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All sources NASA NTRS DOE OSTI

DOE OSTI2021

Evaluating the Benefits of Bayesian Hierarchical Methods for Analyzing Heterogeneous Environmental Datasets: A Case Study of Marine Organic Carbon Fluxes

Large compilations of heterogeneous environmental observations are increasingly available as public databases, allowing researchers to test hypotheses across datasets. Statistical complexities arise when analyzing compiled data due to unbalanced spatial sampling, variable environmental context, mixed measurement techniques, and other reasons. Hierarchical Bayesian modeling is increasingly used in environmental science to describe these complexities, however few studies explicitly compare the utility of hierarchical Bayesian models to simpler and more commonly applied methods. Here we demonstrate the utility of the hierarchical Bayesian approach with application to a large compiled environmental dataset consisting of 5,741 marine vertical organic carbon flux observations from 407 sampling locations spanning eight biomes across the global ocean. We fit a global scale Bayesian hierarchical model that describes the vertical profile of organic carbon flux with depth. Profile parameters within a particular biome are assumed to share a common deviation from the global mean profile. Individual station-level parameters are then modeled as deviations from the common biome-level profile. The hierarchical approach is shown to have several benefits over simpler and more common data aggregation methods. First, the hierarchical approach avoids statistical complexities introduced due to unbalanced sampling and allows for flexible incorporation of spatial heterogeneitites in model parameters. Second, the hierarchical approach uses the whole dataset simultaneously to fit the model parameters which shares information across datasets and reduces the uncertainty up to 95% in individual profiles. Third, the Bayesian approach incorporates prior scientific information about model parameters; for example, the non-negativity of chemical concentrations or mass-balance, which we apply here. We explicitly quantify each of these properties in turn. We emphasize the generality of the hierarchical Bayesian approach for diverse environmental applications and its increasing feasibility for large datasets due to recent developments in Markov Chain Monte Carlo algorithms and easy-to-use high-level software implementations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss

Proteinaceous aggregates containing ?-synuclein protein called Lewy bodies in the substantia nigra is a hallmark of Parkinson’s disease. The molecular mechanisms of Lewy body formation and associated neuronal loss remain largely unknown. To gain insights on proteins and pathways associated with Lewy body pathology, we performed quantitative profiling of the proteome. We analyzed substantia nigra tissue from 51 subjects arranged into three groups: cases with Lewy body pathology, Lewy body-negative controls with matching neuronal loss and controls with no neuronal loss. Using label-free LC-MS/MS approach we quantified the 2,963 most abundant proteins. Statistical testing for differential protein abundance, followed by pathway enrichment and Bayesian learning of the causal network structure were performed to identify likely drivers of Lewy body formation and dopaminergic neuronal loss. The identified pathways include (1) Arp2/3 complex-mediated actin nucleation; (2) synaptic function; (3) poly(A) RNA binding; (4) basement membrane and endothelium; and (5) hydrogen peroxide metabolic process. According to the data, the endothelial/basement membrane pathway is tightly connected with both pathologies and likely to be one of the drivers of the neuronal loss. The poly(A) RNA-binding proteins, including the ones relevant to other neurodegenerative disorders (e.g. TDP-43 and FUS) have strong inverse correlation with Lewy bodies and may reflect alternative mechanism of nigral neurodegeneration.

Petyuk, Vladislav A.↗

DOE OSTI2022

Bayesian characterization of uncertainties surrounding fluvial flood hazard estimates

Fluvial floods drive severe risk to riverine communities. There is strong evidence of increasing flood hazards in many regions around the world. The choice of methods and assumptions used in flood hazard estimates can impact the design of risk management strategies. In this study, we characterize the expected flood hazards conditioned on the uncertain model structures, model parameters, and prior distributions of the parameters. We construct a Bayesian framework for river stage return level estimation using a nonstationary statistical model that relies exclusively on the Indian Ocean Dipole Index. We show that ignoring uncertainties can lead to biased estimation of expected flood hazards. We find that the considered model parametric uncertainty is more influential than model structures and model priors. Our results highlight the importance of incorporating uncertainty in extreme flood stage estimates, and are of practical use for informing water infrastructure designs in a changing climate.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Characterizing and Mitigating Intraday Variability: Reconstructing Source Structure in Accreting Black Holes with mm-VLBI

