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All sources NASA NTRS DOE OSTI

DOE OSTI2024

A consistent dataset for the net income distribution for 190 countries and aggregated to 32 geographical regions from 1958 to 2015

Abstract. Data on income distributions within and across countries are becoming increasingly important for informing analysis of income inequality and understanding the distributional consequences of climate change. While datasets on income distribution collected from household surveys are available for multiple countries, these datasets often do not represent the same concept of inequality (or income concept) and therefore make comparisons across countries, over time and across datasets difficult. Here, we present a consistent dataset of income distributions across 190 countries from 1958 to 2015 measured in terms of net income. We complement the observed values in this dataset with values imputed from a summary measure of the income distribution, specifically the Gini coefficient. For the imputation, we use a recently developed nonparametric principal-component-based approach that shows an excellent fit to data on income distributions compared to other approaches. We also present another version of this dataset aggregated from the country level to 32 geographical regions. Our dataset is developed for the purpose of calibrating models such as integrated human–Earth system models with detailed data on income distributions. This dataset will enable more robust analysis of income distribution at multiple scales. The latest version of our data are available on Zenodo: https://doi.org/10.5281/zenodo.7093997 (Narayan et al., 2022b).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Online mapping and forecasting of epidemics using open-source indicators

Open-source indicators have been proposed as a way of tracking and forecasting disease outbreaks. Some, such are meteorological data, are readily available as reanalysis products. Others, such as those derived from our online behavior (web searches, media article etc.) are gathered easily and are more timely than public health reporting. In this study we investigate how these datastreams may be combined to provide useful epidemiological information. The investigation is performed by building data assimilation systems to track influenza in California and dengue in India. The first does not suffer from incomplete data and was chosen to explore disease modeling needs. The second explores the case when observational data is sparse and disease modeling complexities are beside the point. The two test cases are for opposite ends of the disease tracking spectrum. We find that data assimilation systems that produce disease activity maps can be constructed. Further, being able to combine multiple open-source datastreams is a necessity as any one individually is not very informative. The data assimilation systems have very little in common except that they contain disease models, calibration algorithms and some ability to impute missing data. Thus while the data assimilation systems share the goal for accurate forecasting, they are practically designed to compensate for the shortcomings of the datastreams. Thus we expect them to be disease and location-specific.

42 ENGINEERING↗

DOE OSTI2016

A hybrid computational strategy to address WGS variant analysis in >5000 samples

Abstract Background The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies. Results We present a high throughput framework including multiple variant callers for single nucleotide variant (SNV) calling, which leverages hybrid computing infrastructure consisting of cloud AWS, supercomputers and local high performance computing infrastructures. We present a novel binning approach for large scale joint variant calling and imputation which can scale up to over 10,000 samples while producing SNV callsets with high sensitivity and specificity. As a proof of principle, we present results of analysis on Cohorts for Heart And Aging Research in Genomic Epidemiology (CHARGE) WGS freeze 3 dataset in which joint calling, imputation and phasing of over 5300 whole genome samples was produced in under 6 weeks using four state-of-the-art callers. The callers used were SNPTools, GATK-HaplotypeCaller, GATK-UnifiedGenotyper and GotCloud. We used Amazon AWS, a 4000-core in-house cluster at Baylor College of Medicine, IBM power PC Blue BioU at Rice and Rhea at Oak Ridge National Laboratory (ORNL) for the computation. AWS was used for joint calling of 180 TB of BAM files, and ORNL and Rice supercomputers were used for the imputation and phasing step. All other steps were carried out on the local compute cluster. The entire operation used 5.2 million core hours and only transferred a total of 6 TB of data across the platforms. Conclusions Even with increasing sizes of whole genome datasets, ensemble joint calling of SNVs for low coverage data can be accomplished in a scalable, cost effective and fast manner by using heterogeneous computing platforms without compromising on the quality of variants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

On the Impact of Income, Age, and Travel Distance on the Value of Time

The value of time (VOT) is a fundamental component used in transportation modeling, policy analysis, and economic appraisal. Decades of research and practice have empirically estimated the VOT across many factors (e.g., mode, purpose, time, comfort, etc.), yet little is known about its underlying form. Although it is well established that VOT can vary, it is still unclear whether patterns exist in this variation. The objective of this paper is not to merely estimate the VOT, but to model the VOT across multiple continuous and interacting variables. The purpose is to reveal its functional form with respect to mode, age, gender, purpose, income, and time of day to provide a generalizable understanding for future research and practice. Such an understanding can help develop simpler models and reduce the need for bespoke estimations for every conceivable variable perturbation. This research utilized a household travel survey containing 14,159 reported trips with imputed travel time and costs for the alternative mode choices. The average overall estimated VOT is 40.32 $/h, with results showing VOT varying log-linearly with income and trip distance, but following a Gaussian function (normal curve) with age. Overall, the results show that travel distance dominates VOT variation, which increases exponentially at a rate that is 3.61 times higher per mile of distance than per $10,000 of income, and that VOT by age peaks at age 54. This basic understanding of how the VOT varies sets the foundation for answering the subsequent question for why it might vary.

Engineering↗

NASA NTRS1988

Multiple input/output random vibration control system

A multi-input/output random vibration control algorithm was developed based on system identification concepts derived from random vibration spectral analysis theory. The unique features of the algorithm are: (1) the number of input excitors and the number of output control responses need not be identical; (2) the system inverse response matrix is obtained directly from the input/output spectral matrix; and (3) the system inverse response matrix is updated every control loop cycle to accommodate system amplitude nonlinearities. A laboratory demonstration case of two imputs with three outputs is presented to demonstrate the system capabilities.

