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At least 163 records · Page 9

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DOE OSTI2025

High-throughput spin-bath characterization of spin defects in semiconductors

Detailed knowledge of the local environments of spin defects in semiconductors, such as nitrogenvacancy (NV) centers in diamond or divacancies in silicon carbide, is crucial for optimizing control and entanglement protocols in quantum sensing and information applications. However, at present a direct experimental characterization of individual defect environments is not scalable, as conventional spin-bath measurements are time consuming and difficult to automate. Achieving high-throughput characterization requires short experiments to probe the spin bath. However, with fewer and noisier measurements, the inverse problem of recovering spin-bath properties from measured data becomes ill posed, with multiple spin baths having a high likelihood of yielding the same data. In this work, we present a set of computational tools to resolve the ill-posed inverse problem of recovering the atomic positions and hyperfine couplings of random nuclei surrounding spin defects from sparse, noisy experimental coherence data, which can be obtained in hours. Here, we use a trans-dimensional Bayesian approach that incorporates ab initio data to yield full posterior distributions over nuclear spin environments, enabling robust recovery from limited data. We also provide practical tools and guidelines to determine the limits of detectability for hyperfine couplings under specific dynamical decoupling sequences and sampling conditions. In addition, we demonstrate how the tools developed here, in combination with ab initio simulations of spin baths, can guide the design of efficient experimental protocols for application-specific high-throughput screening. To showcase the utility of our approach, we apply it to design fast dynamical decoupling experiments to characterize the spin baths often individual NV centers in diamond. While the primary focus is on accelerating spin-bath characterization of spin defects, this Bayesian approach also lays the foundation for digital-twin studies of spin defects, where a virtual model of the spin-defect system evolves in real time with ongoing experimental measurements. Together, the set of tools we designed and applied paves the way for scalable deployment of spin defects in semiconductors for quantum sensing and information applications.

Bayesian methods↗

DOE OSTI2020

Three-dimensional traction microscopy accounting for cell-induced matrix degradation

Tractions exerted by cells on the extracellular matrix (ECM) are critical in many important physiological and pathological processes such as embryonic morphogenesis, wound healing, and cancer metastasis. Three-dimensional Traction Microscopy (3DTM) is a tool to quantify cellular tractions by first measuring the displacement field in the ECM in response to these tractions, and then using this measurement to infer tractions. Most applications of 3DTM have assumed that the ECM has spatially-uniform mechanical properties, but cells secrete enzymes that can locally degrade the ECM. In this work, a novel computational method is developed to quantify both cellular tractions and ECM degradation. In particular, the ECM is modeled as a hyperelastic, Neo-Hookean solid, whose material parameters are corrupted by a single degradation parameter. The feasibility of determining both the traction and the degradation parameter is first demonstrated by showing the existence and uniqueness of the solution. An inverse problem is then formulated to determine the nodal values of the traction vector and the degradation parameter, with the objective of minimizing the difference between a predicted and measured displacement field, under the constraint that the predicted displacement field satisfies the equation of equilibrium. The inverse problem is solved by means of a gradient-based optimization approach, and the gradient is computed efficiently using appropriately derived adjoint fields. The computational method is validated in-silico using a geometrically realistic neuronal cell model and synthetic traction and degradation fields. It is found that the method accurately recovers both the traction and degradation fields. Moreover, it is found that neglecting ECM degradation can yield significant errors in traction measurements. Finally, our method can extend the range of context where tractions can be appropriately measured.

42 ENGINEERING↗

DOE OSTI2024

Twins in rotational spectroscopy: Does a rotational spectrum uniquely identify a molecule?

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique “fingerprint” of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. Here we demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Bilevel optimization, deep learning and fractional Laplacian regularization with applications in tomography

Here we consider a generalized bilevel optimization framework for solving inverse problems. We introduce fractional Laplacian as a regularizer to improve the reconstruction quality, and compare it with the total variation regularization. We emphasize that the key advantage of using fractional Laplacian as a regularizer is that it leads to a linear operator, as opposed to the total variation regularization which results in a nonlinear degenerate operator. Inspired by residual neural networks, to learn the optimal strength of regularization and the exponent of fractional Laplacian, we develop a dedicated bilevel optimization neural network with a variable depth for a general regularized inverse problem. We illustrate how to incorporate various regularizer choices into our proposed network. As an example, we consider tomographic reconstruction as a model problem and show an improvement in reconstruction quality, especially for limited data, via fractional Laplacian regularization. We successfully learn the regularization strength and the fractional exponent via our proposed bilevel optimization neural network. We observe that the fractional Laplacian regularization outperforms total variation regularization. This is specially encouraging, and important, in the case of limited and noisy data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

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.