The extraordinary physical resolution afforded by the Event Horizon Telescope has opened a window onto the astrophysical phenomena unfolding on horizon scales in two known black holes, M87* and Sgr A*. However, with this leap in resolution has come a new set of practical complications. Sgr A* exhibits intraday variability that violates the assumptions underlying Earth aperture synthesis, limiting traditional image reconstruction methods to short timescales and data sets with very sparse (u, v) coverage. We present a new set of tools to detect and mitigate this variability. We develop a data-driven, model-agnostic procedure to detect and characterize the spatial structure of intraday variability. This method is calibrated against a large set of mock data sets, producing an empirical estimator of the spatial power spectrum of the brightness fluctuations. We present a novel Bayesian noise modeling algorithm that simultaneously reconstructs an average image and statistical measure of the fluctuations about it using a parameterized form for the excess variance in the complex visibilities not otherwise explained by the statistical errors. These methods are validated using a variety of simulated data, including general relativistic magnetohydrodynamic simulations appropriate for Sgr A* and M87*. We find that the reconstructed source structure and variability are robust to changes in the underlying image model. We apply these methods to the 2017 EHT observations of M87*, finding evidence for variability across the EHT observing campaign. The variability mitigation strategies presented are widely applicable to very long baseline interferometry observations of variable sources generally, for which they provide a data-informed averaging procedure and natural characterization of inter-epoch image consistency.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2010

Separating Gravitational Wave Signals from Instrument Artifacts

Central to the gravitational wave detection problem is the challenge of separating features in the data produced by astrophysical sources from features produced by the detector. Matched filtering provides an optimal solution for Gaussian noise, but in practice, transient noise excursions or "glitches" complicate the analysis. Detector diagnostics and coincidence tests can be used to veto many glitches which may otherwise be misinterpreted as gravitational wave signals. The glitches that remain can lead to long tails in the matched filter search statistics and drive up the detection threshold. Here we describe a Bayesian approach that incorporates a more realistic model for the instrument noise allowing for fluctuating noise levels that vary independently across frequency bands, and deterministic "glitch fitting" using wavelets as "glitch templates", the number of which is determined by a trans-dimensional Markov chain Monte Carlo algorithm. We demonstrate the method's effectiveness on simulated data containing low amplitude gravitational wave signals from inspiraling binary black hole systems, and simulated non-stationary and non-Gaussian noise comprised of a Gaussian component with the standard LIGO/Virgo spectrum, and injected glitches of various amplitude, prevalence, and variety. Glitch fitting allows us to detect significantly weaker signals than standard techniques.

Littenberg, Tyson B.↗

NASA NTRS2017

A Survey of Eight Hot Jupiters in Secondary Eclipse Using WIRCam at CFHT

We present near-infrared high-precision photometry for eight transiting hot Jupiters observed during their predicted secondary eclipses. Our observations were carried out using the staring mode of the WIRCam instrument on the Canada-France-Hawaii Telescope (CFHT).We present the observing strategies and data reduction methods which delivered time series photometry with statistical photometric precision as low as 0.11 percent. We performed a Bayesian analysis to model the eclipse parameters and systematics simultaneously. The measured planet-to-star flux ratios allowed us to constrain the thermal emission from the day side of these hot Jupiters, as we derived the planet brightness temperatures. Our results combined with previously observed eclipses reveal an excess in the brightness temperatures relative to the blackbody prediction for the equilibrium temperatures of the planets for a wide range of heat redistribution factors. We find a trend that this excess appears to be larger for planets with lower equilibrium temperatures. This may imply some additional sources of radiation, such as reflected light from the host star and/or thermal emission from residual internal heat from the formation of the planet.

