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DOE OSTI2023

Image-based solar estimates

An example device is configured to determine, based on a sky image of a portion of sky over a power distribution network and using a convolutional neural network (CNN)-based image regression model, an estimated global horizontal irradiance (GHI) value and manage or control the power distribution network using the estimated GHI value. The device may also be configured to determine, based on GHI values and aggregate load values for at least a portion of the power distribution network, using a Bayesian Structural Time Series model, an estimated photovoltaic power output value for the at least a portion of the power distribution network. The device may manage or control the power distribution network using the estimated photovoltaic power output value.

Bernstein, Andrey↗

DOE OSTI2022

Autodifferentiable Spectrum Model for High-dispersion Characterization of Exoplanets and Brown Dwarfs

We present an autodifferentiable spectral modeling of exoplanets and brown dwarfs. This model enables a fully Bayesian inference of the high-dispersion data to fit the ab initio line-by-line spectral computation to the observed spectrum by combining it with the Hamiltonian Monte Carlo in recent probabilistic programming languages. An open-source code, ExoJAX, developed in this study, was written in Python using the GPU/TPU compatible package for automatic differentiation and accelerated linear algebra, JAX. We validated the model by comparing it with existing opacity calculators and a radiative transfer code and found reasonable agreements for the output. As a demonstration, we analyzed the high-dispersion spectrum of a nearby brown dwarf, Luhman 16 A, and found that a model including water, carbon monoxide, and H 2 /He collision-induced absorption was well fitted to the observed spectrum (R = 10 5 and 2.28-2.30 μm). As a result, we found that T0 = 1295$^{-32}_{+35}$ K at 1 bar and C/O = 0.62 ± 0.03, which is slightly higher than the solar value. This work demonstrates the potential of a full Bayesian analysis of brown dwarfs and exoplanets as observed by high-dispersion spectrographs and also directly imaged exoplanets as observed by high-dispersion coronagraphy.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

A neural-network-enhanced parameter-varying framework for multi-objective model predictive control applied to buildings

Management of the electrical grid is becoming more complex due to the increased penetration of alternative energy generation technologies and a broadening diversity of electric loads. This complexity creates challenges in balancing demand and generation that can increase the potential for grid instabilities. One effective way to address this issue is to leverage previously unexploited demand flexibility through advanced control strategies. In this work, we propose an advanced control method, called adaptive neural parameter-varying model predictive control (ANPV-MPC), to control the temperature and energy consumption of a building via its Heating, Ventilation, and Air Conditioning system. ANPV-MPC combines key ideas in parameter-varying control, adaptive control, and online learning strategies to bridge the gap between computationally efficient linear model predictive control and more accurate nonlinear model predictive control. The novelty in ANPV-MPC is the use of a physics-inspired Bayesian neural network to estimate the coefficients of the parameter-varying linear control model. The Bayesian neural network additionally provides uncertainty estimates, triggering online training to capture evolving building system conditions. We show that ANPV-MPC can approximate the building system dynamics with a 28.39% higher accuracy than traditional linear model predictive control, resulting in 36.23% better control performance without increasing complexity of the optimal control problem. ANPV-MPC also adapts in real time to previously unseen conditions using online learning, further improving its performance.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

PyApprox: A software package for sensitivity analysis, Bayesian inference, optimal experimental design, and multi-fidelity uncertainty quantification and surrogate modeling

PyApprox is a Python-based one-stop-shop for probabilistic analysis of numerical models such as those used in the earth, environmental and engineering sciences. Easy to use and extendable tools are provided for constructing surrogates, sensitivity analysis, Bayesian inference, experimental design, and forward uncertainty quantification. The algorithms implemented represent a wide range of methods for model analysis developed over the past two decades, including recent advances in multi-fidelity approaches that use multiple model discretizations and/or simplified physics to significantly reduce the computational cost of various types of analyses. An extensive set of Benchmarks from the literature is also provided to facilitate the easy comparison of new or existing algorithms for a wide range of model analyses. Here, this paper introduces PyApprox and its various features, and presents results demonstrating the utility of PyApprox on a benchmark problem modeling the advection of a tracer in groundwater.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

An Empirical Model For Intrinsic Alignments: Insights From Cosmological Simulations

