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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cross-national analysis of food security drivers: comparing results based on the Food Insecurity Experience Scale and Global Food Security Index

Abstract The second UN Sustainable Development Goal establishes food security as a priority for governments, multilateral organizations, and NGOs. These institutions track national-level food security performance with an array of metrics and weigh intervention options considering the leverage of many possible drivers. We studied the relationships between several candidate drivers and two response variables based on prominent measures of national food security: the 2019 Global Food Security Index (GFSI) and the Food Insecurity Experience Scale’s (FIES) estimate of the percentage of a nation’s population experiencing food security or mild food insecurity (FI ). We compared the contributions of explanatory variables in regressions predicting both response variables, and we further tested the stability of our results to changes in explanatory variable selection and in the countries included in regression model training and testing. At the cross-national level, the quantity and quality of a nation’s agricultural land were not predictive of either food security metric. We found mixed evidence that per-capita cereal production, per-hectare cereal yield, an aggregate governance metric, logistics performance, and extent of paid employment work were predictive of national food security. Household spending as measured by per-capita final consumption expenditure (HFCE) was consistently the strongest driver among those studied, alone explaining a median of 92% and 70% of variation (based on out-of-sample R 2 ) in GFSI and FI , respectively. The relative strength of HFCE as a predictor was observed for both response variables and was independent of the countries used for model training, the transformations applied to the explanatory variables prior to model training, and the variable selection technique used to specify multivariate regressions. The results of this cross-national analysis reinforce previous research supportive of a causal mechanism where, in the absence of exceptional local factors, an increase in income drives increase in food security. However, the strength of this effect varies depending on the countries included in regression model fitting. We demonstrate that using multiple response metrics, repeated random sampling of input data, and iterative variable selection facilitates a convergence of evidence approach to analyzing food security drivers.

42 ENGINEERING↗
DOE OSTI2023

Development of Building Design Optimization Methodology: Residential Building Applications

Building design optimization is a highly complex problem, requiring long computational running processes because of the many options that exist when a building is being designed. This paper introduces an integrated approach through which to perform this optimization within an acceptable time frame. The approach includes the methods of variable selection, model simplification, and a sequential optimization process. Using singular value decomposition, a large number of design variables is reduced to a smaller subset that can be solved more quickly through the optimization algorithm. To expedite the variable selection process, a modeling approach that quickly simulates annual energy consumption was developed to replace full annual energy simulations. The developed methodology was applied to two residential buildings in the US, and the results are discussed herein. To assess the accuracy of the integrated optimization methodology, the optimized life cycle costs are compaa variables demonstrating the strongest contributions in the optimization study were identified. The proposed methodology significantly shortened the time requirements for the optimization processes of the two case studies by 74% and 84%; the optimized life cycle costs were within 0.05% and 0.06%, respectively, of the optimum point.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2019

Extending Classification Algorithms to Case-Control Studies

Classification is a common technique applied to ’omics data to build predictive models and identify potential markers of biomedical outcomes. Despite the prevalence of case-control studies, the number of classification methods available to analyze data generated by such studies is extremely limited. Conditional logistic regression is the most commonly used technique, but the associated modeling assumptions limit its ability to identify a large class of sufficiently complicated ’omic signatures. We propose a data preprocessing step which generalizes and makes any linear or nonlinear classification algorithm, even those typically not appropriate for matched design data, available to be used to model case-control data and identify relevant biomarkers in these study designs. We demonstrate on simulated case-control data that both the classification and variable selection accuracy of each method is improved after applying this processing step and that the proposed methods are comparable to or outperform existing variable selection methods. Finally, we demonstrate the impact of conditional classification algorithms on a large cohort study of children with islet autoimmunity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions

Belowground microbial communities strongly influence ecosystem function such that predicting function may rely on understanding ecological processes that assemble communities. Uncertainty remains, however, in what governs the relative contributions of different ecological processes. To help fill this knowledge gap we test the general hypothesis that both initial state and degree of change in environmental conditions govern the relative contributions of different ecological assembly processes. To do so we leveraged regional-scale nutrient and organic matter addition experiments and used soil organic matter (SOM) as a proxy of integrated soil environmental conditions. Consistent with our hypothesis, we found that both the initial amount of SOM and the degree of change in SOM—in response to nutrient addition—influenced the relative contributions of different ecological assembly processes. These influences were most clearly observed at the regional scale, suggesting potential scale dependence. More specifically, nutrient additions homogenized bacterial community composition due to enhanced influences of homogenizing dispersal when SOM content was initially high. In contrast, nutrient additions led to divergence in community composition due to variable selection when initial SOM was low and/or when SOM increased significantly in response to nutrient additions. Our findings indicate important connections among initial conditions, degree of change in environmental variables, and microbial community assembly processes that may influence ecosystem processes. These conceptual inferences highlight a need to strengthen connections between ecological theory and biogeochemical modeling.

Feng, Youzhi↗
DOE OSTI2022

Effects of random forest modeling decisions on biogeochemical time series predictions

Abstract Random forests (RF) are an increasingly popular machine learning approach used to model biogeochemical processes in the Earth system. While RF models are robust to many assumptions that complicate deterministic models, there are several important parameterization decisions for appropriate use and optimal model fit. We explored the role that parameter decisions, including training/testing data splitting strategies, variable selection, and hyperparameters play on RF goodness‐of‐fit by constructing models using 1296 unique parameter combinations to predict concentrations of nitrate, a key nutrient for biogeochemical cycling in aquatic ecosystems. Models were built on long‐term, publicly available water quality and meteorology time series collected by the National Estuarine Research Reserve monitoring network for two contrasting ecosystems representing freshwater and brackish estuaries. We found that accounting for temporal dependence when splitting data into training and testing subsets was key for avoiding over‐estimation of model predictive power. In addition, variable selection, the ratio of training to testing data, and to a lesser degree, variables per split and number of trees, were significant parameters for optimizing RF goodness‐of‐fit. We also explored how model parameter decisions influenced interpretation of the relative importance of predictors to the model, and model predictor‐dependent variable relationships, with results suggesting that both data structure and model parameterization influence these factors. Because much of the current RF literature is written for the computational and statistical science communities, the primary goal of this study is to provide guidelines for aquatic scientists new to machine learning to apply RF techniques appropriately to aquatic biogeochemical datasets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Robust Measurement of Stellar Streams around the Milky Way: Correcting Spatially Variable Observational Selection Effects in Optical Imaging Surveys

Observations of density variations in stellar streams are a promising probe of low-mass dark matter substructure in the Milky Way. However, survey systematics such as variations in seeing and sky brightness can also induce artificial fluctuations in the observed densities of known stellar streams. These variations arise because survey conditions affect both object detection and star–galaxy misclassification rates. To mitigate these effects, we use Balrog synthetic source injections in the Dark Energy Survey (DES) Y3 data to calculate detection rate variations and classification rates as functions of survey properties. We show that these rates are nearly separable with respect to survey properties and can be estimated with sufficient statistics from the synthetic catalogs. Applying these corrections reduces the standard deviation of relative detection rates across the DES footprint by a factor of 5, and our corrections significantly change the inferred linear density of the Phoenix stream when including faint objects. Additionally, for artificial streams with DES-like survey properties we are able to recover density power spectra with reduced bias. We also find that uncorrected power-spectrum results for Legacy Survey of Space and Time (LSST)-like data can be around 5 times more biased, highlighting the need for such corrections in future ground-based surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Predictive analytics of selections of russet potatoes

