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DOE OSTI2025

MINE: maximally informative next experiment—toward a new GWAS experimental design and methodology

Abstract The computational methodology of Genome Wide Association Studies (GWAS) currently has several limitations: (i) the number of observations (rows) on a quantitative trait tends to be smaller than the number of single nucleotide polymorphisms (SNPs) (columns) in the design matrix; (ii) each SNP is usually modeled separately, failing to acknowledge interaction between each other (ie epistasis); (iii) there is implicit linkage disequilibrium (LD) between neighboring SNPs due to their linkage. To overcome these issues, we developed a tool that uses ensemble methods to fit mixed linear models to GWAS data, and these ensemble methods include the development of a new experimental design approach in GWAS, which uses the resultant models and data to select the next informative experiment over time. This new adaptive and staged approach for GWAS experimental design was developed and tested in a 3 yr adaptive model-guided discovery experiment against a fixed classical design. In Sorghum bicolor a total of 79, 86, and 78 accessions were tested in years 1, 2, and 3, respectively out of 343 accessions available in the Bioenergy Association Panel (BAP) each identified for 232,303 SNPs, 1 every 2–3 kb in the genomes. We demonstrated the feasibility of MINE enacted with 8 people in the field per year over 3 yr vs in 1 large classical design enacted with 20 people in 1 yr. The MINE results for chromosomal regions identified controlling dry weight were confirmed against results from previous sorghum GWAS experiments and 1 large classical design for the BAP panel.

Genetics & Heredity↗

NASA NTRS2011

Prediction of Weather Impacted Airport Capacity using Ensemble Learning

Ensemble learning with the Bagging Decision Tree (BDT) model was used to assess the impact of weather on airport capacities at selected high-demand airports in the United States. The ensemble bagging decision tree models were developed and validated using the Federal Aviation Administration (FAA) Aviation System Performance Metrics (ASPM) data and weather forecast at these airports. The study examines the performance of BDT, along with traditional single Support Vector Machines (SVM), for airport runway configuration selection and airport arrival rates (AAR) prediction during weather impacts. Testing of these models was accomplished using observed weather, weather forecast, and airport operation information at the chosen airports. The experimental results show that ensemble methods are more accurate than a single SVM classifier. The airport capacity ensemble method presented here can be used as a decision support model that supports air traffic flow management to meet the weather impacted airport capacity in order to reduce costs and increase safety.

Weather impact↗

DOE OSTI2022

Prescreening-Based Subset Selection for Improving Predictions of Earth System Models With Application to Regional Prediction of Red Tide

We present the ensemble method of prescreening-based subset selection to improve ensemble predictions of Earth system models (ESMs). In the prescreening step, the independent ensemble members are categorized based on their ability to reproduce physically-interpretable features of interest that are regional and problem-specific. The ensemble size is then updated by selecting the subsets that improve the performance of the ensemble prediction using decision relevant metrics. We apply the method to improve the prediction of red tide along the West Florida Shelf in the Gulf of Mexico, which affects coastal water quality and has substantial environmental and socioeconomic impacts on the State of Florida. Red tide is a common name for harmful algal blooms that occur worldwide, which result from large concentrations of aquatic microorganisms, such as dinoflagellate Karenia brevis, a toxic single celled protist. We present ensemble method for improving red tide prediction using the high resolution ESMs of the Coupled Model Intercomparison Project Phase 6 (CMIP6) and reanalysis data. The study results highlight the importance of prescreening-based subset selection with decision relevant metrics in identifying non-representative models, understanding their impact on ensemble prediction, and improving the ensemble prediction. These findings are pertinent to other regional environmental management applications and climate services. Additionally, our analysis follows the FAIR Guiding Principles for scientific data management and stewardship such that data and analysis tools are findable, accessible, interoperable, and reusable. As such, the interactive Colab notebooks developed for data analysis are annotated in the paper. This allows for efficient and transparent testing of the results’ sensitivity to different modeling assumptions. Moreover, this research serves as a starting point to build upon for red tide management, using the publicly available CMIP, Coordinated Regional Downscaling Experiment (CORDEX), and reanalysis data.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions

