A Guided Approach To Learning From Discrete Dislocation Dynamics Simulations
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Discrete Dislocation Dynamics, Bayesian optimizati↗
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Neural network approaches versus statistical methods in classification of multisource remote sensing data
Neural network learning procedures and statistical classificaiton methods are applied and compared empirically in classification of multisource remote sensing and geographic data. Statistical multisource classification by means of a method based on Bayesian classification theory is also investigated and modified. The modifications permit control of the influence of the data sources involved in the classification process. Reliability measures are introduced to rank the quality of the data sources. The data sources are then weighted according to these rankings in the statistical multisource classification. Four data sources are used in experiments: Landsat MSS data and three forms of topographic data (elevation, slope, and aspect). Experimental results show that two different approaches have unique advantages and disadvantages in this classification application.
Benediktsson, Jon A.↗
Game Theoretic Approach for Understanding and Modeling Clinical Pathways (Stable Ischemic Heart Disease)
This research develops a game-theoretic agent model for stable ischemic heart disease (SIHD) clinical decisions, incorporating aspects of Bayesian game theory to model hidden information such as the patient’s true underlying medical condition(s). Preexisting observational medical data contained in the United States Department of Veterans Affairs (VA) Corporate Data Warehouse (CDW) is analyzed to obtain the required game-theoretic parameter values. Various statistical adjustments are performed to correct for bias in the preexisting treatment protocol selections and to obtain game-theoretic parameter values for contrafactual treatment protocol choices. Once the game-theoretic parameter values are determined, clinical pathways can be viewed as being mathematical strategies for playing the game and thus can be studied and evaluated using the techniques of game theory.
59 BASIC BIOLOGICAL SCIENCES↗
Probabilistic assessment of cloud fraction using Bayesian blending of independent datasets: Feasibility study of a new method
We describe and evaluate a novel method to blend two observed cloud fraction (CF) datasets through Bayesian posterior estimation. The research reported here is a feasibility study designed to explore the method. In this proof‐of‐concept study, we illustrate the approach using specific observational datasets from the U. S. Department of Energy Atmospheric Radiation Measurement Program's Southern Great Plains site in the central United States, but the method is quite general and is readily applicable to other datasets. The total sky image (TSI) camera observations are used to determine the prior distribution. A regression model and the active remote sensing of clouds (ARSCL) radar/lidar observations are used to determine the likelihood function. The posterior estimate is a probability density function (pdf) of the CF whose mean is taken to be the optimal blend of the two observations. The data at hourly, daily, 5‐day, monthly, and annual time scales are considered. Some physical and probabilistic properties of the CFs are explored from radar/lidar, camera, and satellite observations and from simulations using the Community Atmosphere Model (CAM5). Our results imply that (a) the Beta distribution is a reasonable model for CF for both short‐ and long‐time means, the 5‐day data are skewed right, and the annual data are almost normally distributed, and (b) the Bayesian method developed successfully yields a pdf of CF, rather than a deterministic CF value, and it is feasible to blend the TSI and ARSCL data with a capability for bias correction.
58 GEOSCIENCES↗
Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach
Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate translation, mRNA secondary structure, and/or protein folding. Given the critical link between protein folding and protein function, numerous studies have analyzed the relationship between codon usage and protein structure. The results from these studies have often been contradictory, likely reflecting the differing methods used for measuring codon usage and the failure to appropriately control for confounding factors, such as differences in amino acid usage between protein structures and changes in the frequency of different structures with gene expression. Here we take an explicit population genetics approach to quantify codon-specific shifts in natural selection related to protein structure in S. cerevisiae and E. coli. Unlike other metrics of codon usage, our approach explicitly separates the effects of natural selection, scaled by gene expression, and mutation bias while naturally accounting for a region’s amino acid usage. Bayesian model comparisons suggest selection on codon usage varies only slightly between helix, sheet, and coil secondary structures and, similarly, between structured and intrinsically-disordered regions. Similarly, in contrast to previous findings, we find selection on codon usage only varies slightly at the termini of helices in E. coli. Using simulated data, we show this previous work indicating “non-optimal” codons are enriched at the beginning of helices in S. cerevisiae was due to failure to control for various confounding factors (e.g. amino acid biases, gene expression, etc.), and rather than selection to modulate cotranslational folding. Our results reveal a weak relationship between codon usage and protein structure, indicating that differences in selection on codon usage between structures are slight. In addition to the magnitude of differences in selection between protein structures being slight, the observed shifts appear to be idiosyncratic and largely codon-specific rather than systematic reversals in the nature of selection. Overall, our work demonstrates the statistical power and benefits of studying selective shifts on codon usage or other genomic features from an explicitly evolutionary approach. Limitations of this approach and future potential research avenues are discussed.
