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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 19 records

Gene-Metabolite Association Prediction with Interactive Knowledge Transfer Enhanced Graph for Metabolite Production

Identifying gene targets for enhancing metabolite production in metabolic engineering is challenging due to the vast research literature and the approximation in genome-scale metabolic model (GEM) simulations. Here, to address this, we propose the Gene-Metabolite Association Prediction task, which automates gene discovery for given metabolite-gene pairs, accompanied by a benchmark dataset of 2474 metabolites and 1947 genes for Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is complicated by incomplete metabolic graphs and metabolic heterogeneity. We introduce an Interactive Knowledge Transfer mechanism based on Metabolism Graphs (IKT4Meta) to enhance prediction accuracy by integrating cross-metabolism knowledge. Using Pretrained Language Models (PLMs) to generate inter-graph links mitigates heterogeneity issues, while intra-graph links are propagated via these anchors. Gene-metabolite predictions are then performed on the enriched graphs integrating multiple microorganisms’ knowledge. Experiments show that IKT4Meta outperforms baselines by up to 12.3% in link prediction.

59 BASIC BIOLOGICAL SCIENCES↗

Logic-based analysis of gene expression data predicts association between TNF, TGFB1 and EGF pathways in basal-like breast cancer

For breast cancer, clinically important subtypes are well characterized at the molecular level in terms of gene expression profiles. In addition, signaling pathways in breast cancer have been extensively studied as therapeutic targets due to their roles in tumor growth and metastasis. However, it is challenging to put signaling pathways and gene expression profiles together to characterize biological mechanisms of breast cancer subtypes since many signaling events result from post-translational modifications, rather than gene expression differences. We designed a logic-based computational framework to explain the differences in gene expression profiles among breast cancer subtypes using Pathway Logic and transcriptional network information. Pathway Logic is a rewriting-logic-based formal system for modeling biological pathways including post-translational modifications. Our method demonstrated its utility by constructing subtype-specific path from key receptors (TNFR, TGFBR1 and EGFR) to key transcription factor (TF) regulators (RELA, ATF2, SMAD3 and ELK1) and identifying potential association between pathways via TFs in basal-specific paths, which could provide a novel insight on aggressive breast cancer subtypes. Lastly, codes and results are available at http://epigenomics.snu.ac.kr/PL/.

59 BASIC BIOLOGICAL SCIENCES↗

Models, data, and scripts associated with “Prediction of Distributed River Sediment Respiration Rates using Community-Generated Data and Machine Learning”

This data package is associated with the publication “Prediction of Distributed River Sediment Respiration Rates using Community-Generated Data and Machine Learning’’ submitted to the Journal of Geophysical Research: Machine Learning and Computation (Scheibe et al. 2024). River sediment respiration observations are expensive and labor intensive to obtain and there is no physical model for predicting this quantity. The Worldwide Hydrobiogeochemisty Observation Network for Dynamic River Systems (WHONDRS) observational data set (Goldman et al.; 2020) is used to train machine learning (ML) models to predict respiration rates at unsampled sites. This repository archives training data, ML models, predictions, and model evaluation results for the purposes of reproducibility of the results in the associated manuscript and community reuse of the ML models trained in this project. One of the key challenges in this work was to find an optimum configuration for machine learning models to work with this feature-rich (i.e. 100+ possible input variables) data set. Here, we used a two-tiered approach to managing the analysis of this complex data set: 1) a stacked ensemble of ML models that can automatically optimize hyperparameters to accelerate the process of model selection and tuning and 2) feature permutation importance to iteratively select the most important features (i.e. inputs) to the ML models. The major elements of this ML workflow are modular, portable, open, and cloud-based, thus making this implementation a potential template for other applications. This data package is associated with the GitHub repository found at Please see the file level metadata (flmd; “sl-archive-whondrs_flmd.csv”) for a list of all files contained in this data package and descriptions for each. Please see the data dictionary (dd; “sl-archive-whondrs_dd.csv”) for a list of all column headers contained within comma separated value (csv) files in this data package and descriptions for each. The GitHub repository is organized into five top-level directories: (1) “input_data” holds the training data for the ML models; (2) “ml_models” holds machine learning models trained on the data in “input_data”; (3) “scripts” contains data preprocessing and postprocessing scripts and intermediate results specific to this data set that bookend the ML workflow; (4) “examples” contains the visualization of the results in this repository including plotting scripts for the manuscript (e.g., model evaluation, FPI results) and scripts for running predictions with the ML models (i.e., reusing the trained ML models); (5) “output_data” holds the overall results of the ML model on that branch. Each trained ML model resides on its own branch in the repository; this means that inputs and outputs can be different branch-to-branch. Furthermore, depending on the number of features used to train the ML models, the preprocessing and postprocessing scripts, and their intermediate results, can also be different branch-to-branch. The “main-*” branches are meant to be starting points (i.e. trunks) for each model branch (i.e. sprouts). Please see the Branch Navigation section in the top-level README.md in the GitHub repository for more details. There is also one hidden directory “.github/workflows”. This hidden directory contains information for how to run the ML workflow as an end-to-end automated GitHub Action but it is not needed for reusing the ML models archived here. Please the top-level README.md in the GitHub repository for more details on the automation.