Bayesian Analysis↗

DOE OSTI2025

Sensitive Detection of Structural Differences using a Statistical Framework for Comparative Crystallography

Chemical and conformational changes underlie the functional cycles of proteins. Comparative crystallography can reveal these changes over time, over ligands, and over chemical and physical perturbations in atomic detail. A key difficulty, however, is that the resulting observations must be placed on the same scale by correcting for experimental factors. We recently introduced a Bayesian framework for correcting (scaling) X-ray diffraction data by combining deep learning with statistical priors informed by crystallographic theory. To scale comparative crystallography data, we here combine this framework with a multivariate statistical theory of comparative crystallography. By doing so, we find strong improvements in the detection of protein dynamics, element-specific anomalous signal, and the binding of drug fragments.

Hekstra, Doeke R. [Harvard Univ., Cambridge, MA (U↗

DOE OSTI2021

Stopping criteria for ending autonomous, single detector radiological source searches

While the localization of radiological sources has traditionally been handled with statistical algorithms, such a task can be augmented with advanced machine learning methodologies. The combination of deep and reinforcement learning has provided learning-based navigation to autonomous, single-detector, mobile systems. However, these approaches lacked the capacity to terminate a surveying/search task without outside influence of an operator or perfect knowledge of source location (defeating the purpose of such a system). Two stopping criteria are investigated in this work for a machine learning navigated system: one based upon Bayesian and maximum likelihood estimation (MLE) strategies commonly used in source localization, and a second providing the navigational machine learning network with a “stop search” action. A convolutional neural network was trained via reinforcement learning in a 10 m × 10 m simulated environment to navigate a randomly placed detector-agent to a randomly placed source of varied strength (stopping with perfect knowledge during training). The network agent could move in one of four directions (up, down, left, right) after taking a 1 s count measurement at the current location. During testing, the stopping criteria for this navigational algorithm was based upon a Bayesian likelihood estimation technique of source presence, updating this likelihood after each step, and terminating once the confidence of the source being in a single location exceeded 0.9. A second network was trained and tested with similar architecture as the previous but which contained a fifth action: for self-stopping. The accuracy and speed of localization with set detector and source initializations were compared over 50 trials of MLE-Bayesian approach and 1000 trials of the CNN with self-stopping. The statistical stopping condition yielded a median localization error of ~1.41 m and median localization speed of 12 steps. The machine learning stopping condition yielded a median localization error of 0 m and median localization speed of 17 steps. This work demonstrated two stopping criteria available to a machine learning guided, source localization system.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2023

New constraints on sodium production in globular clusters from the Na 23 ( He 3 , d ) Mg 24 reaction

The star-to-star anticorrelation of sodium and oxygen is a defining feature of globular clusters, but, to date, the astrophysical site responsible for this unique chemical signature remains unknown. Sodium enrichment within these clusters depends sensitively on reaction rate of the sodium destroying reactions 23 Na(p, γ) and 23 Na(p,α). In this paper, we report the results of a 23 Na( 3 He,d) 24 Mg transfer reaction carried out at Triangle Universities Nuclear Laboratory using a 21 MeV 3 He beam. Astrophysically relevant states in 24 Mg between 11 < E x < 12 MeV were studied using high-resolution magnetic spectroscopy, thereby allowing the extraction of excitation energies and spectroscopic factors. Bayesian methods are combined with the distorted wave Born approximation to assign statistically meaningful uncertainties to the extracted spectroscopic factors. For the first time, these uncertainties are propagated through to the estimation of proton partial widths. Our experimental data are used to calculate the reaction rate. The impact of the new rates are investigated using asymptotic giant branch star models. Furthermore, it is found that while the astrophysical conditions still dominate the total uncertainty, intramodel variations on sodium production from the 23 Na(p, γ) and 23 Na(p,α) reaction channels are a lingering source of uncertainty.

20 ≤ A ≤ 38↗

NASA NTRS2009

A Method for Retrieving Ground Flash Fraction from Satellite Lightning Imager Data

A general theory for retrieving the fraction of ground flashes in N lightning observed by a satellite-based lightning imager is provided. An "exponential model" is applied as a physically reasonable constraint to describe the measured optical parameter distributions, and population statistics (i.e., mean, variance) are invoked to add additional constraints to the retrieval process. The retrieval itself is expressed in terms of a Bayesian inference, and the Maximum A Posteriori (MAP) solution is obtained. The approach is tested by performing simulated retrievals, and retrieval error statistics are provided. The ability to retrieve ground flash fraction has important benefits to the atmospheric chemistry community. For example, using the method to partition the existing satellite global lightning climatology into separate ground and cloud flash climatologies will improve estimates of lightning nitrogen oxides (NOx) production; this in turn will improve both regional air quality and global chemistry/climate model predictions.

