Bengi: a Bayesian ENGine for Insights Phase II Report
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Explore the source record for details and available documents.
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Explore the source record for details and available documents.
Explore the source record for details and available documents.
Explore the source record for details and available documents.
Explore the source record for details and available documents.
Here, this paper presents the development and demonstration of massively parallel probabilistic machine learning (ML) and uncertainty quantification (UQ) capabilities within the Multiphysics Object-Oriented Simulation Environment (MOOSE), an open-source computational platform for parallel finite element and finite volume analyses. In addressing the computational expense and uncertainties inherent in complex multiphysics simulations, this paper integrates Gaussian process (GP) variants, active learning, Bayesian inverse UQ, adaptive forward UQ, Bayesian optimization, evolutionary optimization, and Markov chain Monte Carlo (MCMC) within MOOSE. It also elaborates on the interaction among key MOOSE systems — Sampler, MultiApp, Reporter, and Surrogate — in enabling these capabilities. The modularity offered by these systems enables development of a multitude of probabilistic ML and UQ algorithms in MOOSE. Example code demonstrations include parallel active learning and parallel Bayesian inference via active learning. The impact of these developments is illustrated through five applications relevant to computational energy applications: UQ of nuclear fuel fission product release, using parallel active learning Bayesian inference; very rare events analysis in nuclear microreactors using active learning; advanced manufacturing process modeling using multi-output GPs (MOGPs) and dimensionality reduction; fluid flow using deep GPs (DGPs); and tritium transport model parameter optimization for fusion energy, using batch Bayesian optimization. These capabilities are part of the MOOSE framework.
This paper proposes novel noise-free Bayesian optimization strategies that rely on a random exploration step to enhance the accuracy of Gaussian process surrogate models. The new algorithms retain the ease of implementation of the classical GP-UCB algorithm, but the additional random exploration step accelerates their convergence, nearly achieving the optimal convergence rate. Furthermore, to facilitate Bayesian inference with intractable likelihoods, we propose to utilize optimization iterates for maximum a posteriori estimation to build a Gaussian process surrogate model for the unnormalized log-posterior density. We provide bounds for the Hellinger distance between the true and the approximate posterior distributions in terms of the number of design points. We demonstrate the effectiveness of our Bayesian optimization algorithms in nonconvex benchmark objective functions, in a machine learning hyperparameter tuning problem, and in a black-box engineering design problem. The effectiveness of our posterior approximation approach is demonstrated in two Bayesian inference problems for parameters of dynamical systems.
We present a frequentist analysis of clustering measurements from Data Release 1 of the Dark Energy Spectroscopic Instrument (DESI) using the standard profile likelihood method. While Bayesian inferences for effective field theory models of galaxy clustering can be highly sensitive to prior choices for extended cosmological models, frequentist inferences are not susceptible to such effects. We compare frequentist and Bayesian constraints for the parameter set {σ 8 , H 0 , Ω m , w 0 , w a } using the full-shape power spectrum multipoles, post-reconstruction baryon acoustic oscillation (BAO) measurements, and external datasets from the CMB and type Ia supernovae measurements. The frequentist confidence intervals are significantly shifted relative to the Bayesian credible intervals for the w 0 w a CDM model, unless supernovae data are included. When DESI full-shape and BAO data are fit jointly, we obtain the following 1σ frequentist confidence intervals for ΛCDM (w 0 w a CDM): σ 8 = 0.863 +0.048 -0.040 , H 0 = 68.96 +0.81 -0.80 km s -1 Mpc -1 , Ω m = 0.3034 ± 0.0110 (σ 8 = 0.782 +0.060 -0.036 , H 0 = 63.7 +4.2 -2.0 km s -1 Mpc -1 , Ω m = 0.378 +0.024 -0.047 , w 0 = -0.16 +0.10 -0.50 , w a = -3.0 +1.7 ), corresponding to 0.8σ, 0.3σ, 0.7σ (2.1σ, 4.1σ, 6.5σ, 6.3σ, 6.6σ) shifts between the maximum likelihood estimate and the Bayesian posterior mean for ΛCDM (w 0 w a CDM) respectively.
As Li-ion batteries become more essential in today's economy, tools need to be developed to accurately and rapidly diagnose a battery's internal state-of-health. Using a Li-ion battery's (high-rate) voltage response, it is proposed to determine a battery's internal state through Bayesian calibration. However, Bayesian calibration is notoriously slow and requires thousands of model runs. To accelerate parameter inference using Bayesian calibration, a surrogate model is developed to replace the underlying physics-based Li-ion model. Developing a surrogate model for rapid Bayesian calibration analysis is discussed for both the single particle model (SPM) and the pseudo two-dimensional (P2D) model. Surrogate models are constructed using physics-informed neural networks (PINNs) that encode the influence of internal properties on observed voltage responses. In practice, a neural network can be trained by: 1) using simulation results of the physics-based model (i.e., a data-loss approach); 2) using the residuals of the governing equations themselves (i.e., a physics-loss approach); or 3) using a combination of simulation results and governing equation residuals. In the present work, PINNs are developed using a variety of training losses and neural network architectures. In this analysis, it is shown that a PINN surrogate model can be reliably trained with only physics-informed loss. However, using a coupled data-informed and physics-loss approach produced the most accurate PINNs.
