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DOE OSTI2024

Manifold Learning: What, How, and Why

Manifold learning (ML), also known as nonlinear dimension reduction, is a set of methods to find the low-dimensional structure of data. Dimension reduction for large, high-dimensional data is not merely a way to reduce the data; the new representations and descriptors obtained by ML reveal the geometric shape of high-dimensional point clouds and allow one to visualize, denoise, and interpret them. This review presents the underlying principles of ML, its representative methods, and their statistical foundations, all from a practicing statistician's perspective. It describes the trade-offs and what theory tells us about the parameter and algorithmic choices we make in order to obtain reliable conclusions.

Mathematics↗

DOE OSTI2016

WEC Design Response Toolbox v. 1.0

The WEC Design Response Toolbox (WDRT) is a numerical toolbox for design-response analysis of wave energy converters (WECs). The WDRT was developed during a series of efforts to better understand WEC survival design. The WDRT has been designed as a tool for researchers and developers, enabling the straightforward application of statistical and engineering methods. The toolbox includes methods for short-term extreme response, environmental characterization, long-term extreme response and risk analysis, fatigue, and design wave composition.

Coe, Ryan↗

DOE OSTI2023

Robust Machine Learning

UQ4ML is a code repository for a set of tools for the development of robust machine learning methods, uncertainty quantification and explainability of machine learning methods. The goal of these tools is to develop more robust and statistically rigorous machine learning methods for scientific applications. These tools are developed in Python, a high-level programming language that takes advantage of the Python ecosystem of high-quality open-source packages for machine learning.

Oyen, Diane↗

DOE OSTI2020

Path Properties of Atmospheric Transitions: Illustration with a Low-Order Sudden Stratospheric Warming Model

Many rare weather events, including hurricanes, droughts, and floods, dramatically impact human life. To accurately forecast these events and characterize their climatology requires specialized mathematical techniques to fully leverage the limited data that are available. Here we describe transition path theory (TPT), a framework originally developed for molecular simulation, and argue that it is a useful paradigm for developing mechanistic understanding of rare climate events. TPT provides a method to calculate statistical properties of the paths into the event. As an initial demonstration of the utility of TPT, we analyze a low-order model of sudden stratospheric warming (SSW), a dramatic disturbance to the polar vortex that can induce extreme cold spells at the surface in the midlatitudes. SSW events pose a major challenge for seasonal weather prediction because of their rapid, complex onset and development. Climate models struggle to capture the long-term statistics of SSW, owing to their diversity and intermittent nature. We use a stochastically forced Holton–Mass-type model with two stable states, corresponding to radiative equilibrium and a vacillating SSW-like regime. In this stochastic bistable setting, from certain probabilistic forecasts TPT facilitates estimation of dominant transition pathways and return times of transitions. These “dynamical statistics” are obtained by solving partial differential equations in the model’s phase space. With future application to more complex models, TPT and its constituent quantities promise to improve the predictability of extreme weather events through both generation and principled evaluation of forecasts.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer

It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. “Universal proteins” have been used to infer the organismal phylogeny, but have been criticized as being only the “tree of one percent.” Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees – a “treecloud” – for each, as well as for a concatenated dataset based on putative “universal proteins.” We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS). We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the “tree of one percent” is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Estimation of Radiation Doses to U.S. Military Test Participants from Nuclear Testing: A Comparison of Historical Film-Badge Measurements, Dose Reconstruction and Retrospective Biodosimetry