13C↗

Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits

Abstract Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.

59 BASIC BIOLOGICAL SCIENCES↗

An Experimental Study of Uncertainty Considerations Associated with Predicting Auto-ignition Timing using Livengood-Wu Integral Method

The application of the Livengood-Wu (LW) integral method as a tool to estimate knock onset in spark ignited (SI) engines and combustion phasing in advanced compression ignition (ACI) engines has been demonstrated through simulations several times. In this study, the effect of uncertainties associated with parameters required for the LW integral method, when used as a tool for model based control of ignition timing in an ACI engine, were experimentally studied using five full boiling range gasoline fuels. As a first step, the method was applied to experimental data from a rapid compression machine and it was found that the ability of the LW integral method to predict ignition timing was very sensitive to the performance of the chemical kinetic model of each fuel. The method was subsequently applied to experimental data from a single-cylinder gasoline engine with simple approximations for the LW integral input parameters, and it was found that the predicted time of ignition was significantly different from the actual start of combustion. Systematic evaluation of various parametric uncertainties conducted thereafter showed that the uncertainty in cylinder charge temperature has the greatest influence. Improved methods of estimating cylinder charge temperature are proposed to account for the previously determined corrections, to enable the use of the LW integral method for model based control of ignition timing.

Compression Ignition↗

Automated Cloud Based Long Short-Term Memory Neural Network Based SWE Prediction

Snow derived water is a critical component of the US water supply. Measurements of the Snow Water Equivalent (SWE) and associated predictions of peak SWE and snowmelt onset are essential inputs for water management efforts. This paper aims to develop an integrated framework for real-time data ingestion, estimation, prediction and visualization of SWE based on daily snow datasets. In particular, we develop a data-driven approach for estimating and predicting SWE dynamics using the Long Short-Term Memory neural network (LSTM) method. Our approach uses historical datasets (precipitation, air temperature, SWE, and snow thickness) collected at NRCS Snow Telemetry (SNOTEL) stations to train the LSTM network and current year data to predict SWE behavior. The performance of our prediction was compared for different prediction dates and prediction training datasets. Our results suggest that the proposed LSTM network can be an efficient tool for forecasting the SWE timeseries, as well as Peak SWE and snowmelt timing. Results showed that the window size impacts the model performance (where the Nash Sutcliffe efficiency (NSE) ranged from 0.96 to 0.85 and the Rooted Mean Square Error (RMSE) ranged from 0.038 to 0.07) with an optimum number that should be calibrated for different stations and climate conditions. In addition, by implementing the LSTM prediction capability in a cloud based site-monitoring platform, we automate model-data integration. By making the data accessible through a graphical web interface and an underlying API which exposes both training and prediction capabilities. The associated results can be made easily accessible to a broad range of stakeholders.