Alchemical relative binding free energy calculations have recently found important applications in drug optimization. A series of congeneric compounds are generated from a preidentified lead compound, and their relative binding affinities to a protein are assessed in order to optimize candidate drugs. While methods based on equilibrium thermodynamics have been extensively studied, an approach based on nonequilibrium methods has recently been reported together with claims of its superiority. However, these claims pay insufficient attention to the basis and reliability of both methods. Here we report a comparative study of the two approaches across a large data set, comprising more than 500 ligand transformations spanning in excess of 300 ligands binding to a set of 14 diverse protein targets. Ensemble methods are essential to quantify the uncertainty in these calculations, not only for the reasons already established in the equilibrium approach but also to ensure that the nonequilibrium calculations reside within their domain of validity. If and only if ensemble methods are applied, we find that the nonequilibrium method can achieve accuracy and precision comparable to those of the equilibrium approach. Compared to the equilibrium method, the nonequilibrium approach can reduce computational costs but introduces higher computational complexity and longer wall clock times. There are, however, cases where the standard length of a nonequilibrium transition is not sufficient, necessitating a complete rerun of the entire set of transitions. This significantly increases the computational cost and proves to be highly inconvenient during large-scale applications. Our findings provide a key set of recommendations that should be adopted for the reliable implementation of nonequilibrium approaches to relative binding free energy calculations in ligand-protein systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Methods for Incorporating Model Uncertainty into Exoplanet Atmospheric Analysis

A key goal of exoplanet spectroscopy is to measure atmospheric properties, such as abundances of chemical species, in order to connect them to our understanding of atmospheric physics and planet formation. In this new era of high-quality JWST data, it is paramount that these measurement methods are robust. When comparing atmospheric models to observations, multiple candidate models may produce reasonable fits to the data. Typically, conclusions are reached by selecting the best-performing model according to some metric. This ignores model uncertainty in favor of specific model assumptions, potentially leading to measured atmospheric properties that are overconfident and/or incorrect. In this paper, we compare three ensemble methods for addressing model uncertainty by combining posterior distributions from multiple analyses: Bayesian model averaging, a variant of Bayesian model averaging using leave-one-out predictive densities, and stacking of predictive distributions. We demonstrate these methods by fitting the Hubble Space Telescope (HST) + Spitzer transmission spectrum of the hot Jupiter HD 209458b using models with different cloud and haze prescriptions. All of our ensemble methods lead to uncertainties on retrieved parameters that are larger but more realistic and consistent with physical and chemical expectations. Since they have not typically accounted for model uncertainty, uncertainties of retrieved parameters from HST spectra have likely been underreported. We recommend stacking as the most robust model combination method. Our methods can be used to combine results from independent retrieval codes and from different models within one code. They are also widely applicable to other exoplanet analysis processes, such as combining results from different data reductions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Progress in Normalizing Flows for 4d Gauge Theories

Normalizing flows have arisen as a tool to accelerate Monte Carlo sampling for lattice field theories. This work reviews recent progress in applying normalizing flows to 4-dimensional nonabelian gauge theories, focusing on two advancements: an architectural improvement referred to as learned active loops, and the application of correlated ensemble methods to QCD with N f = 2 dynamical fermions.

Abbott, Ryan [Massachusetts Institute of Technolog↗

DOE OSTI2021

EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning

Characterizing the functional properties of plant acyl-ACP thioesterases (TEs), a key enzyme class used in the production of renewable oleochemicals in microbial hosts, experimentally, can be an expensive and time consuming process since it requires manual screening of thousands of candidates in a database. Using amino acid sequence to computationally predict an enzyme’s function might accelerate this process; however obtaining the necessary amount of information on previously characterized enzymes and their respective sequences required by standard Machine Learning (ML) based approaches to accurately infer sequence-function relationships can be prohibitive, especially with a low-throughput testing cycle. Experimental noise, unbalanced dataset where high sequence similarity does not always imply identical functional properties will further prevent robust prediction performance. Herein we present a ML method, Ensemble method for enZyme Classification (EnZymClass), that is specifically designed to address these issues. We used EnZymClass to classify TEs into short, long and mixed free fatty acid substrate specificity categories. While general guidelines for inferring substrate specificity have been proposed before, prediction of chain-length preference from primary sequence has remained elusive for plant acyl-ACP TEs. By applying EnZymClass to a subset of TEs in the ThYme database, we identified two medium chain TEs, ClFatB3 and CwFatB2, with previously uncharacterized activity in E. coli fatty acid production hosts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Inference of relative permeability curves in reservoir rocks with ensemble Kalman method

Not provided.