59 BASIC BIOLOGICAL SCIENCES↗
Inter-Domain Fusion for Enhanced Intrusion Detection in Power Systems: An Evidence Theoretic and Meta-Heuristic Approach
False alerts due to misconfigured or compromised intrusion detection systems (IDS) in industrial control system (ICS) networks can lead to severe economic and operational damage. However, research using deep learning to reduce false alerts often requires the physical and cyber sensor data to be trustworthy. Implicit trust is a major problem for artificial intelligence or machine learning (AI/ML) in cyber-physical system (CPS) security, because when these solutions are most urgently needed is also when they are most at risk (e.g., during an attack). To address this, the Inter-Domain Evidence theoretic Approach for Inference (IDEA-I) is proposed that reframes the detection problem as how to make good decisions given uncertainty. Specifically, an evidence theoretic approach leveraging Dempster–Shafer (DS) combination rules and their variants is proposed for reducing false alerts. A multi-hypothesis mass function model is designed that leverages probability scores obtained from supervised-learning classifiers. Using this model, a location-cum-domain-based fusion framework is proposed to evaluate the detector’s performance using disjunctive, conjunctive, and cautious conjunctive rules. The approach is demonstrated in a cyber-physical power system testbed, and the classifiers are trained with datasets from Man-In-The-Middle attack emulation in a large-scale synthetic electric grid. For evaluating the performance, we consider plausibility, belief, pignistic, and general Bayesian theorem-based metrics as decision functions. To improve the performance, a multi-objective-based genetic algorithm is proposed for feature selection considering the decision metrics as the fitness function. Finally, we present a software application to evaluate the DS fusion approaches with different parameters and architectures.
42 ENGINEERING↗
AI-assisted transport of radioactive ion beams
Beams of radioactive heavy ions allow researchers to study rare and unstable atomic nuclei, shedding light into the internal structure of exotic nuclei and on how chemical elements are formed in stars. However, the extraction and transport of radioactive beams rely on time-consuming expert-driven tuning methods, where hundreds of parameters are manually optimized. Here, in this study, we introduce a system that employs Artificial Intelligence (AI), specifically utilizing Bayesian Optimization, to assist in the transport process of radioactive beams. We apply our methodology to real-life scenarios showing advantages when compared with standard tuning methods. This AI-assisted approach can be extended to other radioactive beam facilities around the world to improve operational efficiency and enhance scientific output.
43 PARTICLE ACCELERATORS↗
Practical and Optimal Sequential Bayesian Experimental Design for Complex Systems Incorporating Human Experimenter Preferences (Final Scientific/Technical Report)
Experiments are indispensable for developing models of complex systems. Carefully designed experiments can provide substantial savings for these expensive data-acquisition opportunities. However, designs based on heuristics are often suboptimal for systems with multiphysics, nonlinear dynamics, and uncertain and noisy environments. Optimal experimental design, while leveraging predictive models, seeks to systematically quantify and maximize the value of experiments. In this project, we focused on the design of multiple experiments, where current approaches are largely suboptimal: batch-design does not adapt to new data acquired during the experiment campaign (no feedback), and greedy/myopic design ignores future dynamics and consequences (no lookahead). We developed the mathematical framework and computational methods for sequential optimal experimental design (sOED) for complex systems. We enabled tractable model-based sOED in a rigorous manner through novel algorithms based on reinforcement learning, and investigated the effects of human experimenters on the design process. Our methods are fully Bayesian, able to quantify and update uncertainty in a principled manner. The traits aimed by our approach—mathematical rigor and optimality, human effects and uncertainty quantification, computational practicality—are crucial for elevating the standards of artificial intelligence (AI) to support decision-making in scientific domains, and contribute toward trust and realistic adoption of AI in experimental design practice.