54 ENVIRONMENTAL SCIENCES↗

Assessing decadal variability of subseasonal forecasts of opportunity using explainable AI

Abstract Identifying predictable states of the climate system allows for enhanced prediction skill on the generally low-skill subseasonal timescale via forecasts with higher confidence and accuracy, known as forecasts of opportunity. This study takes a neural network approach to explore decadal variability of subseasonal predictability, particularly during forecasts of opportunity. Specifically, this work quantifies subseasonal prediction skill provided by the tropics within the Community Earth System Model Version 2 (CESM2) Large Ensemble and assesses how this skill evolves on decadal timescales. Utilizing the networks’ confidence and explainable artificial intelligence, physically meaningful sources of predictability associated with periods of enhanced skill are identified. Using these networks, we find that tropically-driven subseasonal predictability varies on decadal timescales during forecasts of opportunity. Further, we investigate the drivers of the low frequency modulation of the tropical-extratropical teleconnection and discuss the implications. Analysis is extended to ECMWF Reanalysis v5 data, revealing that the relationships learned within the CESM2-Large Ensemble holds in modern reanalysis data. These results indicate that the neural networks are capable of identifying predictable decadal states of the climate system within CESM2 that are useful for making confident, accurate subseasonal precipitation predictions in the real world.

54 ENVIRONMENTAL SCIENCES↗

Quantified uncertainties in fission yields from machine learning

As machine learning methods gain traction in the nuclear physics community, especially those methods that aim to propagate uncertainties to unmeasured quantities, it is important to understand how the uncertainty in the training data coming either from theory or experiment propagates to the uncertainty in the predicted values. Gaussian Processes and Bayesian Neural Networks are being more and more widely used, in particular to extrapolate beyond measured data. However, studies are typically not performed on the impact of the experimental errors on these extrapolated values. In this work, we focus on understanding how uncertainties propagate from input to prediction when using machine learning methods. We use a Mixture Density Network (MDN) to incorporate experimental error into the training of the network and construct uncertainties for the associated predicted quantities. Systematically, we study the effect of the size of the experimental error, both on the reproduced training data and extrapolated predictions for fission yields of actinides.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids

This dataset contains all data used in the paper "Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids". The dataset includes genotypes and phenotypic data from two autotetraploid species Miscanthus sacchariflorus and Vaccinium corymbosum that was used used for genome wide association studies and genomic prediction and the scripts used in the analysis. In this V2, 2 files have the raw data are added: "Miscanthus_sacchariflorus_RADSeq.vcf" is the VCF file with the raw SNP calls of the Miscanthus sacchariflorus data used for genotype calling using the 6 genotype calling methods. "Blueberry_data_read_depths.RData" is the a RData file with the read depth data that was used for genotype calling in the Blueberry dataset.

allelic dosage↗

High-resolution modeling of indoor radon exposure with uncertainty quantification in Utah

Indoor radon accounts for 37% of population-level exposure to ionizing radiation in the United States. However, radon metrics are typically reported at coarse spatial scales, potentially obscuring meaningful local variation. We developed a high-resolution modeling framework to estimate indoor radon concentrations across Utah while explicitly quantifying predictive uncertainty. A total of 19,497 residential radon measurements collected between 2006 and 2017 were combined with environmental and housing characteristics and analyzed using a geospatial neural network that accommodates spatial dependence and nonlinear associations. Predictions were generated on a uniform hexagonal grid at 0.73 km2 resolution (H3 level 8). Out-of-sample predictions aggregated to the H3 level 8 grid showed good agreement with observed concentrations (Pearson r=0.64), while household-level predictions exhibited more moderate agreement (r=0.45). The model produced well-calibrated uncertainty estimates, with 24.1% of held-out observations exceeding the predicted 75th-percentile threshold. Maps of predicted radon concentrations and the probability of exceeding the U.S. EPA action level of 148 Bq/m3 (4 pCi/L) revealed substantial fine-scale spatial heterogeneity that was not apparent in conventional coarse-resolution summaries, with greater local variability observed in densely monitored urban counties than in sparsely sampled regions. High-resolution radon models that explicitly quantify uncertainty provide a useful framework for characterizing the spatial distribution of indoor radon and identifying areas of elevated exceedance risk. These findings highlight the value of fine-scale monitoring data and uncertainty-aware modeling approaches for radon exposure assessment, environmental risk characterization, and radon-related health research.