Diagnosing the internal state of Li-ion batteries is critical for battery research, operation of real-world systems, and prognostic evaluation of remaining lifetime. By using physics-based models to perform probabilistic parameter estimation via Bayesian calibration, diagnostics can account for the uncertainty due to model fitness, data noise, and the observability of any given parameter. However, Bayesian calibration in Li-ion batteries using electrochemical data is computationally intensive even when using a fast surrogate in place of physics-based models, requiring many thousands of model evaluations. A fully amortized alternative is neural posterior estimation (NPE). NPE shifts the computational burden from the parameter estimation step to data generation and model training, reducing the parameter estimation time from minutes to milliseconds, enabling real-time applications. The present work shows that NPE can infer parameters equally or more accurately than Bayesian calibration, even if it leads to higher voltage reconstruction errors. We also demonstrate that the higher computational costs for data generation are tractable even in high-dimensional cases (ranging from 6 to 27 estimated parameters). The NPE method also offers several interpretability advantages over Bayesian calibration, such as local parameter sensitivity to specific regions of the voltage curve. The NPE method is demonstrated using an experimental fast charge dataset, with parameter estimates validated against measurements of loss of lithium inventory and loss of active material. The implementation is made available in a companion repository (https://github.com/NatLabRockies/BatFIT).
Fast analysis of collective Thomson scattering ion acoustic wave features using a deep convolutional neural network model is presented. The network was trained from spectra to predict the plasma parameters, including ion velocities, population fractions, and ion and electron temperatures. A fully kinetic particle-in-cell simulation was used to model a laboratory astrophysics experiment and simulate a diagnostic image of the ion acoustic wave feature. Network predictions were compared with Bayesian inference of the plasma model parameters for both the simulated and experimentally measured images. Both approaches were fairly accurate predicting the simulated image and the network predictions matched a good portion of the Bayesian results for the experimentally measured image. The Bayesian approach is more robust to noise and motivates future work to train deep learning models with realistic noise. The advantage of the deep learning model is making thousands of predictions in a few hundred milliseconds, compared to a few seconds to minutes per prediction for the optimization and Bayesian approaches presented here. The results demonstrate promising capabilities of deep learning models to analyze Thomson data orders of magnitude faster than conventional methods when using the neural network for standalone analysis. If more rigorous analysis is needed, neural network predictions can be used to quickly initialize other optimization methods and increase chances of success. This is especially useful when the dataset becomes very large or highly dimensional and manually refining initial conditions for the entire dataset are no longer tractable.
Differential cross section measurements are the currency of scientific exchange in particle and nuclear physics. A key challenge for these analyses is the correction for detector distortions, known as deconvolution or unfolding. Binned unfolding of cross section measurements traditionally rely on the regularized inversion of the response matrix that represents the detector response, mapping pre-detector (`particle level') observables to post-detector (`detector level') observables. In this paper we introduce Neural Posterior Unfolding, a modern, Bayesian approach that leverages normalizing flows for unfolding. By using normalizing flows for neural posterior estimation, NPU offers several key advantages including implicit regularization through the neural network architecture, fast amortized inference that eliminates the need for repeated retraining, and direct access to the full uncertainty in the unfolded result. In addition to introducing NPU, we implement a classical Bayesian unfolding method called Fully Bayesian Unfolding (FBU) in modern Python so it can also be studied. These tools are validated on simple Gaussian examples and then tested on simulated jet substructure examples from the Large Hadron Collider (LHC). We find that the Bayesian methods are effective and worth additional development to be analysis ready for cross section measurements at the LHC and beyond.
Agent-based simulation provides a powerful tool for in silico system modeling. However, these simulations do not provide built-in methods for uncertainty quantification (UQ). Within these types of models a typical approach to UQ is to run multiple realizations of the model then compute aggregate statistics. This approach is limited due to the compute time required for a solution. When faced with an emerging biothreat, public health decisions need to be made quickly and solutions for integrating near real-time data with analytic tools are needed. We propose an integrated Bayesian UQ framework for agent-based models based on sequential Monte Carlo sampling. Given streaming or static data about the evolution of an emerging pathogen this Bayesian framework provides a distribution over the parameters governing the spread of a disease through a population. These estimates of the spread of a disease may be provided to public health agencies seeking to abate the spread. By coupling agent-based simulations with Bayesian modeling in a data assimilation, our proposed framework provides a powerful tool for modeling dynamical systems in silico. We propose a method which reduces model error and provides a range of realistic possible outcomes. Moreover, our method addresses two primary limitations of ABMs: the lack of UQ and an inability to assimilate data. Our proposed framework combines the flexibility of an agent-based model with UQ provided by the Bayesian paradigm in a workflow which scales well to HPC systems. We provide algorithmic details and results on a simulated outbreak with both static and streaming data.