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Results for “Bayesian imaging”
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Examination of nucleon distribution with Bayesian imaging for isobar collisions
Relativistic collision of isobaric systems is found to be valuable in differentiating the nucleon distributions for nuclei with the same mass number. In recent contrast experiment of $^{96}_{44}$Ru + $^{96}_{44}$Ru versus $^{96}_{40}$Zr + $^{96}_{40}$Zr collisions at $\sqrt{s_{NN}}$ = 200 GeV, the ratios of multiplicity distribution, elliptic flow, triangular flow, and radial flow are precisely measured and found to be significantly different from unity, indicating the difference in the shapes of the isobar pair. Here, in this work, we investigate the feasibility of nuclear structure reconstruction from heavy-ion collision observables. We perform Bayesian Inference with employing the Monte-Carlo Glauber model as an estimator of the mapping from nuclear structure to the final state observables and to provide the mock data for reconstruction. By varying combination of observables included in the mock data, we find it plausible to infer Woods–Saxon parameters from the observables. We also observe that single-system multiplicity distribution for the isobar system, rather than their ratio, is crucial to simultaneously determine the nuclear structure for the isobar system.
Radiation image reconstruction and uncertainty quantification using a Gaussian process prior
We propose a complete framework for Bayesian image reconstruction and uncertainty quantification based on a Gaussian process prior (GPP) to overcome limitations of maximum likelihood expectation maximization (ML-EM) image reconstruction algorithm. The prior distribution is constructed with a zero-mean Gaussian process (GP) with a choice of a covariance function, and a link function is used to map the Gaussian process to an image. Unlike many other maximum a posteriori approaches, our method offers highly interpretable hyperparamters that are selected automatically with the empirical Bayes method. Furthermore, the GP covariance function can be modified to incorporate a priori structural priors, enabling multi-modality imaging or contextual data fusion. Lastly, we illustrate that our approach lends itself to Bayesian uncertainty quantification techniques, such as the preconditioned Crank–Nicolson method and the Laplace approximation. The proposed framework is general and can be employed in most radiation image reconstruction problems, and we demonstrate it with simulated free-moving single detector radiation source imaging scenarios. We compare the reconstruction results from GPP and ML-EM, and show that the proposed method can significantly improve the image quality over ML-EM, all the while providing greater understanding of the source distribution via the uncertainty quantification capability. Furthermore, significant improvement of the image quality by incorporating a structural prior is illustrated.
Sequential Image Recovery Using Joint Hierarchical Bayesian Learning
Abstract Recovering temporal image sequences (videos) based on indirect, noisy, or incomplete data is an essential yet challenging task. We specifically consider the case where each data set is missing vital information, which prevents the accurate recovery of the individual images. Although some recent (variational) methods have demonstrated high-resolution image recovery based on jointly recovering sequential images, there remain robustness issues due to parameter tuning and restrictions on the type of sequential images. Here, we present a method based on hierarchical Bayesian learning for the joint recovery of sequential images that incorporates prior intra- and inter-image information. Our method restores the missing information in each image by “borrowing” it from the other images. More precisely, we couple sequential images by penalizing their pixel-wise difference. The corresponding penalty terms (one for each pixel and pair of subsequent images) are treated as weakly-informative random variables that favor small pixel-wise differences but allow occasional outliers. As a result, all of the individual reconstructions yield improved accuracy. Our method can be used for various data acquisitions and allows for uncertainty quantification. Some preliminary results indicate its potential use for sequential deblurring and magnetic resonance imaging.