We extend current models of the halo occupation distribution (HOD) to include a flexible, empirical framework for the forward modeling of the intrinsic alignment (IA) of galaxies. A primary goal of this work is to produce mock galaxy catalogs for the purpose of validating existing models and methods for the mitigation of IA in weak lensing measurements. This technique can also be used to produce new, simulation-based predictions for IA and galaxy clustering. Our model is probabilistically formulated, and rests upon the assumption that the orientations of galaxies exhibit a correlation with their host dark matter (sub)halo orientation or with their position within the halo. We examine the necessary components and phenomenology of such a model by considering the alignments between (sub)halos in a cosmological dark matter only simulation. We then validate this model for a realistic galaxy population in a set of simulations in the Illustris-TNG suite. We create an HOD mock with Illustris-like correlations using our method, constraining the associated IA model parameters, with the $\mathcal{X}$$^{2}_{dof}$ between our model’s correlations and those of Illustris matching as closely as 1.4 and 1.1 for orientation–position and orientation–orientation correlation functions, respectively. By modeling the misalignment between galaxies and their host halo, we show that the 3-dimensional two-point position and orientation correlation functions of simulated (sub)halos and galaxies can be accurately reproduced from quasi-linear scales down to 0.1 $\mathcal{h}$ –1 Mpc. We also find evidence for environmental influence on IA within a halo. Our publicly-available software provides a key component enabling efficient determination of Bayesian posteriors on IA model parameters using observational measurements of galaxy-orientation correlation functions in the highly nonlinear regime.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Human limits in machine learning: prediction of potato yield and disease using soil microbiome data

Abstract Background The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide one of the first comprehensive investigations into the predictive potential of machine learning models for understanding the connections between soil and biological phenotypes. We investigate an integrative framework performing accurate machine learning-based prediction of plant performance from biological, chemical, and physical properties of the soil via two models: random forest and Bayesian neural network. Results Prediction improves when we add environmental features, such as soil properties and microbial density, along with microbiome data. Different preprocessing strategies show that human decisions significantly impact predictive performance. We show that the naive total sum scaling normalization that is commonly used in microbiome research is one of the optimal strategies to maximize predictive power. Also, we find that accurately defined labels are more important than normalization, taxonomic level, or model characteristics. ML performance is limited when humans can’t classify samples accurately. Lastly, we provide domain scientists via a full model selection decision tree to identify the human choices that optimize model prediction power. Conclusions Our study highlights the importance of incorporating diverse environmental features and careful data preprocessing in enhancing the predictive power of machine learning models for soil and biological phenotype connections. This approach can significantly contribute to advancing agricultural practices and soil health management.

Aghdam, Rosa↗

DOE OSTI2023

Probabilistic Physics-Informed Graph Convolutional Network for Active Distribution System Voltage Prediction

Here this letter proposes a novel data-driven probabilistic physics-informed graph convolutional network (GCN) for active distribution system voltage prediction with PVs and EVs. It leverages both measurements and network topology to accurately and efficiently predict node voltages without the need for an accurate distribution system power flow model. The dropout-enabled Bayesian inference is developed to achieve uncertainty quantification of the voltage prediction. Thanks to the network model embedding, it also has robustness against topology changes, a key difference with existing machine learning-based approaches. Comparison results with other state-of-the-art machine learning methods on a realistic 759-node distribution system demonstrate that the proposed method can achieve better accuracy and robustness under different scenarios.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Applications of emulation and Bayesian methods in heavy-ion physics

Abstract Heavy-ion collisions provide a window into the properties of many-body systems of deconfined quarks and gluons. Understanding the collective properties of quarks and gluons is possible by comparing models of heavy-ion collisions to measurements of the distribution of particles produced at the end of the collisions. These model-to-data comparisons are extremely challenging, however, because of the complexity of the models, the large amount of experimental data, and their uncertainties. Bayesian inference provides a rigorous statistical framework to constrain the properties of nuclear matter by systematically comparing models and measurements. This review covers model emulation and Bayesian methods as applied to model-to-data comparisons in heavy-ion collisions. Replacing the model outputs (observables) with Gaussian process emulators is key to the Bayesian approach currently used in the field, and both current uses of emulators and related recent developments are reviewed. The general principles of Bayesian inference are then discussed along with other Bayesian methods, followed by a systematic comparison of seven recent Bayesian analyses that studied quark-gluon plasma properties, such as the shear and bulk viscosities. The latter comparison is used to illustrate sources of differences in analyses, and what it can teach us for future studies.

Paquet, Jean-François (ORCID:0000000187368171)↗

DOE OSTI2021

A Bayesian nonparametric analysis for zero-inflated multivariate count data with application to microbiome study

High-throughput sequencing technology has enabled researchers to profile microbial communities from a variety of environments, but analysis of multivariate taxon count data remains challenging. Here, we develop a Bayesian nonparametric (BNP) regression model with zero inflation to analyse multivariate count data from microbiome studies. A BNP approach flexibly models microbial associations with covariates, such as environmental factors and clinical characteristics. The model produces estimates for probability distributions which relate microbial diversity and differential abundance to covariates, and facilitates community comparisons beyond those provided by simple statistical tests. We compare the model to simpler models and popular alternatives in simulation studies, showing, in addition to these additional community-level insights, it yields superior parameter estimates and model fit in various settings. The model's utility is demonstrated by applying it to a chronic wound microbiome data set and a Human Microbiome Project data set, where it is used to compare microbial communities present in different environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Analytical methods for superresolution dislocation identification in dark-field X-ray microscopy

