 3D landmark positions using the current camera pose estimations (via an optimal ray projection method), and then improves the camera pose estimates using the 3D landmark positions. Finally, it extracts image patches for each landmark from auto-selected key frames and constructs the landmark database. The landmark database can then be used to estimate future camera poses (and therefore localize a robotic vehicle that may be carrying the cameras) by matching current imagery to landmark database image patches and using the known 3D landmark positions to estimate the current pose.

Wolf, Michael↗
NASA NTRSDate not supplied

High Performance Access to Archival Data Stored in HDF4 and HDF5 on Cloud Object Stores Without Reformatting the Files

Cloud computing offers numerous advantages for users of extensive Earth science data collections. These benefits encompass direct online access to data files and granules from any location, scalable access supporting parallel computing workflows, and flexible computing tools enabling innovative experimentation with processing techniques. However, older archival file formats designed for distinct computing systems hinder efficient access to decade-long time-series data when compared to data stored in modern cloud-optimized formats like Web Object Stores (WOS), exemplified by Amazon Web Services’ Simple Storage Service (S3). We describe DMR++ (Dataset Metadata Response plus plus), a technology facilitating efficient access to HDF5 (Hierarchical Data Format, version 5) and HDF4 files stored on WOS systems without requiring data reformatting. DMR++ achieves performance comparable to technologies like Zarr while preserving the original file structure, a substantial benefit considering the vast quantity of archival files held by organizations such as NASA. Moreover, DMR++ typically outperforms cloud-optimized versions of HDF5. Essentially an XML (Extensible Markup Language) document usually stored alongside the described data, DMR++ can also be generated on-the-fly but is generally created during data staging to the WOS. Archival files that use HDF4/5 often store large arrays of numerical data. The data in these files is often compressed, typically reducing their size by a factor of four or more. To achieve efficient access to portions of those arrays, they are 'chunked' into smaller sub-arrays, each individually compressed. The chunk size is a compromise, where spinning disks can efficiently access data in smaller chunks while S3 favors larger chunks. A simple optimization of aggregating smaller chunks that are stored adjacently, transferring them in a single access and then individually decompressing them will improve performance. NASA data pose an additional challenge: special Application Programmer Interface (API) libraries are often needed to compute some variables. These libraries are incompatible with WOS environments. Our solution involves storing computed values in the DMR++ document or a companion file, making them accessible like other variables and eliminating the need for specialized APIs. We outline specific optimizations for both satellite grid and swath data stored in HDF4-EOS2 (Earth Observing System).

James Gallagher↗
DOE OSTI2014

Radiation effects in concrete for nuclear power plants, Part II: Perspective from micromechanical modeling

The need to understand and characterize the effects of neutron irradiation on concrete has become urgent because of the possible extension of service life of many nuclear power generating stations. Current knowledge is primarily based on a collection of data obtained in test reactors. These results are inherently difficult to interpret because materials and testing conditions are inconsistent. A micromechanical approach based on the Hashin composite sphere model is presented to derive a first-order separation of the effects of radiation on cement paste and aggregate, and, also, on their interaction. Although the scarcity of available data limits the validation of the model, it appears that, without negating a possible gamma-ray induced effect, the neutron-induced damage and swelling of aggregate plays a predominant role on the overall concrete expansion and the damage of the cement paste. Finally, the radiation-induced volumetric expansion (RIVE) effects can also be aided by temperature elevation and shrinkage in the cement paste.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