Satellite Image Algorithms
Presented by Conner Hatton at SIAM UQ Conference in Trieste, Italy, on February 27th, 2024. Conference details available online at https://www.siam.org/conferences/cm/conference/uq24
Bayesian Spatially Varying Multi-Regularization Image Deblurring
Many scientific experiments such as those found in astronomy, geology, microbiology, and X-ray radiography require the use of high-energy instruments to capture images. Since blur and noise are inevitably present in any imaging system, the images must be \deblurred" to extract the full information content. Mathematically, image deblurring is an ill-posed inverse problem that requires regularization. The regularization, in turn, has a large effect on the deblurred image: different regularization strengths, and types, lead to drastically different reconstructions. Moreover, many images contain a mixture of smooth and sharp features which suggests the use of multi-regularization, i.e., varying the type of regularization (e.g. Tikhonov or total variation) across the image. We address these issues by formulating the image deblurring problem within a hierarchical Bayesian framework in which we spatially adapt the strength of the regularization and also vary the regularization type across the image. In this way, the image itself, along with corresponding regularization strength at each pixel, are described jointly by a posterior distribution which we can sample by Markov chain Monte Carlo (MCMC) methods. We illustrate our techniques on simplified test problems and apply them to high-energy X-ray images taken at the Nevada National Security Site. Numerical tests show that our new method is robustly applicable and increases the quality of the image reconstruction when compared to other (Bayesian) methods.
Statistical modelling and Bayesian inversion for a Compton imaging system: application to radioactive source localization
Abstract This paper presents a statistical forward model for a Compton imaging system, called Compton imager. This system, under development at the University of Illinois Urbana Champaign, is a variant of Compton cameras with a single type of sensors which can simultaneously act as scatterers and absorbers. This imager is convenient for imaging situations requiring a wide field of view. The proposed statistical forward model is then used to solve the inverse problem of estimating the location and energy of point-like sources from observed data. This inverse problem is formulated and solved in a Bayesian framework by using a Metropolis within Gibbs algorithm for the estimation of the location, and an expectation-maximization algorithm for the estimation of the energy. This approach leads to more accurate estimation when compared with the deterministic standard back-projection approach, with the additional benefit of uncertainty quantification in the low photon imaging setting.
Target Detection on Hyperspectral Images Using MCMC and VI Trained Bayesian Neural Networks.
Abstract not provided.
Target Detection on Hyperspectral Images Using MCMC and VI Trained Bayesian Neural Networks.
Abstract not provided.
Bayesian Spatially Varying Multi-regularization Image Deblurring
Presentation to be presented during the MSTS Science and Technology Work-in-Progress Seminar (Webex) scheduled for November 16, 2021.
Statistical Estimation of Strain Using Spatial Correlation Functions
Ex-situ estimation of strains from deformed micrographs is not possible as there are no persistent features which can be tracked. Two point spatial statistics enable the rigorous quantification of spatial patterns in heterogeneous media. In this paper, we propose a novel method for estimating strains directly from dissimilar micrographs using a continuum mechanics approach. Rather than operating directly on images from sequential frames, as is done in digital image correlation, we operate on different microstructure realizations. This is made possible by comparing the spatial autocorrelation maps of deformed and undeformed micrographs rather than direct comparison of images. Additionally, a Bayesian framework is proposed for quantifying uncertainty. We first illustrate the efficacy of this method on speckle pattern images from digital image correlation experiments. Then, we demonstrate that the method is capable of operating on dissimilar micrographs using deformed synthetic binary microstructures. Finally, we present a case study on polycrystalline additively manufactured 316L deformed via tension. The proposed method works well and we discuss implications and limitations of the presented work.
Lowering the computational barrier: Partially Bayesian neural networks for transparency in medical imaging AI
Deep Neural Networks (DNNs) can provide clinicians with fast and accurate predictions that are highly valuable for high-stakes medical decision-making, such as in brain tumor segmentation and treatment planning. However, these models largely lack transparency about the uncertainty in their predictions, potentially giving clinicians a false sense of reliability that may lead to grave consequences in patient care. Growing calls for Transparent and Responsible AI have promoted Uncertainty Quantification (UQ) to capture and communicate uncertainty in a systematic and principled manner. However, traditional Bayesian UQ methods remain prohibitively costly for large, million-dimensional tumor segmentation DNNs such as the U-Net. In this work, we discuss a computationally-efficient UQ approach via the partially Bayesian neural networks (pBNN). In pBNN, only a single layer, strategically selected based on gradient-based sensitivity analysis, is targeted for Bayesian inference. We illustrate the effectiveness of pBNN in capturing the full uncertainty for a 7.8-million parameter U-Net. We also demonstrate how practitioners and model developers can use the pBNN's predictions to better understand the model's capabilities and behavior.
