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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The trailing edge is everywhere: tree rings reveal the transient risk of extinction hidden inside climate envelope forecasts

Given the importance of climate in shaping species’ geographic distributions, climate change poses an existential threat to biodiversity. Climate envelope modeling, the predominant approach used to quantify this threat, presumes that individuals in populations respond to climate variability and change according to species-level responses inferred from spatial occurrence data—such that individuals at the cool edge of a species’ distribution should benefit from warming (the “leading edge”), whereas individuals at the warm edge should suffer (the “trailing edge”). Using 1,558 tree-ring time series of an aridland pine (Pinus edulis) collected at 977 locations across the species’ distribution, we found that trees everywhere grow less in warmer-than-average and drier-than-average years. Ubiquitous negative temperature sensitivity indicates that individuals across the entire distribution should suffer with warming—the entire distribution is a trailing edge. Species-level responses to spatial climate variation are opposite in sign to individual-scale responses to time-varying climate for approximately half the species’ distribution with respect to temperature and the majority of the species’ distribution with respect to precipitation. These findings, added to evidence from the literature for scale-dependent climate responses in hundreds of species, suggest that correlative, equilibrium-based range forecasts may fail to accurately represent how individuals in populations will be impacted by changing climate. A scale-dependent view of the impact of climate change on biodiversity highlights the transient risk of extinction hidden inside climate envelope forecasts and the importance of evolution in rescuing species from extinction whenever local climate variability and change exceeds individual-scale climate tolerances.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Tree rings reveal the transient risk of extinction hidden inside climate envelope forecasts

Given the importance of climate in shaping species’ geographic distributions, climate change poses an existential threat to biodiversity. Climate envelope modeling, the predominant approach used to quantify this threat, presumes that individuals in populations respond to climate variability and change according to species-level responses inferred from spatial occurrence data—such that individuals at the cool edge of a species’ distribution should benefit from warming (the “leading edge”), whereas individuals at the warm edge should suffer (the “trailing edge”). Using 1,558 tree-ring time series of an aridland pine (Pinus edulis) collected at 977 locations across the species’ distribution, we found that trees everywhere grow less in warmer-than-average and drier-than-average years. Ubiquitous negative temperature sensitivity indicates that individuals across the entire distribution should suffer with warming—the entire distribution is a trailing edge. Species-level responses to spatial climate variation are opposite in sign to individual-scale responses to time-varying climate for approximately half the species’ distribution with respect to temperature and the majority of the species’ distribution with respect to precipitation. These findings, added to evidence from the literature for scale-dependent climate responses in hundreds of species, suggest that correlative, equilibrium-based range forecasts may fail to accurately represent how individuals in populations will be impacted by changing climate. A scale-dependent view of the impact of climate change on biodiversity highlights the transient risk of extinction hidden inside climate envelope forecasts and the importance of evolution in rescuing species from extinction whenever local climate variability and change exceeds individual-scale climate tolerances.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Bridging the Flux Gap: Sap Flow Measurements Reveal Species-Specific Patterns of Water Use in a Tallgrass Prairie

Woody encroachment, the process through which woody plants (trees and shrubs) replace grasses and wildflowers in grassland ecosystems, is occurring globally. Because woody plants use water differently (e.g., rates, soil depths of uptake, and time periods of activity) than grasses, woody encroachment could potentially change the water cycle in grasslands. In order to understand how grassland water use might change with ongoing woody encroachment, we measured continuous rates of water loss in common plant species in a North American grassland. Furthermore, we found that the main encroaching shrub in this grassland used more water over time than grasses or wildflowers. Additionally, this shrub and grasses used a large amount of water at night compared to wildflowers. Finally, we found that different weather conditions had different impacts on how water was used by woody plants, grasses, and wildflowers. We suggest that woody encroachment might reduce the amount of water stored in grasslands, which could alter the composition of grassland plants in the future.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Tracing the impacts of Mount Pinatubo eruption on regional climate using spatially-varying changepoint detection

Significant events, such as volcanic eruptions, can have global and long-lasting impacts on climate. These global impacts, however, are not uniform across space and time. Understanding how the Mt. Pinatubo eruption affects global and regional climate is of great interest for predicting the impact on climate due to similar events as well as understanding the possible effect of the stratospheric aerosol injections proposed to combat climate change. While many studies illustrated the impact of the Pinatubo eruption on a global scale, studies at a fine regional scale are scarce. Here, we propose a Bayesian spatially-varying changepoint detection and estimation method to trace the impact of Mt. Pinatubo eruption on regional climate. Our approach takes into account the diffusing nature and spatial correlation of the climate changes attributed to the volcanic eruption. We illustrate our method and demonstrate its advantages over an existing changepoint detection method through simulations. Finally, we apply our method to monthly stratospheric aerosol optical depth and surface temperature data from 1985 to 1995 to detect and estimate changepoints following the 1991 Mt. Pinatubo eruption. Our results quantitatively characterize the spatial pattern of the eruption’s impact on regional climate, complementing the previous studies on the global impact of the Pinatubo eruption.