Retrospective radiation dose estimations, whether based on physical or biological measurements, or on theoretical dose reconstruction, are limited in their precision and reliability, particularly for exposures that occurred many decades ago. Here, we studied living U.S. military test participants, believed to have received high-dose radiation exposures during nuclear testing-related activities approximately six decades ago, with two primary goals in mind. The first was to compare three different approaches of assessing past radiation exposures: 1. Historical personnel monitoring data alone; 2. Dose reconstruction based on varying levels of completeness of individual information, which can include film badge data; and 3. Retrospective biodosimetry using chromosome aberrations in peripheral blood lymphocytes. The second goal was to use the collected data to make the best possible estimates of bone marrow dose received by a group with the highest military recorded radiation doses of any currently living military test participants. Six nuclear test participants studied had been on Rongerik Atoll during the 1954 CASTLE Bravo nuclear test. Another six were present at the Nevada Test Site (NTS) and/or Pacific Proving Ground (PPG) and were believed to have received relatively high-dose exposures at those locations. All were interviewed, and all provided a blood sample for cytogenetic analysis. Military dose records for each test participant, as recorded in the Defense Threat Reduction Agency's Nuclear Test Review and Information System, were used as the basis for historical film badge records and provided exposure scenario information to estimate dose via dose reconstruction. Dose to bone marrow was also estimated utilizing directional genomic hybridization (dGH) for high-resolution detection of radiation-induced chromosomal translocations and inversions, the latter being demonstrated for the first time for the purpose of retrospective biodosimetry. As the true dose for each test participant is not known these many decades after exposure, this study gauged the congruence of different methods by assessing the degree of correlation and degree of systematic differences. Overall, the best agreement between methods, defined by statistically significant correlations and small systematic differences, was between doses estimated by a dose reconstruction methodology that exploited all the available individual detail and the biodosimetry methodology derived from a weighted average dose determined from chromosomal translocation and inversion rates. Employing such a strategy, we found that the Rongerik veterans who participated in this study appear to have received, on average, bone marrow equivalent doses on the order of 300–400 mSv, while the NTS/ PPG participants appear to have received approximately 250–300 mSv. The results show that even for nuclear events that occurred six decades in the past, biological signatures of exposure are still present, and when taken together, chromosomal translocations and inversions can serve as reliable retrospective biodosimeters, particularly on a group-average basis, when doses received are greater than statistically-determined detection limits for the biological assays used.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2017

Comparison of Experimental Methods for Estimating Matrix Diffusion Coefficients for Contaminant Transport Modeling

Diffusion cell and diffusion wafer experiments were conducted to compare methods for estimating matrix diffusion coefficients in rock core samples from Pahute Mesa at the Nevada Nuclear Security Site (NNSS). A diffusion wafer method, in which a solute diffuses out of a rock matrix that is pre-saturated with water containing the solute, is presented as a simpler alternative to the traditional through-diffusion (diffusion cell) method. Both methods yielded estimates of matrix diffusion coefficients that were within the range of values previously reported for NNSS volcanic rocks. The difference between the estimates of the two methods ranged from 14 to 30%, and there was no systematic high or low bias of one method relative to the other. From a transport modeling perspective, these differences are relatively minor when one considers that other variables (e.g., fracture apertures, fracture spacings) influence matrix diffusion to a greater degree and tend to have greater uncertainty than diffusion coefficients. For the same relative random errors in concentration measurements, the diffusion cell method yields diffusion coefficient estimates that have less uncertainty than the wafer method. However, the wafer method is easier and less costly to implement and yields estimates more quickly, thus allowing a greater number of samples to be analyzed for the same cost and time. Given the relatively good agreement between the methods, and the lack of any apparent bias between the methods, the diffusion wafer method appears to offer advantages over the diffusion cell method if better statistical representation of a given set of rock samples is desired.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2018

Accelerating Feldman-Cousins on NOvA using NERSC Supercomputers

When fitting to data with low stats and near physical boundaries, extra measures need to be taken to ensure proper statistical coverage. The method NOvA uses is called the Feldman-Cousins procedure, which entails fitting thousands of independent pseudoexperiments to generate acceptance intervals that are then used to correct our fits. The scale required by the Feldman Cousins procedure makes it extremely computationally intensive. In past analyses, it has taken up to several weeks to complete, bottlenecking our final results. Here I present recent work by members of the NOvA experiment and the SciDAC4 collaboration to enable the use of the super-computing facilities at NERSC to process our Feldman-Cousins corrections over 150x faster, allowing us to do more studies, increase the precision of our fits, and produce results quickly.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

We Know Where We Don't Know: 3D Bayesian CNNs for Credible Geometric Uncertainty

Deep learning has been successfully applied to the segmentation of 3D Computed Tomography (CT) scans. Establishing the credibility of these segmentations requires uncertainty quantification (UQ) to identify untrustworthy predictions. Recent UQ architectures include Monte Carlo dropout networks (MCDNs), which approximate deep Gaussian processes, and Bayesian neural networks (BNNs), which learn the distribution of the weight space. BNNs are advantageous over MCDNs for UQ but are thought to be computationally infeasible in high dimension, and neither architecture has produced interpretable geometric uncertainty maps. We propose a novel 3D Bayesian convolutional neural network (BCNN), the first deep learning method which generates statistically credible geometric uncertainty maps and scales for application to 3D data. We present experimental results on CT scans of graphite electrodes and laser-welded metals and show that our BCNN outperforms an MCDN in recent uncertainty metrics. The geometric uncertainty maps generated by our BCNN capture distributions of sigmoid values that are interpretable as confidence intervals, critical for applications that rely on deep learning for high-consequence decisions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