Wu, Yunhan [ORNL] (ORCID:0000000178842994)↗

Synthesis of Mg2IrH5: A potential pathway to high-Tc hydride superconductivity at ambient pressure

Following long-standing predictions associated with hydrogen, high-temperature superconductivity has recently been observed in several hydride-based materials. Nevertheless, these high-Tc phases only exist at extremely high pressures, and achieving high transition temperatures at ambient pressure remains a major challenge. Recent predictions of the complex hydride Mg2IrH6 may help overcome this challenge with calculations of high-Tc superconductivity (65K

High-temperature superconductors↗

Updating and Refining BISON TRISO Assessment

Several advanced reactor concepts consider tristructural isotropic (TRISO) fuel in their designs. To support the advanced reactor industry, the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program within the U.S. Department of Energy (DOE) is developing modeling and simulation capabilities within the BISON fuel performance code. Assessment of these capabilities against available experi- mental data, such as the Advanced Gas Reactor (AGR) program, is essential in instilling confidence in the code predictions. Associated uncertainties in model inadequacy, experimental measurements, and manufacturing are also of importance. This report discusses the updating and standardization of the existing assessment suite in BISON for TRISO fuel performance analysis. The cases considered the AGR-1, AGR-2, and AGR-3/4 experimental programs. The report also includes a preliminary investigation into the sources of model inadequacy associated with silver (Ag) release fractions using the AGR-2 Compact 2-1-2 as a case study. The results indicate that uncertainties in the operating temperatures supplied to the model and the form of those temperature conditions (spatially averaged versus spatially resolved) both affect Ag release predictions. This suggests that previously observed model inadequacy can be attributed to both physical models and the operating conditions supplied to them. These findings will be leveraged to guide development of assessment cases for additional experiments and refinement of physical models for behaviors that potentially influence Ag release, such as palladium penetration.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities

Viruses play important roles in the ocean’s biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities or how they interact with their free-living or particle-attached microbial hosts. We analysed 58 viral communities associated with size-fractionated free-living (0.2–0.8 μm) and particle-attached (0.8–20 μm) cellular metagenomes from bathypelagic (2150–4018 m deep) microbiomes obtained during the Malaspina expedition. These metagenomes yielded 6631 viral sequences, 91% of which were novel, and 67 represented high-quality genomes. Taxonomic classification assigned 53% of the viral sequences to families of tailed viruses from the order Caudovirales. Computational host prediction associated 886 viral sequences to dominant members of the deep ocean microbiome, such as Alphaproteobacteria (284), Gammaproteobacteria (241), SAR324 (23), Marinisomatota (39), and Chloroflexota (61). Free-living and particle-attached viral communities had markedly distinct taxonomic composition, host prevalence, and auxiliary metabolic gene content, which led to the discovery of novel viral-encoded metabolic genes involved in the folate and nucleotide metabolisms. Water mass age emerged as an important factor driving viral community composition. We postulated this was due to changes in quality and concentration of dissolved organic matter acting on the host communities, leading to an increase of viral auxiliary metabolic genes associated with energy metabolism among older water masses. These results shed light on the mechanisms by which environmental gradients of deep ocean ecosystems structure the composition and functioning of free-living and particle-attached viral communities.

