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298 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗
DOE OSTI2025

Influence of background sources and topographic resolution in the Weather Research and Forecasting Model on xenon plume characteristics at monitoring stations

For many atmospheric monitoring applications, networks of measurement sites—such as the radionuclide stations of the International Monitoring System—can be sparse. With measurement locations potentially hundreds to thousands of kilometers from a release it is important to quantify the effects of physical processes on transport and dispersion of plumes between source and measurement locations. This study addresses the effects of background sources and topography resolution near the release location of radionuclides. We use the Weather Research and Forecasting (WRF) model with inline chemistry to investigate (1) how an additional, time-varying source of 133 Xe, such as an operational medical isotope production facility, contributes to activity concentration measurements at monitoring sites, and (2) how complex topography influences on atmospheric conditions near emission sources impact plume concentrations at varying distances from the source. Two 133 Xe emission sources, including (1) a high flux rate of short duration representing an explosive event, and (2) a variable and continuous background source, are simulated. The continuous background source contributes significantly to total 133 Xe concentrations at several monitoring stations. Further, a WRF simulation at 9 km horizontal resolution is compared with a nested grid simulation, where the innermost domain has a resolution of 1 km. Increased topographic resolution leads to an improved representation of plume responses to local winds, with topographic influences greatest at locations closest to the sources. Differences between the two domain resolutions decrease at greater distances from the sources, as plumes have time to spread and mix and are influenced by synoptic scale circulation patterns that are represented similarly in both simulations.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRSDate not supplied

Remote Sensing of Lineage Functional Types for Modeling and Monitoring Biodiversity

Hyperspectral remote sensing has the potential to continuously scale plant function and plant diversity information from landscape to global extents. Numerous studies have indicated that VSWIR (400-2500 nm) reflectance properties of vegetation capture evolutionarily conserved biochemical, structural, and other functional attributes of plant species. Spectral properties conserved in plants provide the opportunity to both 1) aggregate species into lineages with improved classification accuracy and 2) link those lineages directly to plant traits. Full realization of this goal will enable parameterization of Land Surface Models (LSMs) with remotely sensed information, e.g., canopy nitrogen, and better representations of biodiversity and functional diversity in biogeographic studies. In this study, we use hyperspectral AVIRIS data from the 2013 HyspIRI campaign over the Southern Sierra Nevada, California flight box to investigate the potential for incorporating evolutionary thinking into landcover classification. We link the airborne hyperspectral data with vegetation plot data from roughly 1372 surveys and a phylogeny representing 1361 species. We aggregate species into lineages ranging from species level groups down to similar number of Plant Functional Types as often used in LSMs. We assessed the ability of Random Forest and Partial Least Squares Discriminant Analysis to discriminate across these different phylogenetic scales and determine the optimal number of lineages to classify. Although there are some temporal and spatial differences in our training data, our best approaches achieved moderate classification accuracy (Kappa > 0.65). Given an optimal number of lineages, we explored approaches to improve classifications including machine learning and unmixing approaches. This work suggests that lineage-based methods may be a promising way to leverage the huge amounts of data that will come from high resolution and high return interval hyperspectral data planned for the Surface Biology and Geology mission with sparsely sampled existing ground-based ecological data.

Hyperspectral↗
DOE OSTI2020

Causal Interactions between Southern Ocean Polynyas and High-Latitude Atmosphere–Ocean Variability