We explore the application of machine learning algorithms specifically to enhance the selection process of Russet potato (Solanum tuberosum L.) clones in breeding trials by predicting their suitability for advancement. This study addresses the challenge of efficiently identifying high-yield, disease-resistant, and climate-resilient potato varieties that meet processing industry standards. Leveraging manually collected data from trials in the state of Oregon, we investigate the potential of a wide variety of state-of-the-art binary classification models. The dataset includes 1086 clones, with data on 38 attributes recorded for each clone, focusing on yield, size, appearance, and frying characteristics, with several control varieties planted consistently across four Oregon regions from 2013 to 2021. We conduct a comprehensive analysis of the dataset that includes preprocessing, feature engineering, and imputation to address missing values. We focus on several key metrics such as accuracy, F1-score, and Matthews correlation coefficient (MCC) for model evaluation. The top-performing models, namely a feedforward neural network classifier (Neural Net), a histogram-based gradient boosting classifier (HGBC), and a support vector machine classifier (SVM), demonstrate consistent and significant results. To further validate our findings, we conducted a simulation study using the aims, data-generating mechanisms, estimands, methods, and performance measures (ADEMP) framework, simulating different data-generating scenarios to assess model robustness and performance through true positive, true negative, false positive, and false negative distributions, area under the receiver operating characteristic curve (AUC-ROC) and MCC. The simulation results highlight that non-linear models like SVM and HGBC consistently show higher AUC-ROC and MCC than logistic regression, thus outperforming the traditional linear model across various distributions, and emphasizing the importance of model selection and tuning in agricultural trials. Variable selection further enhances model performance and identifies influential features in predicting trial outcomes. The findings emphasize the potential of machine learning in streamlining the selection process for potato varieties, offering benefits such as increased efficiency, substantial cost savings, and judicious resource utilization. Our study contributes insights into precision agriculture and showcases the relevance of advanced technologies for informed decision-making in breeding programs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization

Abstract Background Microbiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome. In the presence of such confounding, variable selection and estimation procedures may have unsatisfactory performance in identifying microbial features with an effect on the outcome. Results In this manuscript, we aim to estimate population-level effects of individual microbiome features while controlling for confounding by a categorical variable. Due to the high dimensionality and confounding-induced correlation between features, we propose feature screening, selection, and estimation conditional on each stratum of the confounder followed by a standardization approach to estimation of population-level effects of individual features. Comprehensive simulation studies demonstrate the advantages of our approach in recovering relevant features. Utilizing a potential-outcomes framework, we outline assumptions required to ascribe causal, rather than associational, interpretations to the identified microbiome effects. We conducted an agricultural study of the rhizosphere microbiome of sorghum in which nitrogen fertilizer application is a confounding variable. In this study, the proposed approach identified microbial taxa that are consistent with biological understanding of potential plant-microbe interactions. Conclusions Standardization enables more accurate identification of individual microbiome features with an effect on the outcome of interest compared to other variable selection and estimation procedures when there is confounding by a categorical variable.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data

High-dimensional mixed-effects models are an increasingly important form of regression in which the number of covariates rivals or exceeds the number of samples, which are collected in groups or clusters. The penalized likelihood approach to fitting these models relies on a coordinate descent algorithm that lacks guarantees of convergence to a global optimum. Here, we empirically study the behavior of this algorithm on simulated and real examples of three types of data that are common in modern biology: transcriptome, genome-wide association, and microbiome data. Our simulations provide new insights into the algorithm’s behavior in these settings, and, comparing the performance of two popular penalties, we demonstrate that the smoothly clipped absolute deviation (SCAD) penalty consistently outperforms the least absolute shrinkage and selection operator (LASSO) penalty in terms of both variable selection and estimation accuracy across omics data. To empower researchers in biology and other fields to fit models with the SCAD penalty, we implement the algorithm in a Julia package, HighDimMixedModels.jl .