97 MATHEMATICS AND COMPUTING↗
Deriving cloud droplet number concentration from surface-based remote sensors with an emphasis on lidar measurements
Abstract. Given the importance of constraining cloud droplet number concentrations (Nd) in low-level clouds, we explore two methods for retrieving Nd from surface-based remote sensing that emphasize the information content in lidar measurements. Because Nd is the zeroth moment of the droplet size distribution (DSD), and all remote sensing approaches respond to DSD moments that are at least 2 orders of magnitude greater than the zeroth moment, deriving Nd from remote sensing measurements has significant uncertainty. At minimum, such algorithms require the extrapolation of information from two other measurements that respond to different moments of the DSD. Lidar, for instance, is sensitive to the second moment (cross-sectional area) of the DSD, while other measures from microwave sensors respond to higher-order moments. We develop methods using a simple lidar forward model that demonstrates that the depth to the maximum in lidar-attenuated backscatter (Rmax) is strongly sensitive to Nd when some measure of the liquid water content vertical profile is given or assumed. Knowledge of Rmax to within 5 m can constrain Nd to within several tens of percent. However, operational lidar networks provide vertical resolutions of > 15 m, making a direct calculation of Nd from Rmax very uncertain. Therefore, we develop a Bayesian optimal estimation algorithm that brings additional information to the inversion such as lidar-derived extinction and radar reflectivity near the cloud top. This statistical approach provides reasonable characterizations of Nd and effective radius (re) to within approximately a factor of 2 and 30 %, respectively. By comparing surface-derived cloud properties with MODIS satellite and aircraft data collected during the MARCUS and CAPRICORN II campaigns, we demonstrate the utility of the methodology.
54 ENVIRONMENTAL SCIENCES↗
Bayesian calibration of bubble size dynamics applied to CO 2 gas fermenters
To accelerate the scale-up of gaseous CO 2 fermentation reactors, computational models need to predict gas-to-liquid mass transfer which requires capturing the bubble size dynamics, i.e. bubble breakup and coalescence. However, the applicability of existing models beyond air–water mixtures remains to be established. Here, an inverse modeling approach, accelerated with a neural network surrogate, calibrates the breakup and coalescence closure models, that are used in class methods for population balance modeling (PBM). The calibration is performed based on experimental results obtained in a CO 2 -air–water-coflowing bubble column reactor. Bayesian inference is used to account for noise in the experimental dataset and bias in the simulation results. To accurately capture gas holdup and interphase mass transfer, the results show that the breakage rate needs to be increased by one order of magnitude. In conclusion, the inferred model parameters are then used on a separate configuration and shown to also improve bubble size distribution predictions.
09 BIOMASS FUELS↗
Bayesian weighting of climate models based on climate sensitivity
Using climate model ensembles containing members that exhibit very high climate sensitivities to increasing CO 2 concentrations can result in biased projections. Various methods have been proposed to ameliorate this ‘hot model’ problem, such as model emulators or model culling. Here, we utilize Bayesian Model Averaging as a framework to address this problem without resorting to outright rejection of models from the ensemble. Taking advantage of multiple lines of evidence used to construct the best estimate of the earth’s climate sensitivity, the Bayesian Model Averaging framework produces an unbiased posterior probability distribution of model weights. The updated multi-model ensemble projects end-of-century global mean surface temperature increases of 2 °C for a low emissions scenario (SSP1-2.6) and 5 °C for a high emissions scenario (SSP5-8.5). These estimates are lower than those produced using a simple multi-model mean for the CMIP6 ensemble. The results are also similar to results from a model culling approach, but retain some weight on low-probability models, allowing for consideration of the possibility that the true value could lie at the extremes of the assessed distribution. Our results showcase Bayesian Model Averaging as a path forward to project future climate change that is commensurate with the available scientific evidence.