Koshak, William J.↗

NASA NTRS1994

Operations for Learning with Graphical Models

This paper is a multidisciplinary review of empirical, statistical learning from a graphical model perspective. Well-known examples of graphical models include Bayesian net- works, directed graphs representing a Markov chain, and undirected networks representing a Markov field. These graphical models are extended to model data analysis and empirical learning using the notation of plates. Graphical operations for simplifying and manipulating a problem are provided including decomposition, differentiation, and the manipulation of probability models from the exponential family. These operations adapt existing techniques from statistics and automatic differentiation to graphs. Two standard algorithm schemes for learning are reviewed in a graphical framework: Gibbs sampling and the expectation maximization algorithm. Some algorithms are developed in this graphical framework including a generalized version of linear regression, techniques for feed-forward networks, and learning Gaussian and discrete Bayesian networks from data. The paper concludes by sketching some implications for data analysis and summarizing some popular algorithms that fall within the framework presented. The main original contributions here are the decomposition techniques and the demonstration that graphical models provide a framework for understanding and developing complex learning algorithms.

Buntine, Wray L.↗

DOE OSTI2022

Uncertainty quantification in breakup reactions

Breakup reactions are one of the favored probes to study loosely bound nuclei, particularly those in the limit of stability forming a halo. In order to interpret such breakup experiments, the continuum discretized coupled channel method is typically used. In this study, the first Bayesian analysis of a breakup reaction model is performed. Herein we use a combination of statistical methods together with a three-body reaction model (the continuum discretized coupled channel method) to quantify the uncertainties on the breakup observables due to the parameters in the effective potential describing the loosely bound projectile of interest. The combination of tools we develop opens the path for a Bayesian analysis of not only breakup processes, but also a wide array of complex processes that require computationally intensive reaction models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Multi-objective Bayesian alloy design using multi-task Gaussian processes

In design applications, correlations among material properties (such as the tendency for stronger materials to be less ductile) are often neglected. This approach is echoed in multi-objective optimization techniques which treat each performance characteristic as an independent objective, aiming to optimize scalar functions and find optimal Pareto fronts. However, this overlooks the statistical relationships between performance characteristics inherent in a material system. To address this, we propose the use of Bayesian optimization, a highly efficient black-box optimization algorithm known for constructing Gaussian processes (GPs) – uncorrelated surrogates - to model objective functions. Rather than evaluating multiple GPs for each objective function separately, we argue for a shift towards jointly modeling these objective functions, considering their statistical correlations. This integrated approach utilizes naturally occurring relationships among material properties, providing additional information to enhance the performance of the design framework. This requires the replacement of multiple independent GPs with a single multi-task GP, employing a correlation matrix to construct a multi-task kernel function, wherein each task corresponds to a single objective function. Here, we anticipate this refined methodology will better leverage material correlations, improving design optimization results.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Forest aboveground biomass estimation through integration of sentinel-2 and PALSAR-2 time series: assessing models trained on GEDI and field inventory benchmarks