Abstract Weddell Sea open-ocean polynyas have been observed to occasionally release heat from the deep ocean to the atmosphere, indicating that their sporadic appearances may be an important feature of high-latitude atmosphere–ocean variability. Yet, observations of the phenomenon are sparse and many standard-resolution models represent these features poorly, if at all. We use a fully coupled, synoptic-scale preindustrial control simulation of the Energy Exascale Earth System Model (E3SMv0-HR) to effectively simulate open-ocean polynyas and investigate their role in the climate system. Our approach employs statistical tests of Granger causality to diagnose local and remote drivers of, and responses to, polynya heat loss on interannual to decadal time scales. First, we find that polynya heat loss Granger causes a persistent increase in surface air temperature over the Weddell Sea, strengthening the local cyclonic wind circulation. Along with responding to polynyas, atmospheric conditions also facilitate their development. When the Southern Ocean experiences a rapid poleward shift in the circumpolar westerlies following a prolonged negative phase of the southern annular mode (SAM), Weddell Sea salinity increases, promoting density destratification and convection in the water column. Finally, we find that the reduction of surface heat fluxes during periods of full ice cover is not fully compensated by ocean heat transport into the high latitudes. This imbalance leads to a buildup of ocean heat content that supplies polynya heat loss. These results disentangle the complex, coupled climate processes that both enable the polynya’s existence and respond to it, providing insights to improve the representation of these highly episodic sea ice features in climate models.

Kaufman, Zachary S.↗
DOE OSTI2016

Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks

Spatial gene expression patterns enable the detection of local covariability and are extremely useful for identifying local gene interactions during normal development. The abundance of spatial expression data in recent years has led to the modeling and analysis of regulatory networks. The inherent complexity of such data makes it a challenge to extract biological information. We developed staNMF, a method that combines a scalable implementation of nonnegative matrix factorization (NMF) with a new stability-driven model selection criterion. When applied to a set of Drosophila early embryonic spatial gene expression images, one of the largest datasets of its kind, staNMF identified 21 principal patterns (PP). Providing a compact yet biologically interpretable representation of Drosophila expression patterns, PP are comparable to a fate map generated experimentally by laser ablation and show exceptional promise as a data-driven alternative to manual annotations. Our analysis mapped genes to cell-fate programs and assigned putative biological roles to uncharacterized genes. Finally, we used the PP to generate local transcription factor regulatory networks. Spatially local correlation networks were constructed for six PP that span along the embryonic anterior-posterior axis. Using a two-tail 5% cutoff on correlation, we reproduced 10 of the 11 links in the well-studied gap gene network. In conclusion, the performance of PP with the Drosophila data suggests that staNMF provides informative decompositions and constitutes a useful computational lens through which to extract biological insight from complex and often noisy gene expression data.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

Image Dis-Integration for Improved Plasmasphere Visualization

Traditionally, study of the plasmasphere has involved terrestrial observation of local characteristics. Global modeling of the plasmasphere in such an observation regime made use of an ensemble of (sparse) local measurements. Recently, sensors aboard the IMAGE (Imager for Magnetopause-to-Aurora Global Exploration) satellite (in particular, the EUV (Extreme Ultra Violet) Imager) have created the potential for truly global study of the plasmasphere. IMAGE was launched in spring of 2000 in an orbit with apogee altitude 7.2 R E (Earth radii) and perigee altitude 1000 km. IMAGE's EUV sensor allows an external view of the distribution of cold plasma in the plasmasphere to be acquired. EUV is designed to image light emission at 30.4 nanometers, which is the emission wavelength of the He + ion in the presence of solar radiation. He + makes up approximately 15-20% of the plasma in the plasmasphere, thus imaging of He + enables determination of plasma distribution. The EUV instrument provides a 90° by 84° field of view which is imaged as an equally spaced 150x140 pixel array on a spherical imaging surface. The EUV produces an image approximately every 10 minutes when the sensor is operating. Since EUV images contain line-of-sight integrations of plasma distributions, they do not directly express equatorial plane density (which would enable comparison of observed plasma distributions with predictions from models). Furthermore, the plasma density at any point in three-space is not known. The goal of our work was development of a technique that can enable plasma density to be determined throughout three-space. Our approach to creation of a three-space representation of the plasma distribution involves disintegrating the EUV lines of sight to form a volumetric map of plasma densities.