LBNL CRADA (FP00009949) with the American Public Power Association: Electricity Reliability Metrics, Analysis, and Planning (Final Technical Report)

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

Electricity Reliability Metrics, Analysis, and Planning (CRADA Final Report)

LBNL and APPA (the team) jointly examined the extent to which differences in distribution feeder characteristics are correlated with differences in their reliability performance when exposed to three different types of natural hazards (wildlife, weather, and vegetation). The team employed data-driven approaches to quantify the relationships between various measures of feeder reliability and a suite of feeder characteristics individually and jointly via a statistically-based clustering method. The team developed suggestions on how comparisons across groupings of feeders and review of the relative contributions of the constituents of SAIFI and SAIDI could be used to help prioritize utility actions to improve reliability. However, they also caution that their suggestions require further evaluation because they are based on only one year of information from a modest number of small utilities.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2016

AGC-1 Irradiation Induced Property Changes Analysis Report: Dynamic Elastic Modulus

Recent analyses of some of the test property data from the AGC-1 creep capsule are reported. Specifically the analyses of data for the effects of compressive creep strain on the Dynamic elastic modulus (by the fundamental frequency and ultrasonic velocity/tof methods) are reported. Statistical “t” testing was used to establish the statistical significance of any differences observed between the Dynamic elastic modulus of the creep (irradiated with compressive stress) and the control (irradiated without stress) specimens. Compressive creep strain does have a small effect on Dynamic elastic modulus, reducing it at the higher doses as volume turnaround is approached.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Baseline Cost Model for Hydropower: Documentation (2025)

Hydropower currently contributes about 80 GW of conventional and 23 GW of pumped storage capacity to the United States (US) power grid. Previous studies have estimated a considerable amount of remaining US hydropower resources, including non-powered dams (NPD) (Hadjerioua et al., 2012), new stream-reach developments (NSD) (Kao et al., 2014), pumped storage hydropower (PSH) and canal/conduit (Kao et al., 2022). The combined theoretical capacity potential of these various hydropower resources is comparable to the existing US hydropower capacity. There is a continuing interest in developing this hydropower potential, particularly to help meet the increasing demand for electricity. However, available data (Sasthav and Oladosu, 2022) show that the rate of new hydropower development has slowed considerably over time despite the interest of industry stakeholders. This is partly due to the competition from other energy resources and from the highly dispersed nature of remaining hydropower resources, which lead to high information requirements for evaluating the feasibility of potential projects. Cost information provides the most succinct summary of the feasibility of a potential hydropower project required by stakeholders, including developers, investors, policymakers, consumer groups, etc., considering investment options. The best estimates of hydropower costs can be obtained through detailed engineering design and cost assessments of individual projects. However, this approach has high data and resource (time, funds, cross-disciplinary expertise) requirements that render it inapplicable for rapid cost estimation with limited data. Although innovative approaches can overcome some of these impediments (see Oladosu and Ma, 2024 for such an application to potential NPD projects), the development of such approaches still requires significant amounts of resources and are not generally applicable to all hydropower project types. Therefore, statistical and parametric methods using simpler cost specifications remain of significant utility to hydropower stakeholders and are, at the least, complementary to more detailed approaches, particularly when evaluating many potential projects.

13 HYDRO ENERGY↗

DOE OSTI2025

Neutrino Induced Charged Current Coherent Pion Production for Constraining the Muon Neutrino Flux at DUNE

We study neutrino induced charge current coherent pion production (νμ CC-Coh π) as a tool for constraining the neutrino flux at the Deep Underground Neutrino Experiment (DUNE). The neutrino energy and flavor in the process can be directly reconstructed from the outgoing particles, making it especially useful to specifically constrain the muon neutrino component of the total flux. The cross section of this process can be obtained using the Adler relation with the π-Ar elastic scattering cross section, taken either from external data or, as we explore, from a simultaneous measurement in the DUNE near detector. We develop a procedure that leverages νμ CC-Coh π events to fit for the neutrino flux while simultaneously accounting for relevant effects in the cross section. We project that this method has the statistical power to constrain the uncertainty on the normalization of the flux at its peak to a few percent. This study demonstrates the potential utility of aνμ CC-Coh π flux constraint, though further work will be needed to determine the range of validity and precision of the Adler relation upon which it relies, as well as to measure the π-Ar elastic scattering cross section to the requisite precision. We discuss the experimental and phenomenological developments necessary to unlock the νμ CC-Coh π process as a "standard candle'' for neutrino experiments.