Chemistry↗

NASA NTRS2004

Virtual Sensors: Using Data Mining to Efficiently Estimate Spectra

Detecting clouds within a satellite image is essential for retrieving surface geophysical parameters, such as albedo and temperature, from optical and thermal imagery because the retrieval methods tend to be valid for clear skies only. Thus, routine satellite data processing requires reliable automated cloud detection algorithms that are applicable to many surface types. Unfortunately, cloud detection over snow and ice is difficult due to the lack of spectral contrast between clouds and snow. Snow and clouds are both highly reflective in the visible wavelen,ats and often show little contrast in the thermal Infrared. However, at 1.6 microns, the spectral signatures of snow and clouds differ enough to allow improved snow/ice/cloud discrimination. The recent Terra and Aqua Moderate Resolution Imaging Spectro-Radiometer (MODIS) sensors have a channel (channel 6) at 1.6 microns. Presently the most comprehensive, long-term information on surface albedo and temperature over snow- and ice-covered surfaces comes from the Advanced Very High Resolution Radiometer ( AVHRR) sensor that has been providing imagery since July 1981. The earlier AVHRR sensors (e.g. AVHRR/2) did not however have a channel designed for discriminating clouds from snow, such as the 1.6 micron channel available on the more recent AVHRR/3 or the MODIS sensors. In the absence of the 1.6 micron channel, the AVHRR Polar Pathfinder (APP) product performs cloud detection using a combination of time-series analysis and multispectral threshold tests based on the satellite's measuring channels to produce a cloud mask. The method has been found to work reasonably well over sea ice, but not so well over the ice sheets. Thus, improving the cloud mask in the APP dataset would be extremely helpful toward increasing the accuracy of the albedo and temperature retrievals, as well as extending the time-series of albedo and temperature retrievals from the more recent sensors to the historical ones. In this work, we use data mining methods to construct a model of MODIS channel 6 as a function of other channels that are common to both MODIS and AVHRR. The idea is to use the model to generate the equivalent of MODIS channel 6 for AVHRR as a function of the AVHRR equivalents to MODIS channels. We call this a Virtual Sensor because it predicts unmeasured spectra. The goal is to use this virtual channel 6. to yield a cloud mask superior to what is currently used in APP . Our results show that several data mining methods such as multilayer perceptrons (MLPs), ensemble methods (e.g., bagging), and kernel methods (e.g., support vector machines) generate channel 6 for unseen MODIS images with high accuracy. Because the true channel 6 is not available for AVHRR images, we qualitatively assess the virtual channel 6 for several AVHRR images.

Srivastava, Ashok↗

NASA NTRS2016

Similar Estimates of Temperature Impacts on Global Wheat Yield by Three Independent Methods

The potential impact of global temperature change on global crop yield has recently been assessed with different methods. Here we show that grid-based and point-based simulations and statistical regressions (from historic records), without deliberate adaptation or CO2 fertilization effects, produce similar estimates of temperature impact on wheat yields at global and national scales. With a 1 C global temperature increase, global wheat yield is projected to decline between 4.1% and 6.4%. Projected relative temperature impacts from different methods were similar for major wheat-producing countries China, India, USA and France, but less so for Russia. Point-based and grid-based simulations, and to some extent the statistical regressions, were consistent in projecting that warmer regions are likely to suffer more yield loss with increasing temperature than cooler regions. By forming a multi-method ensemble, it was possible to quantify 'method uncertainty' in addition to model uncertainty. This significantly improves confidence in estimates of climate impacts on global food security.

Climate impacts↗

DOE OSTI2022

A Spatiotemporal-Aware Weighting Scheme for Improving Climate Model Ensemble Predictions

Multimodel ensembling has been widely used to improve climate model predictions, and the improvement strongly depends on the ensembling scheme. In this work, we propose a Bayesian neural network (BNN) ensembling method, which combines climate models within a Bayesian model averaging framework, to improve the predictive capability of model ensembles. Our proposed BNN approach calculates spatiotemporally varying model weights and biases by leveraging individual models' simulation skill, calibrates the ensemble prediction against observations by considering observation data uncertainty, and quantifies epistemic uncertainty when extrapolating to new conditions. More importantly, the BNN method provides interpretability about which climate model contributes more to the ensemble prediction at which locations and times. Thus, beyond its predictive capability, the method also brings insights and understanding of the models to guide further model and data development. In this study, we design experiments using an ensemble of CMIP6 climate model simulations to illustrate the BNN ensembling method's capability with respect to prediction accuracy, interpretability, and uncertainty quantification (UQ). We demonstrate that BNN can correctly assign larger weights to the regions and seasons where the individual model fits the observation better. Moreover, its offered interpretability is consistent with our understanding of localized climate model performance. Additionally, BNN shows an increasing uncertainty when the prediction is farther away from the period with constrained data, which appropriately reflects our trustworthiness of the models in the changing climate.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Predicting Biomass Yields of Advanced Switchgrass Cultivars for Bioenergy and Ecosystem Services Using Machine Learning