Timothy S. Newman↗
DOE OSTI2016

Combined measurement and modeling of the hydrological impact of hydraulic redistribution using CLM4.5 at eight AmeriFlux sites

Effects of hydraulic redistribution (HR) on hydrological, biogeochemical, and ecological processes have been demonstrated in the field, but the current generation of standard earth system models does not include a representation of HR. Though recent studies have examined the effect of incorporating HR into land surface models, few (if any) have done cross-site comparisons for contrasting climate regimes and multiple vegetation types via the integration of measurement and modeling. Here, we incorporated the HR scheme of Ryel et al. (2002) into the NCAR Community Land Model Version 4.5 (CLM4.5), and examined the ability of the resulting hybrid model to capture the magnitude of HR flux and/or soil moisture dynamics from which HR can be directly inferred, to assess the impact of HR on land surface water and energy budgets, and to explore how the impact may depend on climate regimes and vegetation conditions. Eight AmeriFlux sites with contrasting climate regimes and multiple vegetation types were studied, including the Wind River Crane site in Washington State, the Santa Rita Mesquite savanna site in southern Arizona, and six sites along the Southern California Climate Gradient. HR flux, evapotranspiration (ET), and soil moisture were properly simulated in the present study, even in the face of various uncertainties. Our cross-ecosystem comparison showed that the timing, magnitude, and direction (upward or downward) of HR vary across ecosystems, and incorporation of HR into CLM4.5 improved the model-measurement matches of evapotranspiration, Bowen ratio, and soil moisture particularly during dry seasons. Lastly, our results also reveal that HR has important hydrological impact in ecosystems that have a pronounced dry season but are not overall so dry that sparse vegetation and very low soil moisture limit HR.

58 GEOSCIENCES↗
DOE OSTI2019

A Multiple Lines of Evidence Approach for Conceptual Site Models in Performance Assessments - 19070

Demonstration of the long-term performance of remediated radioactive waste sites relies on models that evaluate vadose zone and groundwater flow and contaminant transport for thousands of years. Model qualification, verification, and comparisons with data are essential elements to demonstrating the accuracy of long-term performance assessments (PAs). However, comparisons with data are generally limited due to incomplete characterization data and long-time scales. Since PAs support decision making to assure long-term protection of both human health and the environment, a conceptual site model (CSM) is needed to explain the hydrodynamic behavior and account for subsurface heterogeneities in sufficient detail to support confident decisions. In the case of the Waste Management Area (WMA) C PA, where the focus of the effort is on characterizing flow and transport through a thick vadose zone, site-specific data are sparse and larger-scale geologic descriptions are adopted with the risk of losing small scale features that may affect contaminant transport. Features such as horizontal bedding and sloping interfaces between contrasting material types, as well as vertically oriented features such as clastic dikes, may be difficult to delineate from sparse characterization data, but may affect the extent to which contaminants are transported. The PA conducted to identify long-term impacts associated with the closure of the single-shell tank (SST) farm at WMA C adopted an equivalent homogenous medium approach to represent the major stratigraphic units at the site. This approach explicitly represents major stratigraphic units but assigns hydraulic properties that implicitly account for the presence of small-scale heterogeneities and their impact on flow and contaminant transport to the groundwater. The objective of this study is to evaluate the available site-specific and analogue data that can be used to characterize heterogeneity and to assess its impact on fate and transport of contaminants that may lead to different conclusions when compared to the results of the equivalent homogeneous media approach. To this end, a multiple lines of evidence approach was used to construct alternative CSMs based on an evaluation of several types of data. These data include 1) general characteristics and features of the major stratigraphic units from historical descriptions; 2) borehole geologic logs; 3) particle size distribution measurements; 4) moisture content measurements; 5) spectral gamma data; and 6) concentrations of key constituents (i.e., Tc-99) in both the vadose zone and groundwater impacted by past releases. Based on an analysis of the available data, lines of evidence are evaluated for consistency and integrated in a consistent manner into scientifically defensible CSMs. Numerical models are then used to evaluate the impact that the explicit representation of heterogeneities has on contaminant transport. Together, the field data and the numerical modeling results indicate that heterogeneity caused by the small-scale features do not have a significant (i.e. greater than a factor of 2) impact on transport below WMA C relative to peak concentrations and arrival times for potential releases from waste tanks. The results of this study underscore the value of using multiple lines of evidence based on the quantity and quality of available data in developing alternative CSMs and evaluating their relative impact on key transport metrics such as arrival times and peak concentration. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Efficient high-fidelity TRISO statistical failure analysis using Bison: Applications to AGR-2 irradiation testing