Bayesian Target Detection Algorithms for Solid Subpixel Targets in Hyperspectral Images
Not Available
A deep learning approach to fast analysis of collective Thomson scattering spectra
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.
Physics-based reward driven image analysis in microscopy
The rise of electron microscopy has expanded our ability to acquire nanometer and atomically resolved images of complex materials. The resulting vast datasets are typically analyzed by human operators, an intrinsically challenging process due to the multiple possible analysis steps and the corresponding need to build and optimize complex analysis workflows. We present a methodology based on the concept of a Reward Function coupled with Bayesian Optimization, to optimize image analysis workflows dynamically. The Reward Function is engineered to closely align with the experimental objectives and broader context and is quantifiable upon completion of the analysis. Here, cross-section, high-angle annular dark field (HAADF) images of ion-irradiated (Y, Dy)Ba 2 Cu 3 O 7–δ thin-films were used as a model system. The reward functions were formed based on the expected materials density and atomic spacings and used to drive multi-objective optimization of the classical Laplacian-of-Gaussian (LoG) method. These results can be benchmarked against the DCNN segmentation. This optimized LoG* compares favorably against DCNN in the presence of the additional noise. We further extend the reward function approach towards the identification of partially-disordered regions, creating a physics-driven reward function and action space of high-dimensional clustering. We pose that with correct definition, the reward function approach allows real-time optimization of complex analysis workflows at much higher speeds and lower computational costs than classical DCNN-based inference, ensuring the attainment of results that are both precise and aligned with the human-defined objectives.
Physics Discovery in Nanoplasmonic Systems via Autonomous Experiments in Scanning Transmission Electron Microscopy
Abstract Physics‐driven discovery in an autonomous experiment has emerged as a dream application of machine learning in physical sciences. Here, this work develops and experimentally implements a deep kernel learning (DKL) workflow combining the correlative prediction of the target functional response and its uncertainty from the structure, and physics‐based selection of acquisition function, which autonomously guides the navigation of the image space. Compared to classical Bayesian optimization (BO) methods, this approach allows to capture the complex spatial features present in the images of realistic materials, and dynamically learn structure–property relationships. In combination with the flexible scalarizer function that allows to ascribe the degree of physical interest to predicted spectra, this enables physical discovery in automated experiment. Here, this approach is illustrated for nanoplasmonic studies of nanoparticles and experimentally implemented in a truly autonomous fashion for bulk‐ and edge plasmon discovery in MnPS 3 , a lesser‐known beam‐sensitive layered 2D material. This approach is universal, can be directly used as‐is with any specimen, and is expected to be applicable to any probe‐based microscopic techniques including other STEM modalities, scanning probe microscopies, chemical, and optical imaging.
Sparse Data Machine Learning Integration with Theory, Experiment and Uncertainty Quantification: Process-Structure-Property-Performance of Friction Deformation Processing
Computer vision and deep learning tools that advance the ability to establish processing-structure-property-performance (PSPP) relations are presented. The Bayesian binning method for image segmentation enables quantitative analysis of microstructural features in an automated way, while the analysis of shapes and relative orientation of these features reveals local deformation maps indicative of both, material flow and residual stresses due to materials processing. The deep learning method leads to the previous knowledge agnostic mapping of empirically observed microstructural zones in friction stir welding (FSW) process and synthetic microstructure generation capability that is statistically equivalent to experimentally collected data.
Autonomous convergence of STM control parameters using Bayesian optimization
Scanning tunneling microscopy (STM) is a widely used tool for atomic imaging of novel materials and their surface energetics. However, the optimization of the imaging conditions is a tedious process due to the extremely sensitive tip–surface interaction, thus limiting the throughput efficiency. In this paper, we deploy a machine learning (ML)-based framework to achieve optimal atomically resolved imaging conditions in real time. The experimental workflow leverages the Bayesian optimization (BO) method to rapidly improve the image quality, defined by the peak intensity in the Fourier space. The outcome of the BO prediction is incorporated into the microscope controls, i.e., the current setpoint and the tip bias, to dynamically improve the STM scan conditions. We present strategies to either selectively explore or exploit across the parameter space. As a result, suitable policies are developed for autonomous convergence of the control parameters. The ML-based framework serves as a general workflow methodology across a wide range of materials.