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Results for “Bayesian statistical modeling”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A Bayesian Approach for Characterizing and Mitigating Gate and Measurement Errors

Various noise models have been developed in quantum computing study to describe the propagation and effect of the noise that is caused by imperfect implementation of hardware. Identifying parameters such as gate and readout error rates is critical to these models. We use a Bayesian inference approach to identify posterior distributions of these parameters such that they can be characterized more elaborately. By characterizing the device errors in this way, we can further improve the accuracy of quantum error mitigation. Experiments conducted on IBM’s quantum computing devices suggest that our approach provides better error mitigation performance than existing techniques used by the vendor. Also, our approach outperforms the standard Bayesian inference method in some scenarios.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A Bayesian analysis of classical shadows

Abstract The method of classical shadows proposed by Huang, Kueng, and Preskill heralds remarkable opportunities for quantum estimation with limited measurements. Yet its relationship to established quantum tomographic approaches, particularly those based on likelihood models, remains unclear. In this article, we investigate classical shadows through the lens of Bayesian mean estimation (BME). In direct tests on numerical data, BME is found to attain significantly lower error on average, but classical shadows prove remarkably more accurate in specific situations—such as high-fidelity ground truth states—which are improbable in a fully uniform Hilbert space. We then introduce an observable-oriented pseudo-likelihood that successfully emulates the dimension-independence and state-specific optimality of classical shadows, but within a Bayesian framework that ensures only physical states. Our research reveals how classical shadows effect important departures from conventional thinking in quantum state estimation, as well as the utility of Bayesian methods for uncovering and formalizing statistical assumptions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Galaxy cluster profiles: a Gaussian mixture model approach to halo miscentering

Measurements of the galaxy density and weak-lensing profiles of galaxy clusters typically rely on an assumed cluster center, which is taken to be the brightest cluster galaxy or other proxies for the true halo center defined as the minimum in the potential well. Departure of the assumed cluster center from the true halo center bias the resultant profile measurements, an effect known as miscentering bias. Currently, miscentering is typically modeled in stacked profiles of clusters with a two parameter model. We use an alternate approach in which the profiles of individual clusters are used with the corresponding likelihood computed using a Gaussian mixture model. We test the approach using halos and the corresponding subhalo profiles from the IllustrisTNG hydrodynamic simulations. We obtain significantly improved estimates of the miscentering parameters for both 3D and projected 2D profiles relevant for imaging surveys. We discuss applications to upcoming cosmological surveys. Our Python package for the Gaussian mixture model is publicly available at https://github.com/KyleMiller1/Halo-Miscentering-Mixture-Model.

Bayesian reasoning↗
DOE OSTI2019

Quantifying correlated truncation errors in effective field theory

Effective field theories (EFTs) organize the description of complex systems into an infinite sequence of decreasing importance. Predictions are made with a finite number of terms, which induces a truncation error that is often left unquantified. Here, we formalize the notion of EFT convergence and propose a Bayesian truncation error model for predictions that are correlated across the independent variables, e.g., energy or scattering angle. Central to our approach are Gaussian processes that encode both the naturalness and correlation structure of EFT coefficients. Our use of Gaussian processes permits efficient and accurate assessment of credible intervals, allows EFT fits to easily include correlated theory errors, and provides analytic posteriors for physical EFT-related quantities such as the expansion parameter. Furthermore, we demonstrate that model-checking diagnostics—applied to the case of multiple curves—are powerful tools for EFT validation. As an example, we assess a set of nucleon-nucleon scattering observables in chiral EFT. In an effort to be self-contained, appendices include thorough derivations of our statistical results. Our methods are packaged in Python code, called gsum, that is available for download on GitHub.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2011

Statistical surrogate models for prediction of high-consequence climate change.