Gorstein, Evan↗
DOE OSTI2020

Probabilistic Forecast of All-Sky Solar Radiation Using Enhanced WRF-Solar: Preprint

This study presents enhancements of the Weather Research and Forecasting model with solar extensions (WRF-Solar) to provide probabilistic forecasts of solar radiation. Our approach builds ensemble WRF-Solar runs by introducing stochastic perturbations of variables that produce the largest uncertainties in predicting surface irradiance and clouds. The key variables are identified using tangent linear sensitivity analysis of six physics packages responsible for all-sky irradiance variability. An optimal strategy to stochastically perturb the selected variables is developed and applied to WRF-Solar to generate ensemble members for day-ahead solar prediction. The National Solar Radiation Database (NSRDB) is used to validate the ensemble forecast at arbitrary locations on the model grid. Preliminary results indicate that the proposed technique can potentially produce WRF-Solar ensembles providing reliable information of solar prediction uncertainty. This study describes the implemented methodology and initial results as well as future research to improve ensemble-based probabilistic forecasts with WRF-Solar.

all-sky↗
DOE OSTI2024

Efficiency of ML Anomaly Detection Triggers for Emerging Jets

Novel machine learning-based anomaly detection Level 1 (L1) triggers are currently under development at CMS, namely AXOL1TL and CICADA. The former employs a variational autoencoder, while the latter utilizes a convolutional autoencoder. These triggers aim to balance rate reduction with model independence, enabling the selection of potentially significant events that might be overlooked by traditional triggers relying on basic kinematic variable selections. Consequently, they have the potential to enhance signals indicative of physics beyond the Standard Model, such as those associated with emerging jets. Such signals are predicted by models featuring a composite dark sector where long-lived particles decay into Standard Model jets with displaced tracks and numerous vertices. This study evaluates the efficiency of these anomaly detection triggers in selecting events with emerging jets produced via the s-channel production of two dark quarks.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Efficiency of ML Anomaly Detection Triggers for Emerging Jets

Novel machine learning-based anomaly detection Level 1 (L1) triggers are currently under development at CMS, namely AXOL1TL and CICADA. The former employs a variational autoencoder, while the latter utilizes a convolutional autoencoder. These triggers aim to balance rate reduction with model independence, enabling the selection of potentially significant events that might be overlooked by traditional triggers relying on basic kinematic variable selections. Consequently, they have the potential to enhance signals indicative of physics beyond the Standard Model, such as those associated with emerging jets. Such signals are predicted by models featuring a composite dark sector where long-lived particles decay into Standard Model jets with displaced tracks and numerous vertices. This study evaluates the efficiency of these anomaly detection triggers in selecting events with emerging jets produced via the s-channel production of two dark quarks.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Efficiency of ML Anomaly Detection Triggers for Emerging Jets

Novel machine learning-based anomaly detection Level 1 (L1) triggers are currently under development at CMS, namely AXOL1TL and CICADA. The former employs a variational autoencoder, while the latter utilizes a convolutional autoencoder. These triggers aim to balance rate reduction with model independence, enabling the selection of potentially significant events that might be overlooked by traditional triggers relying on basic kinematic variable selections. Consequently, they have the potential to enhance signals indicative of physics beyond the Standard Model, such as those associated with emerging jets. Such signals are predicted by models featuring a composite dark sector where long-lived particles decay into Standard Model jets with displaced tracks and numerous vertices. This study evaluates the efficiency of these anomaly detection triggers in selecting events with emerging jets produced via the s-channel production of two dark quarks.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Salinization and sedimentation drive contrasting assembly mechanisms of planktonic and sediment‐bound bacterial communities in agricultural streams