Putnam, Gray [Fermilab]↗

DOE OSTI2022

Deep Generative Models for Materials Discovery and Machine Learning-Accelerated Innovation

Machine learning and artificial intelligence (AI/ML) methods are beginning to have significant impact in chemistry and condensed matter physics. For example, deep learning methods have demonstrated new capabilities for high-throughput virtual screening, and global optimization approaches for inverse design of materials. Recently, a relatively new branch of AI/ML, deep generative models (GMs), provide additional promise as they encode material structure and/or properties into a latent space, and through exploration and manipulation of the latent space can generate new materials. These approaches learn representations of a material structure and its corresponding chemistry or physics to accelerate materials discovery, which differs from traditional AI/ML methods that use statistical and combinatorial screening of existing materials via distinct structure-property relationships. However, application of GMs to inorganic materials has been notably harder than organic molecules because inorganic structure is often more complex to encode. In this work we review recent innovations that have enabled GMs to accelerate inorganic materials discovery. We focus on different representations of material structure, their impact on inverse design strategies using variational autoencoders or generative adversarial networks, and highlight the potential of these approaches for discovering materials with targeted properties needed for technological innovation.

36 MATERIALS SCIENCE↗

DOE OSTI2024

The relationship between stress, anxiety and eating behavior among Chinese students: a cross-sectional study

Background The expansion of higher education and the growing number of college students have led to increased awareness of mental health issues such as stress, anxiety, and eating disorders. In China, the educational system and cultural expectations contribute to the stress experienced by college students. This study aims to clarify the role of anxiety as a mediator in the relationship between stress and eating behaviors among Chinese college students. Methods This study utilized data from the 2021 Psychology and Behavior Investigation of Chinese Residents, which included 1,672 college students under the age of 25. The analysis methods comprised descriptive statistics, t -tests, Pearson correlation analyses, and mediation effect analysis. Results The findings indicate that Chinese college students experience high levels of stress, with long-term stress slightly exceeding short-term stress. Both types of stress were positively correlated with increased anxiety and the adoption of unhealthy eating behaviors. Anxiety was identified as a significant mediator, accounting for 28.3% of the relationship between long-term stress and eating behavior (95% CI = 0.058–0.183). The mediation effect of short-term stress on eating behavior through anxiety was also significant, explaining 61.4% of the total effect (95% CI = 0.185–0.327). Conclusion The study underscores the importance of stress management and mental health services for college students. It recommends a comprehensive approach to reducing external pressures, managing anxiety, and promoting healthy eating behaviors among college students. Suggestions include expanding employment opportunities, providing career guidance, enhancing campus and societal support for holistic development, strengthening mental health services, leveraging artificial intelligence technologies, educating on healthy lifestyles, and implementing targeted health promotion programs.

Chai, Yulin↗

DOE OSTI2017

Low-frequency Carbon Radio Recombination Lines. I. Calculations of Departure Coefficients

In the first paper of this series, we study the level population problem of recombining carbon ions. We focus our study on high quantum numbers, anticipating observations of carbon radio recombination lines to be carried out by the Low Frequency Array. We solve the level population equation including angular momentum levels with updated collision rates up to high principal quantum numbers. We derive departure coefficients by solving the level population equation in the hydrogenic approximation and including low-temperature dielectronic capture effects. Our results in the hydrogenic approximation agree well with those of previous works. When comparing our results including dielectronic capture, we find differences that we ascribe to updates in the atomic physics (e.g., collision rates) and to the approximate solution method of the statistical equilibrium equations adopted in previous studies. A comparison with observations is discussed in an accompanying article, as radiative transfer effects need to be considered.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

A Cross-correlation Study of High-energy Neutrinos and Tracers of Large-scale Structure

The origin of the bulk of the astrophysical neutrinos detected by the IceCube Observatory remains a mystery. Previous source-finding analyses compared the directions of IceCube events and individual sources in astrophysical catalogs. The source association method is technically challenging when the number of source candidates is much larger than the number of the observed astrophysical neutrinos. In this paper, we show that in this large source number regime, a two-point cross-correlation analysis of neutrino data and source catalog can instead be used to constrain potential source populations for the high-energy astrophysical neutrinos, and provide spatial evidence for the existence of astrophysical neutrinos. We present an analysis of the cross-correlation of the IceCube 2010–2012 point-source data and a WISE–2MASS galaxy sample. While we find no significant detection of cross-correlation with the publicly available neutrino data set, we show that, when applied to the full IceCube data, which has a longer observation time and higher astrophysical neutrino purity, our method has sufficient statistical power to detect a cross-correlation signal if the neutrino sources trace the large-scale structure of the universe.

79 ASTRONOMY AND ASTROPHYSICS↗