In safety engineering, performance metrics are defined using probabilistic risk assessments focused on the low-probability, high-consequence tail of the distribution of possible events, as opposed to best estimates based on central tendencies. We frame the climate change problem and its associated risks in a similar manner. To properly explore the tails of the distribution requires extensive sampling, which is not possible with existing coupled atmospheric models due to the high computational cost of each simulation. We therefore propose the use of specialized statistical surrogate models (SSMs) for the purpose of exploring the probability law of various climate variables of interest. A SSM is different than a deterministic surrogate model in that it represents each climate variable of interest as a space/time random field. The SSM can be calibrated to available spatial and temporal data from existing climate databases, e.g., the Program for Climate Model Diagnosis and Intercomparison (PCMDI), or to a collection of outputs from a General Circulation Model (GCM), e.g., the Community Earth System Model (CESM) and its predecessors. Because of its reduced size and complexity, the realization of a large number of independent model outputs from a SSM becomes computationally straightforward, so that quantifying the risk associated with low-probability, high-consequence climate events becomes feasible. A Bayesian framework is developed to provide quantitative measures of confidence, via Bayesian credible intervals, in the use of the proposed approach to assess these risks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

EFIT‐AI: Machine Learning and Artificial Intelligence Assisted Equilibrium Reconstruction for Tokamak Experiments and Burning Plasmas (Final Report)

The EFIT-AI project is creating a modern advanced equilibrium reconstruction code suitable for tokamak experiments of burning plasmas. EFIT [1,2] was the first and is the most extensively used equilibrium reconstruction code in the world. This project builds on the production-level experience and adds key elements as follows. 1. A Model Order Reduction (MOR) version of the two-dimensional (2D) Grad-Shafranov equation solver (EFIT-MORNN) using physics-informed neural networks. 2. Improved optimization and data analysis capabilities using a Bayesian framework enhanced with machine learning. 3. A MOR version of the three-dimensional (3D) perturbed equilibrium reconstruction tool.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2012

Use of Stable Isotopes in Forensic Analysis of Microorganisms

The use of isotopic signatures for forensic analysis of biological materials is well-established, and the same general principles that apply to interpretation of stable isotope content of C, N, O, and H apply to the analysis of microorganisms. Heterotrophic microorganisms derive their isotopic content from their growth substrates, which are largely plant and animal products, and the water in their culture medium. Thus the isotope signatures of microbes are tied to their growth environment. The C, N, O, and H isotope ratios of spores have been demonstrated to constitute highly discriminating signatures for sample matching. They can rule out specific samples of media and/or water as possible production media, and can predict isotope ratio ranges of the culture media and water used to produce a given sample. These applications have been developed and tested through analyses of approximately 250 samples of Bacillus subtilis spores and over 500 samples of culture media, providing a strong statistical basis for data interpretation. A Bayesian statistical framework for integrating stable isotope data with other types of signatures derived from microorganisms has been able to characterize the culture medium used to produce spores of various Bacillus species, leveraging isotopic differences in different medium types and demonstrating the power of data integration for forensic investigations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Multiscale influenza forecasting

Abstract Influenza forecasting in the United States (US) is complex and challenging due to spatial and temporal variability, nested geographic scales of interest, and heterogeneous surveillance participation. Here we present Dante, a multiscale influenza forecasting model that learns rather than prescribes spatial, temporal, and surveillance data structure and generates coherent forecasts across state, regional, and national scales. We retrospectively compare Dante’s short-term and seasonal forecasts for previous flu seasons to the Dynamic Bayesian Model (DBM), a leading competitor. Dante outperformed DBM for nearly all spatial units, flu seasons, geographic scales, and forecasting targets. Dante’s sharper and more accurate forecasts also suggest greater public health utility. Dante placed 1st in the Centers for Disease Control and Prevention’s prospective 2018/19 FluSight challenge in both the national and regional competition and the state competition. The methodology underpinning Dante can be used in other seasonal disease forecasting contexts having nested geographic scales of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Parameter estimation for X-ray scattering analysis with Hamiltonian Markov Chain Monte Carlo

Bayesian-inference-based approaches, in particular the random-walk Markov Chain Monte Carlo (MCMC) method, have received much attention recently for X-ray scattering analysis. Hamiltonian MCMC, a state-of-the-art development in the field of MCMC, has become popular in recent years. It utilizes Hamiltonian dynamics for indirect but much more efficient drawings of the model parameters. We described the principle of the Hamiltonian MCMC for inversion problems in X-ray scattering analysis by estimating high-dimensional models for several motivating scenarios in small-angle X-ray scattering, reflectivity, and X-ray fluorescence holography. Hamiltonian MCMC with appropriate preconditioning can deliver superior performance over the random-walk MCMC, and thus can be used as an efficient tool for the statistical analysis of the parameter distributions, as well as model predictions and confidence analysis.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Bayesian investigation of isochrone consistency using the old open cluster NGC 188