Aerosol optical depth↗
DOE OSTI2024

Assessing heterogeneity of patient and health system delay among TB in a population with internal migrants in China

Backgrounds The diagnostic delay of tuberculosis (TB) contributes to further transmission and impedes the implementation of the End TB Strategy. Therefore, we aimed to describe the characteristics of patient delay, health system delay, and total delay among TB patients in Shanghai, identify areas at high risk for delay, and explore the potential factors of long delay at individual and spatial levels. Method The study included TB patients among migrants and residents in Shanghai between January 2010 and December 2018. Patient and health system delays exceeding 14 days and total delays exceeding 28 days were defined as long delays. Time trends of long delays were evaluated by Joinpoint regression. Multivariable logistic regression analysis was employed to analyze influencing factors of long delays. Spatial analysis of delays was conducted using ArcGIS, and the hierarchical Bayesian spatial model was utilized to explore associated spatial factors. Results Overall, 61,050 TB patients were notified during the study period. Median patient, health system, and total delays were 12 days (IQR: 3–26), 9 days (IQR: 4–18), and 27 days (IQR: 15–43), respectively. Migrants, females, older adults, symptomatic visits to TB-designated facilities, and pathogen-positive were associated with longer patient delays, while pathogen-negative, active case findings and symptomatic visits to non-TB-designated facilities were associated with long health system delays (LHD). Spatial analysis revealed Chongming Island was a hotspot for patient delay, while western areas of Shanghai, with a high proportion of internal migrants and industrial parks, were at high risk for LHD. The application of rapid molecular diagnostic methods was associated with reduced health system delays. Conclusion Despite a relatively shorter diagnostic delay of TB than in the other regions in China, there was vital social-demographic and spatial heterogeneity in the occurrence of long delays in Shanghai. While the active case finding and rapid molecular diagnosis reduced the delay, novel targeted interventions are still required to address the challenges of TB diagnosis among both migrants and residents in this urban setting.

Sun, Ruoyao↗
DOE OSTI2025

Lens Model Accuracy in the Expected LSST Lensed AGN Sample

Strong gravitational lensing of active galactic nuclei (AGN) enables measurements of cosmological parameters through time-delay cosmography (TDC). With data from the upcoming LSST survey, we anticipate using a sample of O(1000) lensed AGN for TDC. To prepare for this dataset and enable this measurement, we construct and analyze a realistic mock sample of 1300 systems drawn from the OM10 (Oguri & Marshall 2010) catalog of simulated lenses with AGN sources at $z<3.1$ in order to test a key aspect of the analysis pipeline, that of the lens modeling. We realize the lenses as power law elliptical mass distributions and simulate 5-year LSST i-band coadd images. From every image, we infer the lens mass model parameters using neural posterior estimation (NPE). Focusing on the key model parameters, $θ_E$ (the Einstein Radius) and $γ_{lens}$ (the projected mass density profile slope), with consistent mass-light ellipticity correlations in test and training data, we recover $θ_E$ with less than 1% bias per lens, 6.5% precision per lens and $γ_{lens}$ with less than 3% bias per lens, 8% precision per lens. We find that lens light subtraction prior to modeling is only useful when applied to data sampled from the training prior. If emulated deconvolution is applied to the data prior to modeling, precision improves across all parameters by a factor of 2. Finally, we combine the inferred lens mass models using Bayesian Hierarchical Inference to recover the global properties of the lens sample with less than 1% bias.