Unruh, James F.↗

NASA NTRS2022

Bayesian Rules of Thumb: Robust Uncertainty Quantification in Early Project Cost Estimation

Systems engineers often make use of cost Rules ofThumb in order to estimate cost during early phases of projectformulation. These Rules of Thumb typically take the form ofa sequence of percentages over which a total cost is allocatedacross NASA WBS elements. Rules of Thumb can then be usedto extrapolate cost from one or more known WBS elements tothe remaining unknown WBS elements, assisting early projectformulation architecture studies (such as those in JPL’s Team Xand A Team).A number of issues can arise when generating and using costRules of Thumb. For example, many records of project costsconsist of incomplete data. Typical methods of dealing withincomplete cost allocation data include (a) ignoring missionswith incomplete data, or (b) taking averages of the non-zero percentagesacross missions, but both of these methods can result inbiased estimates if the existence of incomplete data correlateswith total mission cost or any particular WBS element. Anothercommon example is cost reported in one or more incorrect WBSelements. This is especially prevalent in smaller missions whereit is more common for engineers to perform tasks that fall underthe purview of multiple WBS elements.Furthermore, a Rule of Thumb estimate is typically reported asa point estimate; there is no reported uncertainty around thepercentages used to generate an allocation. Even in the rarecase in which confidence intervals around mean percentages areprovided, there may be positive or negative correlations betweenWBS elements which can skew estimates.Here we attempt to address these problems by formulatingprobabilistic Rules of Thumb in which a distribution of allocationschemes, rather than a single allocation scheme, is generated.We use a bootstrap imputation method to simultaneouslyaccount for uncertainty in the missing data while using allavailable information contained in the dataset. The imputeddatasets are then input into a multivariate Bayesian modelwhich accounts for correlations between WBS elements andproperly accounts for uncertainty in the final Rule of Thumbpercentages and predictions. We describe the mathematicalmodel and provides snippets of R code utilizing the brms(Bayesian Regression Models using Stan) package. To illustratethis model, we generate a Bayesian Level 2 WBS Cost Rule ofThumb for MIDEX (Medium-Class Explorers) missions withdata extracted from NASA’s CADRe. We then compare thismethod’s performance with the classical Rule of Thumb method.

Hooke, Melissa A↗

DOE OSTI2024

Hydrologic connectivity and dynamics of solute transport in a mountain stream: Insights from a long-term tracer test and multiscale transport modeling informed by machine learning

The movement of solutes in a watershed is a complex process with multiple interactions and feedbacks across spatial and temporal scales. Modeling the dynamics of solute transport along diverse hydrologic pathways within watersheds – from hillslopes to stream channels and in and out of the hyporheic zones – is challenging but critically important, as these processes integrate and contribute to the biogeochemical functioning of the river corridor up to the river network scale. Here we use results from a long-term network-scale tracer test at the H.J. Andrews experimental forest in western Cascade Mountains, Oregon, USA to inform a multiscale framework for transport in stream corridors. The framework uses a Lagrangian-based subgrid model to represent the effects of hyporheic exchange flow and advective transport at stream network scales. The spatially and temporally resolved stream discharge needed for the transport model is imputed across the river system by an entity-aware long short-term memory network. Modeled concentrations show good agreements with the observations and exhibit power scaling laws indicative of a very wide range of timescales over which hyporheic exchange flow occurs. Our results demonstrate a data-informed modeling framework that links dynamical processes occurring at small scales to a network context to help understand how changes at reach scale cascade into network-scale effects, providing a useful tool for sustainable river basin management.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Gap-filling eddy covariance methane fluxes: Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands

Time series of methane fluxes measured by eddy-covariance require gap-filling to estimate annual emissions. Gap-filling methane fluxes is challenging because of high variability and complex responses to multiple drivers. To date, there is no widely established gap-filling standard for methane, with regards both to the best model algorithms and predictors. In this study, we address the need for standardization by synthesizing results of gap-filling methods applied at 17 wetland sites spanning boreal to tropical regions including all major wetlands classes and two rice paddies. We introduce new procedures for: 1) creating realistic artificial gap scenarios, 2) training and evaluating gap-filling models without overstating performance, and 3) predicting half-hourly methane fluxes and annual emissions with robust uncertainty estimates. We tested a conventional method (marginal distribution sampling) and four machine learning algorithms - penalized linear regression, artificial neural networks, random forests, and boosted decision trees - and four predictor sets, including temporal, meteorological, ecosystem carbon and energy flux, and soil predictors. We find that the conventional method can achieve similar median performance to the machine learning models but is worse than the best machine learning models and relatively insensitive to predictor choices. Of the machine learning models, decision tree algorithms performed the best in cross-validation experiments, even with a baseline predictor set, and artificial neural networks showed comparable performance when using all predictors. Soil temperature was frequently the most important predictor whilst water table depth was important at sites with substantial water table fluctuations, highlighting the value of data on soil conditions. Raw gap-filling uncertainties from the machine learning models were underestimated and we propose a method to calibrate uncertainties to observations. Finally, we gap-fill and provide summary evaluation metrics for all 81 sites in the FLUXNET-CH4 community dataset and publicly release the python code for model development, evaluation, and uncertainty estimation.

42 ENGINEERING↗