In this work, we develop several inference methods to estimate the position of dislocations from images generated using dark-field X-ray microscopy (DFXM)—achieving superresolution accuracy and principled uncertainty quantification. Using the framework of Bayesian inference, we incorporate models of the DFXM contrast mechanism and detector measurement noise, along with initial position estimates, into a statistical model coupling DFXM images with the dislocation position of interest. We motivate several position estimation and uncertainty quantification algorithms based on this model. We then demonstrate the accuracy of our primary estimation algorithm on synthetic realistic DFXM images of edge dislocations in single-crystal aluminum. We conclude with a discussion of our methods’ impact on future dislocation studies and possible future research avenues.

36 MATERIALS SCIENCE↗

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 OSTI2024

Interpreting strain tensor data to characterize and monitor reservoirs for CO2 storage and other applications

Recent advances in instrumentation have made it feasible to measure the transient strain tensor caused by small changes in fluid volume or pressure in the subsurface and this has opened the door to new opportunities for characterization and monitoring. We have deployed strainmeters and then conducted injection well tests in an underlying reservoir at 530m depth. The resulting data indicated that the horizontal strain at shallow strainmeters (30 to 40m depth) was tensile and the vertical strain was compressive. The radial strain was less than the horizontal strain, and the strain rates decreased from 100 nanostrain/day to roughly 10 n/d over a few days. The signal at two strainmeters at shallow depth were consistent, although the magnitude of the horizontal strains were different reflecting the different radial directions from the well. The signal at a deep strainmeter deployed at reservoir depth was much different, with tensile vertical strains and compressive horizontal strains. These data can be interpreted by inverting poroelastic forward models developed using numerical and analytical methods. The average horizontal strain in the caprock resembles the transient pressure in the underlying reservoir and classic type-curve methods from transient well testing can be used for preliminary interpretations of strain data. We have developed closed-form analytical solutions to a pressurized poroelastic inclusion and inhomogeneity in a half-space. This model is fast and can be inverted to estimate reservoir stiffness and geometry. Numerical models developed using finite element methods allow more details of the subsurface to be included in the inversion, but they require much longer run times and this makes inversion cumbersome using standard methods. We have developed an inversion approach that uses a proxy model created using machine learning to do most of the forward calculations. The proxy model is periodically updated and refined using the finite element model to ensure accuracy. This approach significantly reduces the computational requirements and makes it feasible to use Bayesian inversion with large numerical models. We have shown that the strain tensor in the caprock is sensitive to pressure in the reservoir, boundaries in the reservoir, and pressure in the caprock caused by leaks. These results indicate that coupling strain tensor data with inversion has the potential to help evaluate reservoirs during initial characterization, and to monitor them during the CO2 injection and storage process.

Murdoch, Larry↗

DOE OSTI2020

A Data-Driven Nonparametric Approach for Probabilistic Load-Margin Assessment Considering Wind Power Penetration

A modern power system is characterized by an increasing penetration of wind power, which results in large uncertainties in its states. These uncertainties must be quantified properly; otherwise, the system security may be threatened. Facing this challenge, here we propose a cost-effective, data-driven approach to assessing a power system's load margin probabilistically. Using actual wind data, a kernel density estimator is applied to infer the nonparametric wind speed distributions, which are further merged into the framework of a vine copula. The latter enables us to simulate complex multivariate and highly dependent model inputs with a variety of bivariate copulae that precisely represent the tail dependence in the correlated samples. Furthermore, to reduce the prohibitive computational time of traditional Monte-Carlo simulations that process a large amount of samples, we propose to use a nonparametric, Gaussian-process-emulator-based reduced-order model to replace the original complicated continuation power-flow model through a Bayesian-learning framework. To accelerate the convergence rate of this Bayesian algorithm, a truncated polynomial chaos surrogate, which serves as a highly efficient, parametric Bayesian prior, is developed. This emulator allows us to execute the time-consuming continuation power-flow solver at the sampled values with a negligible computational cost. Results of simulations that are performed on several test systems reveal the impressive performance of the proposed method in the probabilistic load-margin assessment.