Venkatraman, Padmavathi [Illinois U., Urbana; KIPA↗
DOE OSTI2021

Optimal Bayesian supervised domain adaptation for RNA sequencing data

Abstract Motivation When learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited. Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success. But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all. Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks. Results In this article, we develop a generative optimal Bayesian supervised domain adaptation (OBSDA) model that can integrate RNA sequencing (RNA-Seq) data from different domains along with their labels for improving prediction accuracy in the target domain. Our model can be applied in cases where different domains share the same labels or have different ones. OBSDA is based on a hierarchical Bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters. We first provide an efficient Gibbs sampler for parameter inference in OBSDA. Then, we leverage the gene-gene network prior information and construct an informed and flexible variational family to infer the posterior distributions of model parameters. Comprehensive experiments on real-world RNA-Seq data demonstrate the superior performance of OBSDA, in terms of accuracy in identifying cancer subtypes by utilizing data from different domains. Moreover, we show that by taking advantage of the prior network information we can further improve the performance. Availability and implementation The source code for implementations of OBSDA and SI-OBSDA are available at the following link. https://github.com/SHBLK/BSDA. Supplementary information Supplementary data are available at Bioinformatics online.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Hierarchical Bayesian Thermonuclear Rate for the 7 Be(n,p) 7 Li Big Bang Nucleosynthesis Reaction

Big Bang nucleosynthesis provides the earliest probe of standard model physics, at a time when the universe was less than 1000 seconds old. It determines the abundances of the lightest nuclides, which give rise to the subsequent history of the visible matter in the universe. This work derives new 7 Be(n,p) 7 Li thermonuclear reaction rates based on all available experimental information. This reaction sensitively impacts the primordial abundances of 7 Be and 7 Li during big bang nucleosynthesis. We critically evaluate all available data and disregard experimental results that are questionable. For the nuclear model, we adopt an incoherent sum of single-level, two-channel, R -matrix approximation expressions, which are implemented into a hierarchical Bayesian model, to analyze the remaining six data sets we deem most reliable. In the fitting of the data, we consistently model all known sources of uncertainty, including discrepant absolute normalizations of different data sets, and also take the variation of the neutron and proton channel radii into account, hence providing less biased estimates of the 7 Be(n,p) 7 Li thermonuclear rates. From the resulting posteriors, we extract R -matrix parameters ($E_r, γ^2_n, γ^2_p$) and derive excitation energies and partial and total widths. Our fit is sensitive to the contributions of the first three levels above the neutron threshold. Reaction rates were computed by integrating 10,000 samples of the reduced cross section. Our 7 Be(n,p) 7 Li thermonuclear rates have uncertainties between 1.5% and 2.0% at temperatures of ≤1 GK. Finally, we compare our rates to previous results and find that the 7 Be(n,p) 7 Li rates most commonly used in big bang simulations have uncertainties that are too optimistic.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Surface and subsurface oceanographic features drive forage fish distributions and aggregations: Implications for prey availability to top predators in the US Northeast Shelf ecosystem

Abstract Forage fishes are a critical food web link in marine ecosystems, aggregating in a hierarchical patch structure over multiple spatial and temporal scales. Surface‐level forage fish aggregations (FFAs) represent a concentrated source of prey available to surface‐ and shallow‐foraging marine predators. Existing survey and analysis methods are often imperfect for studying forage fishes at scales appropriate to foraging predators, making it difficult to quantify predator–prey interactions. In many cases, general distributions of forage fish species are known; however, these may not represent surface‐level prey availability to predators. Likewise, we lack an understanding of the oceanographic drivers of spatial patterns of prey aggregation and availability or forage fish community patterns. Specifically, we applied Bayesian joint species distribution models to bottom trawl survey data to assess species‐ and community‐level forage fish distribution patterns across the US Northeast Continental Shelf (NES) ecosystem. Aerial digital surveys gathered data on surface FFAs at two project sites within the NES, which we used in a spatially explicit hierarchical Bayesian model to estimate the abundance and size of surface FFAs. We used these models to examine the oceanographic drivers of forage fish distributions and aggregations. Our results suggest that, in the NES, regions of high community species richness are spatially consistent with regions of high surface FFA abundance. Bathymetric depth drove both patterns, while subsurface features, such as mixed layer depth, primarily influenced aggregation behavior and surface features, such as sea surface temperature, sub‐mesoscale eddies, and fronts influenced forage fish diversity. In combination, these models help quantify the availability of forage fishes to marine predators and represent a novel application of spatial models to aerial digital survey data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A Spatiotemporal Prediction Model for Regional Scheduling of Shared Bicycles Based on the INLA Method