59 BASIC BIOLOGICAL SCIENCES↗

Develop a weather-aware climate model to understand and predict extremes and associated power outages and renewable energy shortages with uncertainty-aware and physics-informed machine learning

Focal Area(s): The focus area is predictive modeling through the use of AI techniques and AI-derived model components with a particular emphasis on extreme weather in Atmospheric Science and power outages and shortages in Energy Science. Science Challenge: Predicting weather extremes (e.g., heavy precipitation, strong wind, and large hailstones), and weather-related power system outages and shortages can mitigate economic losses, save lives, support renewables integration, and improve power system resiliency. However, currently, the poor reliability and large uncertainty associated with the weather extreme prediction in the current climate models make the problem intractable. The key challenges are: (1) physical factors like green-house gases (GHGs), aerosols, and land use and land cover (LULC) can significantly impact extreme storms, but the understanding of these impacts is limited, particularly globally; (2) the convective permitting resolutions needed to model severe convective storms and their impacts are computationally prohibitive with global climate models (GCMs); (3) interactions between weather extremes and power system outages are complex and subject to great uncertainty. Current outage prediction models are short lead (~ 3 days), which do not allow for long-time planning of energy production and distribution. Moreover, we have limited capacity to predict weather events leading to sustained shortages in a renewable-energy-dominated power system. These challenges drive motivation for mechanistic understanding and reliable and efficient predictive modeling of extremes and their impacts from the sub-seasonal to long term projections.

54 ENVIRONMENTAL SCIENCES↗

Genome‐wide association and genomic prediction for yield and component traits of Miscanthus sacchariflorus

Abstract Accelerating biomass improvement is a major goal of Miscanthus breeding. The development and implementation of genomic‐enabled breeding tools, like marker‐assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of Miscanthus breeding. The present study conducted genome‐wide association (GWA) and genomic prediction of biomass yield and 14 yield‐components traits in Miscanthus sacchariflorus . We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across 4 years in one subtropical and three temperate locations and genotyped with 268,109 single‐nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported Miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield‐component traits in M. sacchariflorus that may facilitate marker‐assisted breeding for biomass yield. Genomic prediction accuracy for the yield‐related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia ( N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus . This study indicated that MAS and genomic prediction will likely be beneficial for conducting population‐improvement of M. sacchariflorus .

09 BIOMASS FUELS↗

Data for Genome-Wide Association and Genomic Prediction for Yield and Component Traits of Miscanthus sacchariflorus

Accelerating biomass improvement is a major goal of miscanthus breeding. The development and implementation of genomic-enabled breeding tools, like marker-assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of miscanthus breeding. The present study conducted genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus . We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across four years in one subtropical and three temperate locations and genotyped with 268,109 single-nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield-component traits in M. sacchariflorus that may facilitate marker-assisted breeding for biomass yield. Genomic prediction accuracy for the yield-related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia (N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus . This study indicated that MAS and genomic prediction will likely be beneficial for conducting population-improvement of M. sacchariflorus .

Biomass Analytics↗

Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids

Abstract Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost‐efficient genotyping using next‐generation sequencing. However, accurate genotype calling from next‐generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome‐wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype‐calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum , and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype‐calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost‐efficiently implement GWAS and genomic prediction in polyploid crops.

59 BASIC BIOLOGICAL SCIENCES↗

Knowledge-Guided Machine Learning (KGML) Platform to Predict Integrated Water Cycle and Associated extremes

Focal Area(s): Predictive modeling through the use of AI techniques and insight gleaned from complex data (both observed and simulated). Science Challenge: Although advanced predictive capabilities of the water cycle are critical to address environmental needs and develop sustainable solutions for energy demands, there is no robust framework, to say the least, that seamlessly integrates local to intermediate to global scales and a gamut of biogeophysical information to enhance understanding of the integrated water cycle and its associated extremes.

54 ENVIRONMENTAL SCIENCES↗