Abstract Agriculture is the most dominant land use globally and is projected to increase in the future to support a growing human population but also threatens ecosystem structure and services. Bacteria mediate numerous biogeochemical pathways within ecosystems. Therefore, identifying linkages between stressors associated with agricultural land use and responses of bacterial diversity is an important step in understanding and improving resource management. Here, we use the Mississippi Alluvial Plain (MAP) ecoregion, a highly modified agroecosystem, as a case study to better understand agriculturally associated drivers of stream bacterial diversity and assembly mechanisms. In the MAP, we found that planktonic bacterial communities were strongly influenced by salinity. Tolerant taxa increased with increasing ion concentrations, likely driving homogenous selection which accounted for ~90% of assembly processes. Sediment bacterial phylogenetic diversity increased with increasing agricultural land use and was influenced by sediment particle size, with assembly mechanisms shifting from homogenous to variable selection as differences in median particle size increased. Within individual streams, sediment heterogeneity was correlated with bacterial diversity and a subsidy‐stress relationship along the particle size gradient was observed. Planktonic and sediment communities within the same stream also diverged as sediment particle size decreased. Nutrients including carbon, nitrogen, and phosphorus, which tend to be elevated in agroecosystems, were also associated with detectable shifts in bacterial community structure. Collectively, our results establish that two understudied variables, salinity and sediment texture, are the primary drivers of bacterial diversity within the studied agroecosystem, whereas nutrients are secondary drivers. Although numerous macrobiological communities respond negatively, we observed increasing bacterial diversity in response to agricultural stressors including salinization and sedimentation. Elevated taxonomic and phylogenetic bacterial diversity likely increases the probability of detecting community responses to stressors. Thus, bacteria community responses may be more reliable for establishing water quality goals within highly modified agroecosystems that have experienced shifting baselines.

DeVilbiss, Stephen E.↗
DOE OSTI2024

Comparing Sensor Fusion and Multimodal Chemometric Models for Monitoring U(VI) in Complex Environments Representative of Irradiated Nuclear Fuel

Optical sensors and chemometric models were leveraged for the quantification of uranium(VI) (0–100 μg mL –1 ), europium (0–150 μg mL –1 ), samarium (0–250 μg mL –1 ), praseodymium (0–350 μg mL –1 ), neodymium (0–1000 μg mL –1 ), and HNO 3 (2–4 M) with varying corrosion product (iron, nickel, and chromium) levels using laser fluorescence, Raman scattering, and ultraviolet–visible–near-infrared absorption spectra. In this paper, an efficient approach to developing and evaluating tens of thousands of partial least-squares regression (PLSR) models, built from fused optical spectra or multimodal acquisitions, is discussed. Each PLSR model was optimized with unique preprocessing combinations, and features were selected using genetic algorithm filters. The 7-factor D-optimal design training set contained just 55 samples to minimize the number of samples. The performance of PLSR models was evaluated by using an automated latent variable selection script. PLS1 regression models tailored to each species outperformed a global PLS2 model. PLS1 models built using fused spectra data and a multimodal (i.e., analyzed separately) approach yielded similar information, resulting in percent root-mean-square error of prediction values of 0.9–5.7% for the seven factors. Further, the optical techniques and data processing strategies established in this study allow for the direct analysis of numerous species without measuring luminescence lifetimes or relying on a standard addition approach, making it optimal for near-real-time, in situ measurements. Nuclear reactor modeling helped bound training set conditions and identified elemental ratios of lanthanide fission products to characterize the burnup of irradiated nuclear fuel. Leveraging fluorescence, spectrophotometry, experimental design, and chemometrics can enable the remote quantification and characterization of complex systems with numerous species, monitor system performance, help identify the source of materials, and enable rapid high-throughput experiments in a variety of industrial processes and fundamental studies.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Machine learning of factors for improving oyster hatchery production

Oyster aquaculture and restoration in the Chesapeake Bay are vital, yet hatcheries frequently struggle with inconsistent larval growth and sudden mass mortality events. Unpredictable disruptions in larval production cause large economic losses, represent a perceived risk to growers, and impede industry expansion. To better understand associations between production yield and its potential predictors, we applied machine learning (random forest, and neural network) and statistical (generalized additive model) models to a comprehensive dataset of environmental, water quality, and operational parameters from a Maryland oyster hatchery, aiming to identify key yield predictors and develop a robust forecasting tool. We used recursive Boruta algorithm for variable selection, pinpointing critical predictors, and employed cross-validation to fine-tune model settings. Shapley value analysis offered crucial insights into model interpretations, highlighting week number, Normalized Difference Vegetation Index, salinity, turbidity, and fecundity as primary drivers of yield variability. For low-yield cases, salinity-related variables were particularly important. Our findings provide an early warning system for potential production downturns, empowering hatchery operators to make data-driven decisions for optimizing water conditions, feeding schedules, and broodstock management. By boosting predictability and efficiency, this research directly supports economic stability of the oyster industry and ecological health of the Chesapeake Bay.