Accurate and spatially explicit forest Aboveground Biomass (AGB) mapping through remote sensing is critical for quantifying terrestrial carbon stocks and informing effective forest management strategies. However, AGB estimation in dense forests with complex terrain remains challenging due to satellite sensor signal saturation problem (saturation issue occurs in high biomass forests), structural complexity, and limited ground truth for calibration. This study presents a novel framework that integrates multi-temporal Sentinel-2 optical imagery, ALOS PALSAR-2 Synthetic Aperture Radar (SAR) data, and topographic variables with explainable Machine Learning to map AGB across mountainous forests within subtropical and temperate oceanic climate zones of Mexico. We evaluate the effects of temporal granularity and sensor synergy by comparing multiple temporal inputs and sensor configurations (Sentinel-2, PALSAR-2, and their fusion), and assess model performance using two reference datasets: NASA GEDI LiDAR-derived biomass and Mexico’s National Forest and Soil Inventory (INFyS). Our results showed that models trained on INFyS consistently outperformed those trained on GEDI, highlighting limitations in GEDI’s reliability in biomass estimates within this study region. Furthermore, the integration of Sentinel-2 and PALSAR-2 provided improved predictions compared to single-sensor models, particularly when combined with temporally explicit yearly statistics. The best-performing model, which was trained on INFyS data, and considered both Sentinel-2 and PALSAR-2 yearly statistics, as well as topographic variables, achieved an R2 of 0.64, RMSE of 51.10 Mg/ha, and relative RMSE (rRMSE) of 58.69%. Explainable ML analysis identified Sentinel-2 spectral indices and topographic features as key predictors, while PALSAR-2 metrics provided complementary information, partially mitigating saturation effects in high-biomass areas. Specifically, integrating both sensors substantially improved AGB estimation in high biomass forest (≥200 Mg/ha), yielding 98% gains over optical-only model, with resulting estimates exceeding GEDI L4B by 29% and ESA-CCI-BIOMASS by 174%. Terrain-stratified analysis indicated close agreement with GEDI in low-slope areas, with increasing divergence as slope steepness increased, while estimates remained consistently higher than ESA-CCI-BIOMASS across all slope classes. The proposed approach advances multi-sensor fusion and temporal feature engineering for AGB mapping using open-access satellite datasets, providing a scalable and reproducible framework for annual biomass monitoring in topographically complex mountainous forests. The resulting 25 m resolution biomass product has the potential to provide spatially detailed information for forest monitoring and may support applications in carbon accounting and forest management.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Validation Metrics for Fixed Effects and Mixed-Effects Calibration

The modern scientific process often involves the development of a predictive computational model. To improve its accuracy, a computational model can be calibrated to a set of experimental data. A variety of validation metrics can be used to quantify this process. Some of these metrics have direct physical interpretations and a history of use, while others, especially those for probabilistic data, are more difficult to interpret. In this work, a variety of validation metrics are used to quantify the accuracy of different calibration methods. Frequentist and Bayesian perspectives are used with both fixed effects and mixed-effects statistical models. Through a quantitative comparison of the resulting distributions, the most accurate calibration method can be selected. Two examples are included which compare the results of various validation metrics for different calibration methods. It is quantitatively shown that, in the presence of significant laboratory biases, a fixed effects calibration is significantly less accurate than a mixed-effects calibration. This is because the mixed-effects statistical model better characterizes the underlying parameter distributions than the fixed effects model. The results suggest that validation metrics can be used to select the most accurate calibration model for a particular empirical model with corresponding experimental data.

97 MATHEMATICS AND COMPUTING↗

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↗

NASA NTRS1996

Software For Multivariate Bayesian Classification

PHD general-purpose classifier computer program. Uses Bayesian methods to classify vectors of real numbers, based on combination of statistical techniques that include multivariate density estimation, Parzen density kernels, and EM (Expectation Maximization) algorithm. By means of simple graphical interface, user trains classifier to recognize two or more classes of data and then use it to identify new data. Written in ANSI C for Unix systems and optimized for online classification applications. Embedded in another program, or runs by itself using simple graphical-user-interface. Online help files makes program easy to use.

Saul, Ronald↗

NASA NTRS2005

Bayesian Analysis of the Power Spectrum of the Cosmic Microwave Background

There is a wealth of cosmological information encoded in the spatial power spectrum of temperature anisotropies of the cosmic microwave background. The sky, when viewed in the microwave, is very uniform, with a nearly perfect blackbody spectrum at 2.7 degrees. Very small amplitude brightness fluctuations (to one part in a million!!) trace small density perturbations in the early universe (roughly 300,000 years after the Big Bang), which later grow through gravitational instability to the large-scale structure seen in redshift surveys... In this talk, I will discuss a Bayesian formulation of this problem; discuss a Gibbs sampling approach to numerically sampling from the Bayesian posterior, and the application of this approach to the first-year data from the Wilkinson Microwave Anisotropy Probe. I will also comment on recent algorithmic developments for this approach to be tractable for the even more massive data set to be returned from the Planck satellite.

Bayesian inference↗