This paper provides a detailed comparison of the differences in parameters derived for a star cluster from its color–magnitude diagrams (CMDs) depending on the filters and models used. We examine the consistency and reliability of fitting three widely used stellar evolution models to 15 combinations of optical and near-IR photometry for the old open cluster NGC 188. The optical filter response curves match those of theoretical systems and are thus not the source of fit inconsistencies. NGC 188 is ideally suited to this study thanks to a wide variety of high-quality photometry and available proper motions and radial velocities that enable us to remove non-cluster members and many binaries. Our Bayesian fitting technique yields inferred values of age, metallicity, distance modulus, and absorption as a function of the photometric band combinations and stellar models. We show that the historically favored three-band combinations of UBV and VRI can be meaningfully inconsistent with each other and with longer baseline data sets such as UBVRIJHK{sub S}. Differences among model sets can also be substantial. For instance, fitting Yi et al. (2001) and Dotter et al. (2008) models to UBVRIJHK{sub S} photometry for NGC 188 yields the following cluster parameters: age = (5.78 ± 0.03, 6.45 ± 0.04) Gyr, [Fe/H] = (+0.125 ± 0.003, −0.077 ± 0.003) dex, (m−M){sub V} = (11.441 ± 0.007, 11.525 ± 0.005) mag, and A{sub V} = (0.162 ± 0.003, 0.236 ± 0.003) mag, respectively. Within the formal fitting errors, these two fits are substantially and statistically different. Such differences among fits using different filters and models are a cautionary tale regarding our current ability to fit star cluster CMDs. Additional modeling of this kind, with more models and star clusters, and future Gaia parallaxes are critical for isolating and quantifying the most relevant uncertainties in stellar evolutionary models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Interpreting internal consistency of DES measurements

ABSTRACT Bayesian evidence ratios are widely used to quantify the statistical consistency between different experiments. However, since the evidence ratio is prior dependent, the precise translation between its value and the degree of concordance/discordance requires additional information. The most commonly adopted metric, the Jeffreys scale, can falsely suggest agreement between data sets when priors are chosen to be sufficiently wide. This work examines evidence ratios in a DES-Y1 simulated analysis, focusing on the internal consistency between weak lensing and galaxy clustering. We study two scenarios using simulated data in controlled experiments. First, we calibrate the expected evidence ratio distribution given noise realizations around the best-fitting DES-Y1 ΛCDM cosmology. Secondly, we show the behaviour of evidence ratios for noiseless fiducial data vectors simulated using a modified gravity model, which generates internal tension in the LCDM analysis. We find that the evidence ratio of noise realizations generated at all confidence levels was biased towards agreement and show, with a modified gravity model, that the choice of prior could conceal the discrepancies between weak lensing and galaxy clustering induced by prior effects in unlike cosmological models, concluding that the evidence ratio in a DES-Y1 study is, indeed, biased towards agreement. Boundary effects can also influence conclusions about the inconsistency induced by modified gravity, even in a noiseless data vector simulation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Parkes Pulsar Timing Array constraints on ultralight scalar-field dark matter

It is widely accepted that dark matter contributes about a quarter of the critical mass-energy density in our Universe. The nature of dark matter is currently unknown, with the mass of possible constituents spanning nearly one hundred orders of magnitude. The ultralight scalar field dark matter, consisting of extremely light bosons with m~10 –22 eV and often called “fuzzy” dark matter, provides intriguing solutions to some challenges at sub-Galactic scales for the standard cold dark matter model. As shown by Khmelnitsky and Rubakov, such a scalar field in the Galaxy would produce an oscillating gravitational potential with nanohertz frequencies, resulting in periodic variations in the times of arrival of radio pulses from pulsars. The Parkes Pulsar Timing Array (PPTA) has been monitoring 20 millisecond pulsars at two- to three-week intervals for more than a decade. In addition to the detection of nanohertz gravitational waves, PPTA offers the opportunity for direct searches for fuzzy dark matter in an astrophysically feasible range of masses. We analyze the latest PPTA data set which includes timing observations for 26 pulsars made between 2004 and 2016. Here, we perform a search in this data set for evidence of ultralight dark matter in the Galaxy using Bayesian and Frequentist methods. No statistically significant detection has been made. We, therefore, place upper limits on the local dark matter density. Our limits, improving on previous searches by a factor of 2 to 5, constrain the dark matter density of ultralight bosons with m ≤ 10 –23 eV to be below 6 GeV cm –3 with 95% confidence in the Earth neighborhood. Finally, we discuss the prospect of probing the astrophysically favored mass range m ≳ 10 –22 eV with next-generation pulsar timing facilities.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Dark matter voids in the SDSS galaxy survey