59 BASIC BIOLOGICAL SCIENCES↗
Stochastic Reconstruction of Thermal Protection Material Properties from Arc-Jet Experiments
Material response models are used to assess reliability using variances in the bond-line temperature predictions based on uncertainties in trajectory, aerothermal environment, and material properties. A key deficiency in the current approach is that input uncertainties are too often subjective, empirical, or ad-hoc, and are not rigorously linked to the arc-jet test data used to develop the TPS material model. While materials such as PICA are well understood, future missions may require more novel materials such as HEEET where unknown uncertainties have real consequences on the ability to assess reliability. A quantifiable estimate of reliability requires an iterative methodology where the parameters driving the variance in bond-line temperature (for example) are systematically identified. A test campaign to collect data or develop new models can then be identified to reduce those input uncertainties. A Bayesian inference loop defines these connections mathematically, i.e., prior knowledge about uncertainty is updated based on observation. While these concepts are well known (and often applied intuitively in a non-rigorous approach), only recent advances in reduced-order modelling have made them computationally viable methods for engineering. By replacing deterministic inverse methods with stochastic approaches, the hope is new materials proposed for future missions can more rapidly be developed with a greater understanding of the TPS material reliability. Two additional steps for the analysis of arc jet test data are discussed. The first is ability to construct a reduced-order model using material response simulations (Icarus/US3D) of the arc-jet test articles, and the second is the inclusion of this surrogate model in the Bayesian inversion process. Both capabilities will be demonstrated using prior PICA arc-jet test data. The quality of a surrogate model will be investigated and the variances on the calibrated material properties will be compared to our current understanding of the PICA material model.
Material response↗
Sample-Efficient Adaptive Calibration of Quantum Networks Using Bayesian Optimization
All physical systems employed for quantum information tasks must act as unbiased carriers of encoded quantum states. Ensuring such indistinguishability of information carriers is a major challenge in many quantum information applications, including advanced quantum communication protocols. For photons, the workhorses of quantum communication networks, it is difficult to obtain and maintain their indistinguishability because of environment-induced transformations and loss imparted by communication channels, especially in noisy scenarios. Conventional strategies to mitigate these transformations often require hardware or software overhead that is restrictive (e.g., adding noise), infeasible (e.g., on a satellite), or time-consuming for deployed networks. In this work we propose and develop resource-efficient Bayesian optimization techniques to rapidly and adaptively calibrate the indistinguishability of individual photons for quantum networks using only information derived from their measurement. To experimentally validate our approach, we demonstrate the optimization of Hong-Ou-Mandel interference between two photons-a central task in quantum networking- finding rapid, efficient, and reliable convergence towards maximal photon indistinguishability in the presence of high loss and shot noise. We expect our resource-optimized and experimentally friendly methodology will allow fast and reliable calibration of indistinguishable quanta, a necessary task in distributed quantum computing, communications, and sensing, as well as for fundamental investigations.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Estimation of stagnation performance metrics in magnetized liner inertial fusion experiments using Bayesian data assimilation
Here we present a new analysis methodology that allows for the self-consistent integration of multiple diagnostics including nuclear measurements, x-ray imaging, and x-ray power detectors to determine the primary stagnation parameters, such as temperature, pressure, stagnation volume, and mix fraction in magnetized liner inertial fusion (MagLIF) experiments. The analysis uses a simplified model of the stagnation plasma in conjunction with a Bayesian inference framework to determine the most probable configuration that describes the experimental observations while simultaneously revealing the principal uncertainties in the analysis. We validate the approach by using a range of tests including analytic and three-dimensional MHD models. An ensemble of MagLIF experiments is analyzed, and the generalized Lawson criterion χ is estimated for all experiments.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
A scalable design of experiments framework for optimal sensor placement
Here, we present a scalable design of an experiments framework for sensor placement in systems described by partial differential equations (PDEs). In particular, we aim to compute optimal sensor locations by minimizing the uncertainty of parameters estimated from Bayesian inverse problems and where the system. The resulting problem is a computationally intractable mixed-integer nonlinear program constrained by PDEs. We approach this problem with two heuristics used in compressed sensing and optimal control literature: a sparsity-inducing approach and a sum-up rounding approach. We also investigate metrics to guide the design of experiments (the total flow variance and the A-optimal design criterion) and analyze the effect of different noise structures (white and colored). Using an application in natural gas pipelines, we conclude that the sum-up rounding approach approach gives the best results and produces shrinking gaps with increasing mesh resolution. We also observe that convergence for the white noise measurement error case is slower than for the colored noise case. For A-optimal design, the solution is close to a uniform distribution of sensors along the pipeline while for the flow variance design the distribution is unstructured.