Dock-less bicycle-sharing programs have been widely accepted as an efficient mode to benefit health and reduce congestions. And modeling and prediction has always been a core proposition in the field of transportation. Most of the existing demand prediction models for shared bikes take regions as research objects; therefore, a POI-based method can be a beneficial complement to existing research, including zone-level, OD-level, and station-level techniques. Point of interest (POI) is the location description of spatial entities, which can reflect the cycling route characteristics for both commuting and noncommuting trips to a certain extent, and is also the main generating point and attraction point of shared-bike travel flow. In this study, we make an effort to model a POI-level cycling demand with a Bayesian hierarchical method. The proposed model combines the integrated nested Laplace approximation (INLA) and random partial differential equation (SPDE) to cope with the huge computation in the modeling process. In particular, we have adopted the dock-less bicycle-sharing rental records of Mobike as a case study to validate our method; the study area was one of the fastest growing urban districts in Shanghai in August 2016. The operation results show that the method can help better understand, measure, and characterize spatiotemporal patterns of bike-share ridership at the POI level and quantify the impact of the spatiotemporal effect on bicycle-sharing use.

Yu, Zhuoran↗
DOE OSTI2025

Lens Modeling of STRIDES Strongly Lensed Quasars Using Neural Posterior Estimation

Strongly lensed quasars can be used to constrain cosmological parameters through time-delay cosmography. Models of the lens masses are a necessary component of this analysis. To enable time-delay cosmography from a sample of $\mathcal{O}(10^3)$ lenses, which will soon become available from surveys like the Rubin Observatory’s Legacy Survey of Space and Time and the Euclid Wide Survey, we require fast and standardizable modeling techniques. To address this need, we apply neural posterior estimation (NPE) for modeling galaxy-scale strongly lensed quasars from the Strong Lensing Insights into the Dark Energy Survey (STRIDES) sample. NPE brings two advantages: speed and the ability to implicitly marginalize over nuisance parameters. We extend this method by employing sequential NPE to increase precision of mass model posteriors. We then fold individual lens models into a hierarchical Bayesian inference to recover the population distribution of lens mass parameters, accounting for out-of-distribution shift. After verifying our method using simulated analogs of the STRIDES lens sample, we apply our method to 14 Hubble Space Telescope single-filter observations. We find the population mean of the power-law elliptical mass distribution slope, γ lens , to be $\mathcal{M}_γ$ lens = 2.13 ± 0.06. Our result represents the first population-level constraint for these systems. This population-level inference from fully automated modeling is an important stepping stone toward cosmological inference with large samples of strongly lensed quasars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Fully Bayesian Analysis With Model Inadequacy Correction For Nuclear Graphite Property Models With Hierarchical Variance Structure

Nuclear-grade graphites are extensively utilized in the core designs of various advanced nuclear reactors. Within the reactor environment, graphite is subjected to prolonged exposure to extreme conditions, including high temperatures, radiation, and potentially molten salt and oxygen. Such exposure can induce several degradation mechanisms in graphite, such as nonuniform volumetric strains caused by irradiation and thermal expansion, leading to stresses that may compromise the performance of graphite components. Assessing component integrity, forecasting component performance over the reactor's lifespan, and developing design standards necessitate robust tools for predicting fracture initiation and propagation in graphite structural components within nuclear reactors. This code enables the Bayesian calibration of properties for nuclear-grade graphites. Using a hierarchical Bayesian approach, multiple experimental data sources are combined to develop Gaussian process models for the properties. Using the Kennedy O'Hagan framework, the uncertainties due inadequacies in the model and the inherent spread in the experimental data are quantified.

Dhulipala, Som Lakshmi NarasimhaLakshmi Narasimha ↗
DOE OSTI2024

Body size and early marine conditions drive changes in Chinook salmon productivity across northern latitude ecosystems