The production of advanced perennial bioenergy crops within marginal areas of the agricultural landscape is gaining interest due to its potential to sustainably produce feedstocks for biofuels and bioproducts while also improving the sustainability and resilience of commodity crop production. However, predicting the biomass yields of this production system is challenging because marginal areas are often relatively small and spread around agricultural fields and are typically associated with various abiotic conditions that limit crop production. Machine learning (ML) offers a viable solution as a biomass yield prediction tool because it is suited to predicting relationships with complex functional associations. The objectives of this study were to (1) evaluate the accuracy of commonly applied ML algorithms in agricultural applications for predicting the biomass yields of advanced switchgrass cultivars for bioenergy and ecosystem services and (2) determine the most important biomass yield predictors. Datasets on biomass yield, weather, land marginality, soil properties, and agronomic management were generated from three field study sites in two U.S. Midwest states (Illinois and Iowa) over three growing seasons. The ML algorithms evaluated in the study included random forests (RFs), gradient boosting machines (GBMs), artificial neural networks (ANNs), K-neighbors regressor (KNR), AdaBoost regressor (ABR), and partial least squares regression (PLSR). Coefficient of determination (R 2 ) and mean absolute error (MAE) were used to evaluate the predictive accuracy of the tested algorithms. Results showed that the ensemble methods, RF (R 2 = 0.86, MAE = 0.62 Mg/ha), GBM (R 2 = 0.88, MAE = 0.57 Mg/ha), and GBM (R 2 = 0.78, MAE = 0.66 Mg/ha), were the most accurate in predicting biomass yields of the Independence, Liberty, and Shawnee switchgrass cultivars, respectively. This is in agreement with similar studies that apply ML to multi-feature problems where traditional statistical methods are less applicable and datasets used were considered to be relatively small for ANNs. Consistent with previous studies on switchgrass, the most important predictors of biomass yield included average annual temperature, average growing season temperature, sum of the growing season precipitation, field slope, and elevation. This study helps pave the way for applying ML as a management tool for alternative bioenergy landscapes where understanding agronomic and environmental performance of a multifunctional cropping system seasonally and interannually at the sub-field scale is critical.

09 BIOMASS FUELS↗

DOE OSTI2025

MINE: a new way to design genetics experiments for discovery

Abstract The Maximally Informative Next Experiment or MINE is a new experimental design approach for experiments, such as those in omics, in which the number of effects or parameters p greatly exceeds the number of samples n (p > n). Classical experimental design presumes n > p for inference about parameters and its application to p > n can lead to over-fitting. To overcome p > n, MINE is an ensemble method, which makes predictions about future experiments from an existing ensemble of models consistent with available data in order to select the most informative next experiment. Its advantages are in exploration of the data for new relationships with n < p and being able to integrate smaller and more tractable experiments to replace adaptively one large classic experiment as discoveries are made. Thus, using MINE is model-guided and adaptive over time in a large omics study. Here, MINE is illustrated in two distinct multiyear experiments, one involving genetic networks in Neurospora crassa and a second one involving a genome-wide association study in Sorghum bicolor as a comparison to classic experimental design in an agricultural setting.

Biochemistry & Molecular Biology↗

NASA NTRS2021

Exploring uncertainties in global crop yield projections in a large ensemble of crop models and CMIP5 and CMIP6 climate scenarios