What do we know about voids in the dark matter distribution given the Sloan Digital Sky Survey (SDSS) and assuming the ΛCDM model? Recent application of the Bayesian inference algorithm BORG to the SDSS Data Release 7 main galaxy sample has generated detailed Eulerian and Lagrangian representations of the large-scale structure as well as the possibility to accurately quantify corresponding uncertainties. Building upon these results, we present constrained catalogs of voids in the Sloan volume, aiming at a physical representation of dark matter underdensities and at the alleviation of the problems due to sparsity and biasing on galaxy void catalogs. To do so, we generate data-constrained reconstructions of the presently observed large-scale structure using a fully non-linear gravitational model. We then find and analyze void candidates using the VIDE toolkit. Our methodology therefore predicts the properties of voids based on fusing prior information from simulations and data constraints. For usual void statistics (number function, ellipticity distribution and radial density profile), all the results obtained are in agreement with dark matter simulations. Our dark matter void candidates probe a deeper void hierarchy than voids directly based on the observed galaxies alone. The use of our catalogs therefore opens the way to high-precision void cosmology at the level of the dark matter field. We will make the void catalogs used in this work available at http://www.cosmicvoids.net.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Greedy emulators for nuclear two-body scattering

Applications of reduced basis method emulators are increasing in low-energy nuclear physics because they enable fast and accurate sampling of high-fidelity calculations, enabling robust uncertainty quantification. Here, in this paper, we develop, implement, and test two model-driven emulators based on the (Petrov-)Galerkin projection using the prototypical test case of two-body scattering with the Minnesota potential and a more realistic local chiral potential. The high-fidelity scattering equations are solved with the matrix Numerov method, a reformulation of the popular Numerov recurrence relation for solving special second-order differential equations as a linear system of coupled equations. A novel error estimator based on reduced-space residuals is applied to an active learning approach (a greedy algorithm) to choosing training samples (“snapshots”) for the emulator and contrasted with a proper orthogonal decomposition (POD) approach. Both approaches allow for computationally efficient offline-online decompositions, but the greedy approach requires many fewer snapshot calculations. These developments set the groundwork for emulating scattering observables based on chiral nucleon-nucleon and three-nucleon interactions and optical models, where computational speed-ups are necessary for Bayesian uncertainty quantification. Our emulators and error estimators are widely applicable to linear systems.

Bayesian methods↗
DOE OSTI2011

Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites

Finding conserved motifs in genomic sequences represents one of essential bioinformatic problems. However, achieving high discovery performance without imposing substantial auxiliary constraints on possible motif features remains a key algorithmic challenge. This work describes BAMBI—a sequential Monte Carlo motifidentification algorithm, which is based on a position weight matrix model that does not require additional constraints and is able to estimate such motif properties as length, logo, number of instances and their locations solely on the basis of primary nucleotide sequence data. Furthermore, should biologically meaningful information about motif attributes be available, BAMBI takes advantage of this knowledge to further refine the discovery results. In practical applications, we show that the proposed approach can be used to find sites of such diverse DNA-binding molecules as the cAMP receptor protein (CRP) and Din-family site-specific serine recombinases. Results obtained by BAMBI in these and other settings demonstrate better statistical performance than any of the four widely-used profile-based motif discovery methods: MEME, BioProspector with BioOptimizer, SeSiMCMC and Motif Sampler as measured by the nucleotide-level correlation coefficient. Additionally, in the case of Din-family recombinase target site discovery, the BAMBI-inferred motif is found to be the only one functionally accurate from the underlying biochemical mechanism standpoint. C++and Matlab code is available at http://www.ee.columbia.edu/guido/ BAMBI or http://genomics.lbl.gov/BAMBI/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Systematic validation of non-equilibrium thermochemical models using Bayesian inference