Vishwakarma, Srishti [Oak Ridge National Laborator↗
DOE OSTI2019

Quantifying Climate and Catchment Control on Hydrological Drought in the Continental United States

The evolution of hydrological drought events is a result of complex (nonlinear) interactions between climate and catchment processes. To investigate such nonlinear relationship, we integrated a machine learning modeling framework based on the random forest (RF) algorithms with an interpretation framework to quantify the role of climate and catchment controls on hydrological drought. More particularly, our framework interprets a built RF machine-learning model to identify dominant variables and visualize their functional dependence and interaction effects on hydrological drought characteristics utilizing concepts of minimal depth, interactive depth, and partial dependence. We test our proposed modeling framework based on a set of 652 continental United States catchments with minimal human interference for a period of 1979–2010. Application of this framework indicated presence of three distinct drought regimes, which includes, Regime 1: droughts with longer duration, less frequent and lesser intensity; Regime 2: droughts with moderate duration, moderate frequency, and moderate intensity; and Regime 3: droughts with shorter duration, more frequent, and more intense. RF algorithm was able to accurately model the drought characteristics (intensity, duration, and number of events) for all the three drought regimes as a function of selected variables. It was observed that the type of dominant variables as well as their nonlinear functional relationship with hydrological droughts characteristics can vary between three selected regimes. Finally, our interpretation framework indicated that catchment characteristics have a significant role in controlling the hydrologic drought for catchments (regime 1), whereas both climate and catchment characteristics control hydrological drought in regimes 2 and 3.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Effect of Computational Schemes on Coupled Flow and Geo-Mechanical Modeling of CO 2 Leakage through a Compromised Well

Carbon capture, utilization, and storage (CCUS) describes a set of technically viable processes to separate carbon dioxide (CO 2 ) from industrial byproduct streams and inject it into deep geologic formations for long-term storage. Legacy wells located within the spatial domain of new injection and production activities represent potential pathways for fluids (i.e., CO 2 and aqueous phase) to leak through compromised components (e.g., through fractures or micro-annulus pathways). The finite element (FE) method is a well-established numerical approach to simulate the coupling between multi-phase fluid flow and solid phase deformation interactions that occur in a compromised well system. We assumed the spatial domain consists of a three-phases system: a solid, liquid, and gas phase. For flow in the two fluids phases, we considered two sets of primary variables: the first considering capillary pressure and gas pressure (PP) scheme, and the second considering liquid pressure and gas saturation (PS) scheme. Fluid phases were coupled with the solid phase using the full coupling (i.e., monolithic coupling) and iterative coupling (i.e., sequential coupling) approaches. The challenge of achieving numerical stability in the coupled formulation in heterogeneous media was addressed using the mass lumping and the upwinding techniques. Numerical results were compared with three benchmark problems to assess the performance of coupled FE solutions: 1D Terzaghi’s consolidation, Liakopoulos experiments, and the Kueper and Frind experiments. We found good agreement between our results and the three benchmark problems. For the Kueper and Frind test, the PP scheme successfully captured the observed experimental response of the non-aqueous phase infiltration, in contrast to the PS scheme. These exercises demonstrate the importance of fluid phase primary variable selection for heterogeneous porous media. We then applied the developed model to the hypothetical case of leakage along a compromised well representing a heterogeneous media. Considering the mass lumping and the upwinding techniques, both the monotonic and the sequential coupling provided identical results, but mass lumping was needed to avoid numerical instabilities in the sequential coupling. Additionally, in the monolithic coupling, the magnitude of primary variables in the coupled solution without mass lumping and the upwinding is higher, which is essential for the risk-based analyses.

deformation flow↗