Disentangling the influences of climate change from other stressors affecting the population dynamics of aquatic species is particularly pressing for northern latitude ecosystems, where climate‐driven warming is occurring faster than the global average. Chinook salmon (Oncorhynchus tshawytscha) in the Yukon‐Kuskokwim (YK) region occupy the northern extent of their species' range and are experiencing prolonged declines in abundance resulting in fisheries closures and impacts to the well‐being of Indigenous people and local communities. These declines have been associated with physical (e.g., temperature, streamflow) and biological (e.g., body size, competition) conditions, but uncertainty remains about the relative influence of these drivers on productivity across populations and how salmon–environment relationships vary across watersheds. To fill these knowledge gaps, we estimated the effects of marine and freshwater environmental indicators, body size, and indices of competition, on the productivity (adult returns‐per‐spawner) of 26 Chinook salmon populations in the YK region using a Bayesian hierarchical stock‐recruitment model. Across most populations, productivity declined with smaller spawner body size and sea surface temperatures that were colder in the winter and warmer in the summer during the first year at sea. Decreased productivity was also associated with above average fall maximum daily streamflow, increased sea ice cover prior to juvenile outmigration, and abundance of marine competitors, but the strength of these effects varied among populations. Maximum daily stream temperature during spawning migration had a nonlinear relationship with productivity, with reduced productivity in years when temperatures exceeded thresholds in main stem rivers. These results demonstrate for the first time that well‐documented declines in body size of YK Chinook salmon were associated with declining population productivity, while taking climate into account.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Bayesian model mixing with multireference energy density functional

Reliably predicting nuclear properties across the entire chart of isotopes is important for applications ranging from nuclear astrophysics to superheavy science to nuclear technology. To this day, however, all the theoretical models that can scale at the level of the chart of isotopes remain semiphenomenological. Because they are fitted locally, their predictive power can vary significantly; different versions of the same theory provide different predictions. Bayesian model mixing takes advantage of such imperfect models to build a local mixture of a set of models to make improved predictions. Earlier attempts to use Bayesian model mixing for mass table calculations relied on models treated at single-reference energy density functional level, which fail to capture some of the correlations caused by configuration mixing or the restoration of broken symmetries. In this study we have applied Bayesian model mixing techniques within a multireference energy density functional (MR-EDF) framework. We considered predictions of two-particle separation energies from particle number projection or angular momentum projection with four different energy density functionals—a total of eight different MR-EDF models. We used a hierarchical Bayesian stacking framework with a Dirichlet prior distribution over weights together with an inverse log-ratio transform to enable positive correlations between different models. We found that Bayesian model mixing provides significantly improved predictions compared to the participating models. Published by the American Physical Society 2025

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

A framework for strategic discovery of credible neural network surrogate models under uncertainty

The widespread integration of deep neural networks in developing data-driven surrogate models for high-fidelity simulations of complex physical systems highlights the critical necessity for robust uncertainty quantification techniques and credibility assessment methodologies, ensuring the reliable deployment of surrogate models in consequential decision-making. Here, this study presents the Occam Plausibility Algorithm for surrogate models (OPAL-surrogate), providing a systematic framework to uncover predictive neural network-based surrogate models within the large space of potential models, including various neural network classes and choices of architecture and hyperparameters. The framework is grounded in hierarchical Bayesian inferences and employs model validation tests to evaluate the credibility and prediction reliability of the surrogate models under uncertainty. Leveraging these principles, OPAL-surrogate introduces a systematic and efficient strategy for balancing the trade-off between model complexity, accuracy, and prediction uncertainty. The effectiveness of OPAL-surrogate is demonstrated through two modeling problems, including the deformation of porous materials for building insulation and turbulent combustion flow for ablation of solid fuels within hybrid rocket motors.

42 ENGINEERING↗
DOE OSTI2020

On the quantification and efficient propagation of imprecise probabilities with copula dependence

This paper addresses the problem of quantification and propagation of uncertainties associated with dependence modeling when data for characterizing probability models are limited. Practically, the system inputs are often assumed to be mutually independent or correlated by a multivariate Gaussian distribution. However, this subjective assumption may introduce bias in the response estimate if the real dependence structure deviates from this assumption. In this work, we overcome this limitation by introducing a flexible copula dependence model to capture complex dependencies. Here, a hierarchical Bayesian multimodel approach is proposed to quantify uncertainty in dependence model-form and model parameters that result from small data sets. This approach begins by identifying, through Bayesian multimodel inference, a set of candidate marginal models and their corresponding model probabilities, and then estimating the uncertainty in the copula-based dependence structure, which is conditional on the marginals and their parameters. The overall uncertainties integrating marginals and copulas are probabilistically represented by an ensemble of multivariate candidate densities. A novel importance sampling reweighting approach is proposed to efficiently propagate the overall uncertainties through a computational model. Through an example studying the influence of constituent properties on the out-of-plane properties of transversely isotropic E-glass fiber composites, we show that the composite property with copula-based dependence model converges to the true estimate as data set size increases, while an independence or arbitrary Gaussian correlation assumption leads to a biased estimate.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