17 WIND ENERGY↗

DOE OSTI2022

Comprehensive compartmental model and calibration algorithm for the study of clinical implications of the population-level spread of COVID-19: a study protocol

The complex dynamics of the coronavirus disease 2019 (COVID-19) pandemic has made obtaining reliable long-term forecasts of the disease progression difficult. Simple mechanistic models with deterministic parameters are useful for short-term predictions but have ultimately been unsuccessful in extrapolating the trajectory of the pandemic because of unmodelled dynamics and the unrealistic level of certainty that is assumed in the predictions. We propose a 22-compartment epidemiological model that includes compartments not previously considered concurrently, to account for the effects of vaccination, asymptomatic individuals, inadequate access to hospital care, post-acute COVID-19 and recovery with long-term health complications. Additionally, new connections between compartments introduce new dynamics to the system and provide a framework to study the sensitivity of model outputs to several concurrent effects, including temporary immunity, vaccination rate and vaccine effectiveness. Subject to data availability for a given region, we discuss a means by which population demographics (age, comorbidity, socioeconomic status, sex and geographical location) and clinically relevant information (different variants, different vaccines) can be incorporated within the 22-compartment framework. Considering a probabilistic interpretation of the parameters allows the model's predictions to reflect the current state of uncertainty about the model parameters and model states. We propose the use of a sparse Bayesian learning algorithm for parameter calibration and model selection. This methodology considers a combination of prescribed parameter prior distributions for parameters that are known to be essential to the modelled dynamics and automatic relevance determination priors for parameters whose relevance is questionable. This is useful as it helps prevent overfitting the available epidemiological data when calibrating the parameters of the proposed model. Population-level administrative health data will serve as partial observations of the model states.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Exploring experimental conditions to reduce uncertainties in the optical potential

Uncertainty quantification for nuclear theories has gained a more prominent role in the field, with more groups attempting to understand the uncertainties in their calculations. However, recent studies have shown that the uncertainties on the optical potentials are too large for the theory to be useful. The goal of this work is to explore possible experimental conditions that may reduce the uncertainties on elastic scattering and single-nucleon transfer cross sections that come from the fitting of the optical model parameters to experimental data. Using Bayesian methods, we explore the effect of the uncertainties of optical model parameters on the angular grid of the differential cross section, including cross-section data at nearby energies, and changes in the experimental error bars. We also study the effect on the resulting uncertainty when other observables are included in the fitting procedure, particularly the total (reaction) cross sections. We study proton and neutron elastic scattering on 48 Ca and 208 Pb. We explore the parameter space with the Markov-chain Monte Carlo method, produce posterior distributions for the optical model parameters, and construct the corresponding 95% confidence intervals on the elastic-scattering cross sections. We also propagate the uncertainties on the optical potentials to the 48 Ca(d,p) 49 Ca(g.s.) and 208 Pb(d,p) 209 Pb(g.s.) cross sections. We find little sensitivity to the angular grid and an improvement of up to a factor of 2 on the uncertainties by including data at a nearby energy. Although reducing the error bars on the data does reduce the uncertainty, the gain is often considerably smaller than one would naively expect. We also find that the inclusion of total reaction cross section can improve the uncertainty although the magnitude of the effect depends strongly on the cases considered.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Bayesian Active Learning for Scanning Probe Microscopy: From Gaussian Processes to Hypothesis Learning

Recent progress in machine learning methods and the emerging availability of programmable interfaces for scanning probe microscopes (SPMs) have propelled automated and autonomous microscopies to the forefront of attention of the scientific community. However, enabling automated microscopy requires the development of task-specific machine learning methods, understanding the interplay between physics discovery and machine learning, and fully defined discovery workflows. This, in turn, requires balancing the physical intuition and prior knowledge of the domain scientist with rewards that define experimental goals and machine learning algorithms that can translate these to specific experimental protocols. Here, we discuss the basic principles of Bayesian active learning and illustrate its applications for SPM. We progress from the Gaussian process as a simple data-driven method and Bayesian inference for physical models as an extension of physics-based functional fits to more complex deep kernel learning methods, structured Gaussian processes, and hypothesis learning. These frameworks allow for the use of prior data, the discovery of specific functionalities as encoded in spectral data, and exploration of physical laws manifesting during the experiment. Here, the discussed framework can be universally applied to all techniques combining imaging and spectroscopy, SPM methods, nanoindentation, electron microscopy and spectroscopy, and chemical imaging methods and can be particularly impactful for destructive or irreversible measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Quantifying the effect of multiple load flexibility strategies on commercial building electricity demand and services via surrogate modeling

The expansion of commercial building demand response as a demand-side management resource for the electric grid necessitates new decision support resources for customers seeking to assess the benefit–risk tradeoffs of possible strategies for energy flexible building operations. To address this need, we, in this study, develop surrogate models that predict the impacts of several load flexibility strategies on commercial building electricity demand and indoor temperature, focusing on offices and retail buildings at multiple scales. The surrogate models are fit to a synthetic database generated via whole building simulations, which establish the relationships between the key operational features of a given strategy and potential changes in building demand and temperature across a variety of contexts. The surrogate models are translated to a Bayesian framework to allow straightforward communication of uncertainty and parameter updating given new evidence. We find strong predictive performance across the suite of models, underscoring the usefulness of the approach in guiding decisions about implementing load flexibility strategies under a particular set of operational and environmental conditions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