42 ENGINEERING↗
Computationally efficient Bayesian quantum state tomography
We describe a method for Bayesian quantum state estimation combining efficient parameterization, a pseudo-likelihood, and advanced numerical sampling techniques. Examples reveal significant computational speedup, indicating the approach’s promise in practical quantum state tomography.
Lukens, Joseph↗
A New Method to Measure the Post-reionization Ionizing Background from the Joint Distribution of Ly α and Ly β Forest Transmission
The amplitude of the ionizing background that pervades the intergalactic medium (IGM) at the end of the epoch of reionization provides a valuable constraint on the emissivity of the sources that reionized the universe. While measurements of the ionizing background at lower redshifts rely on a simulation-calibrated mapping between the photoionization rate and the mean transmission of the Lyα forest, at z ≳ 6 the IGM becomes increasingly opaque and transmission arises solely in narrow spikes separated by saturated Gunn–Peterson troughs. In this regime, the traditional approach of measuring the average transmission over large ~50 Mpc/h regions is less sensitive and suboptimal. In addition, the five times smaller oscillator strength of the Lyβ transition implies that the Lyβ forest is considerably more transparent at z ≳ 6, even in the presence of contamination by foreground z ~ 5 Lyα forest absorption. We present a novel statistical approach to analyze the joint distribution of transmission spikes in the cospatial z ~ 6 Lyα and Lyβ forests. Our method relies on approximate Bayesian computation (ABC), which circumvents the necessity of computing the intractable likelihood function describing the highly correlated Lyα and Lyβ transmission. We apply ABC to mock data generated from a large-volume hydrodynamical simulation combined with a state-of-the-art model of ionizing background fluctuations in the post-reionization IGM and show that it is sensitive to higher IGM neutral hydrogen fractions than previous techniques. As a proof of concept, we apply this methodology to a real spectrum of a z = 6.54 quasar and measure the ionizing background from 5.4 ≤ z ≤ 6.4 along this sightline with ~0.2 dex statistical uncertainties.
79 ASTRONOMY AND ASTROPHYSICS↗
Online Multi-Modal Learning and Adaptive Information Trajectory Planning for Autonomous Exploration
In robotic information gathering missions, scientists are typically interested in understanding variables which require proxy measurements from specialized sensor suites to estimate. However, energy and time constraints limit how often these sensors can be used in a mission. Robots are also equipped with cheaper to use navigation sensors such as cameras. In this paper, we explore a challenging planning problem in which a robot is required to learn about a scientific variable of interest in an initially unknown environment by planning informative paths and deciding when and where to use its sensors. To tackle this we present two innovations: a Bayesian generative model framework to automatically learn correlations between expensive science sensors and cheaper to use navigation sensors online, and a sampling based approach to plan for multiple sensors while handling long horizons and budget constraints. Our approach does not grow in complexity with data and is anytime making it highly applicable to field robotics. We tested our approach extensively in simulation and validated it with real data collected during the 2014 Mojave Volatiles Prospector Mission. Our planning algorithm performs statistically significantly better than myopic approaches and at least as well as a coverage-based algorithm in an initially unknown environment while having added advantages of being able to exploit prior knowledge and handle other intricacies of the real world without further algorithmic modifications.
learning↗