The validation process proposed by Babuška et al. [1] is applied to thermochemical models describing post-shock flow conditions. In this validation approach, experimental data is involved only in the calibration of the models, and the decision process is based on quantities of interest (QoIs) predicted on scenarios that are not necessarily amenable experimentally. Moreover, uncertainties present in the experimental data, as well as those resulting from an incomplete physical model description, are propagated to the QoIs. We investigate four commonly used thermochemical models: a one-temperature model (which assumes thermal equilibrium among all inner modes), and two-temperature models developed by Macheret et al. [2], Marrone and Treanor [3], and Park [4]. Up to 16 uncertain parameters are estimated using Bayesian updating based on the latest absolute volumetric radiance data collected at the Electric Arc Shock Tube (EAST) installed inside the NASA Ames Research Center. Following the solution of the inverse problems, the forward problems are solved in order to predict the radiative heat flux, QoI, and examine the validity of these models. Our results show that all four models are invalid, but for different reasons: the one-temperature model simply fails to reproduce the data while the two-temperature models exhibit unacceptably large uncertainties in the QoI predictions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2012

Quantitative Phenomena Identification and Ranking Table (QPIRT) for Bayesian uncertainty quantification

Propagating parameter uncertainty for a nuclear reactor system code is a challenging problem due to often non-linear system response to the numerous parameters involved and lengthy computational times; issues that compound when a statistical sampling procedure is adopted, since the code must be run many times. The number of parameters sampled must therefore be limited to as few as possible that still accurately characterize the uncertainty in the system response. A Quantitative Phenomena Identification and Ranking Table (QPIRT) was developed to accomplish this goal. The QPIRT consists of two steps: a 'Top-Down' step focusing on identifying the dominant physical phenomena controlling the system response, and a 'Bottom-Up' step which focuses on determining the correlations from those key physical phenomena that significantly contribute to the response uncertainty. The Top-Down step evaluates phenomena using the governing equations of the system code at nominal parameter values, providing a 'fast' screening step. The Bottom-Up step then analyzes the correlations and models for the phenomena identified from the Top-Down step to find which parameters to sample. The QPIRT, through the Top-Down and Bottom-Up steps thus provides a systematic approach to determining the limited set of physically relevant parameters that influence the uncertainty of the system response. This strategy was demonstrated through an application to the RELAP5-based analysis of a PWR Total Loss of main Feedwater Flow (TLOFW) accident, also known as feed and bleed' scenario, . Ultimately, this work is the first component in a larger task of building a calibrated uncertainty propagation framework. The QPIRT is an essential piece because the uncertainty of those selected parameters will be calibrated to data from both Separate and Integral Effect Tests (SETs and IETs). Therefore the system response uncertainty will incorporate the knowledge gained from the database of past large IETs. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2015

Bayesian inference on the sphere beyond statistical isotropy

We present a general method for Bayesian inference of the underlying covariance structure of random fields on a sphere. We employ the Bipolar Spherical Harmonic (BipoSH) representation of general covariance structure on the sphere. We illustrate the efficacy of the method as a principled approach to assess violation of statistical isotropy (SI) in the sky maps of Cosmic Microwave Background (CMB) fluctuations. SI violation in observed CMB maps arise due to known physical effects such as Doppler boost and weak lensing; yet unknown theoretical possibilities like cosmic topology and subtle violations of the cosmological principle, as well as, expected observational artefacts of scanning the sky with a non-circular beam, masking, foreground residuals, anisotropic noise, etc. We explicitly demonstrate the recovery of the input SI violation signals with their full statistics in simulated CMB maps. Our formalism easily adapts to exploring parametric physical models with non-SI covariance, as we illustrate for the inference of the parameters of a Doppler boosted sky map. Our approach promises to provide a robust quantitative evaluation of the evidence for SI violation related anomalies in the CMB sky by estimating the BipoSH spectra along with their complete posterior.

79 ASTRONOMY AND ASTROPHYSICS↗