The ability of tri-structural isotropic (TRISO) fuel to contain fission products is largely dictated by the quality of the manufacturing process, since most of the fission product release is expected to occur due to coating layer failure in a small number of particles containing defects. The Bison fuel performance code has capabilities to predict failure in individual particles, accounting for the presence of defects, and to apply statistical analysis methods to compute the probability of failure in a set of fuel particles. Bison has recently undergone significant development both to improve its physical representations of fuel particle behavior and to improve the efficiency of its statistical failure calculations. Physical model improvements include new capabilities to account for the pressure generated by fission gases on inner pyrolytic carbon (IPyC) crack surfaces and to use local material coordinate orientation to accurately incorporate the anisotropy in the material properties in aspherical particles. To improve statistical modeling efficiency, a direct integration approach which involves directly integrating the failure probability function associated with statistically varying parameters has been developed. The direct integration approach is much more efficient than the Monte Carlo (MC) schemes commonly employed, and allows Bison to directly run high-dimensional fuel performance models, which improves the accuracy of failure probability calculations. Finally, a set of benchmark problems is considered here to compare the MC and direct integration approaches, and a statistical failure analysis of compacts in the Advanced Gas Reactor (AGR)-2 experiments is performed using the direct integration approach.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Using MODIS estimates of fractional snow cover area to improve streamflow forecasts in interior Alaska

Remotely sensed snow cover observations give an opportunity to improve operational snow melt and stream flow forecasting in remote regions. This is particularly true in Alaska, where remote basins and a spatially and temporally sparse gaging network plague efforts to understand and forecast the hydrology of subarctic boreal basins and where climate change is leading to rapid shifts in basin function. In this study,the operational framework employed by the United States (US) National Weather Service, including the Alaska Pacific River Forecast Center, is adapted to integrate Moderate Resolution Imaging Spectroradiometer (MODIS) remotely sensed observations of fractional snow cover area (fSCA) to determine if these data improve streamflow forecasts in interior Alaska river basins. Two versions of MODIS fSCA are tested against a base case extent of snow cover derived by aerial depletion curves: the MODIS 10A1(MOD10A1) and the MODIS Snow Cover Area and Grain size (MODSCAG) product over the period 2000–2010. Observed runoff is compared to simulated runoff to calibrate both iterations of the model. MODIS-forced simulations haveimproved snow depletion timing compared with snow telemetry sites in the basins, with discernable increases in skill for the streamflow simulations.The MODSCAG fSCA version provides moderate increases in skill but is similar to the MOD10A1 results. The basins with the largest improvement in streamflow simulations have the sparsest streamflow observations.Considering the numerous low-quality gages (discontinuous, short, or unreliable) and ungauged systems throughout the high-latitude regions of the globe, this result is valuable and indicates the utility of the MODIS fSCAdata in these regions. Additionally, while improvements in predicted discharge values are subtle, the snow model better represents the physical conditions of the snow pack and therefore provides more robust simulations,which are consistent with the US National Weather Service's move toward a physically based National Water Model. Physically based models may also be more capable of adapting to changing climates than statistical models corrected to past regimes. This work provides direction for both the Alaska Pacific River Forecast Center and other forecast centers across the US to implement remote-sensing observations within their operational framework, to refine the representation of snow, and to improve streamflow forecasting skill in basins with few or poor-quality observations.

54 ENVIRONMENTAL SCIENCES↗