Concerns over climate change are motivated in large part because of their impact on human society. Assessing the effect of that uncertainty on specific potential impacts is demanding, since it requires a systematic survey over both climate and impacts models. We provide a comprehensive evaluation of uncertainty in projected crop yields for maize, spring and winter wheat, rice, and soybean, using a suite of nine crop models and up to 45 CMIP5 and 34 CMIP6 climate projections for three different forcing scenarios. To make this task computationally tractable, we use a new set of statistical crop model emulators. We find that climate and crop models contribute about equally to overall uncertainty. While the ranges of yield uncertainties under CMIP5 and CMIP6 projections are similar, median impact in aggregate total caloric production is typically more negative for the CMIP6 projections (+1% to −19%) than for CMIP5 (+5% to −13%). In the first half of the 21st century and for individual crops is the spread across crop models typically wider than that across climate models, but we find distinct differences between crops: globally, wheat and maize uncertainties are dominated by the crop models, but soybean and rice are more sensitive to the climate projections. Climate models with very similar global mean warming can lead to very different aggregate impacts so that climate model uncertainties remain a significant contributor to agricultural impacts uncertainty. These results show the utility of large-ensemble methods that allow comprehensively evaluating factors affecting crop yields or other impacts under climate change. The crop model ensemble used here is unbalanced and pulls the assumption that all projections are equally plausible into question. Better methods for consistent model testing, also at the level of individual processes, will have to be developed and applied by the crop modeling community.

crop yield projections↗

DOE OSTI2025

Exploring Data Set Bias and Decision Support with Predictive Uncertainty Through Bayesian Approximations and Convolutional Neural Networks

Individual seismic catalogs can contain multiscale observations from fault level to global scales and associated waveforms from discrete events reflect crustal structure across many different scales and locations. Seismic network aperture, geographic location, and observation distance may not provide informative guidance or intuition on how different catalogs will behave across models trained under different conditions. We rely on uncertainty to provide guardrails for when to trust model decisions, but understanding when our uncertainty is trustworthy is an open challenge. Here, in this work, we explore Bayesian approximation methods for assigning predictive uncertainty in seismic event classification problems. We find that computationally expensive Bayesian approximations do not outperform simple ensemble methods. We also find that when exploiting multiple seismic event catalogs, joint training with data from all the catalogs combined with Bayesian approximations and supervised training for classification can obscure bias and result in less robust uncertainty while also not providing substantial performance benefits compared to training individual models for each catalog.

58 GEOSCIENCES↗

NASA NTRS1990

Statistical properties of ideal three-dimensional magnetohydrodynamics

Classical Gibbs ensemble methods are used to study the spectral structure of three-dimensional ideal MHD in periodic geometry. In this paper the equilibrium ensemble incorporates constraints of total energy, magnetic helicity, and cross helicity. Several new results are proven for ensemble averages, including the constraint that magnetic energy equal or exceed kinetic energy, and that cross helicity represents a constant fraction of magnetic energy across the spectral domain, for arbitrary size systems. Two zero-temperature limits are considered in detail, emphasizing the role of complete and partial condensaiton of spectral quantities to the longest wavelength states. The ensemble predictions are compared to direct numerical solution using a low-order truncation Galerkin spectral code. Implications for spectral transfer of nonequilibrium, dissipative turbulent MHD systems are discussed.

Stribling, T.↗

NASA NTRS2015

Improving Climate Projections Using "Intelligent" Ensembles

Recent changes in the climate system have led to growing concern, especially in communities which are highly vulnerable to resource shortages and weather extremes. There is an urgent need for better climate information to develop solutions and strategies for adapting to a changing climate. Climate models provide excellent tools for studying the current state of climate and making future projections. However, these models are subject to biases created by structural uncertainties. Performance metrics-or the systematic determination of model biases-succinctly quantify aspects of climate model behavior. Efforts to standardize climate model experiments and collect simulation data-such as the Coupled Model Intercomparison Project (CMIP)-provide the means to directly compare and assess model performance. Performance metrics have been used to show that some models reproduce present-day climate better than others. Simulation data from multiple models are often used to add value to projections by creating a consensus projection from the model ensemble, in which each model is given an equal weight. It has been shown that the ensemble mean generally outperforms any single model. It is possible to use unequal weights to produce ensemble means, in which models are weighted based on performance (called "intelligent" ensembles). Can performance metrics be used to improve climate projections? Previous work introduced a framework for comparing the utility of model performance metrics, showing that the best metrics are related to the variance of top-of-atmosphere outgoing longwave radiation. These metrics improve present-day climate simulations of Earth's energy budget using the "intelligent" ensemble method. The current project identifies several approaches for testing whether performance metrics can be applied to future simulations to create "intelligent" ensemble-mean climate projections. It is shown that certain performance metrics test key climate processes in the models, and that these metrics can be used to evaluate model quality in both current and future climate states. This information will be used to produce new consensus projections and provide communities with improved climate projections for urgent decision-making.

Baker, Noel C.↗

NASA NTRS2015

Improving Climate Projections Using "Intelligent" Ensembles

Baker, Noel C.↗