Tarpau, Cécilia (ORCID:0000000286539490)↗

DOE OSTI2026

Regularizing INR with Diffusion Prior for Self-Supervised 3D Reconstruction OF Neutron Computed Tomography Data

Recently, generative diffusion priors have made huge strides as inverse problem solvers, including the ability to be adapted for inference on out-of-distribution data. Concurrently, implicit neural representations (INRs) have emerged as fast and lightweight inverse imaging solvers that are amenable to hybrid approaches that combine learned priors with traditional inverse problem formulations. In this paper, we present a diffusive computed tomography (CT) inversion framework for regularizing INRs called Diffusive INR (DINR), designed to enable high-quality reconstruction from sparse-view neutron CT. Pretrained purely on synthetic data, DINR is evaluated on simulated and experimentally obtained observations of concrete microstructures, where traditional reconstruction methods suffer substantial degradation when the number of views is reduced. Our approach delivers superior performance, reduces reconstruction artifacts, and achieves gains in PSNR and SSIM, enabling accurate micro-structural characterization even under extreme data limitations compared to state-of-the-art sparse-view reconstruction techniques.

Hossain, Maliha [ORNL]↗

DOE OSTI2022

Scientific Computational Imaging Code (SCICO)

Scientific Computational Imaging Code (SCICO) is a Python package for solving the inverse problems that arise in scientific imaging applications. Its primary focus is providing methods for solving ill-posed inverse problems by using an appropriate prior model of the reconstruction space. SCICO includes a growing suite of operators, cost functionals, regularizers, and optimization routines that may be combined to solve a wide range of problems, and is designed so that it is easy to add new building blocks. SCICO is built on top of JAX rather than NumPy, enabling GPU/TPU acceleration, just-in-time compilation, and automatic gradient functionality, which is used to automatically compute the adjoints of linear operators. An example of how to solve a multi-channel tomography problem with SCICO is shown in Figure 1. The SCICO source code is available from GitHub, and pre-built packages are available from PyPI. It has extensive online documentation, including API documentation and usage examples, which can be run online at Google Colab and binder.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Pre-conditioned BFGS-based uncertainty quantification in elastic full-waveform inversion

SUMMARY Full-waveform inversion has become an essential technique for mapping geophysical subsurface structures. However, proper uncertainty quantification is often lacking in current applications. In theory, uncertainty quantification is related to the inverse Hessian (or the posterior covariance matrix). Even for common geophysical inverse problems its calculation is beyond the computational and storage capacities of the largest high-performance computing systems. In this study, we amend the Broyden–Fletcher–Goldfarb–Shanno (BFGS) algorithm to perform uncertainty quantification for large-scale applications. For seismic inverse problems, the limited-memory BFGS (L-BFGS) method prevails as the most efficient quasi-Newton method. We aim to augment it further to obtain an approximate inverse Hessian for uncertainty quantification in FWI. To facilitate retrieval of the inverse Hessian, we combine BFGS (essentially a full-history L-BFGS) with randomized singular value decomposition to determine a low-rank approximation of the inverse Hessian. Setting the rank number equal to the number of iterations makes this solution efficient and memory-affordable even for large-scale problems. Furthermore, based on the Gauss–Newton method, we formulate different initial, diagonal Hessian matrices as pre-conditioners for the inverse scheme and compare their performances in elastic FWI applications. We highlight our approach with the elastic Marmousi benchmark model, demonstrating the applicability of pre-conditioned BFGS for large-scale FWI and uncertainty quantification.

58 GEOSCIENCES↗

DOE OSTI2021

Quantitative imaging and automated fuel pin identification for passive gamma emission tomography

Compliance of member States to the Treaty on the Non-Proliferation of Nuclear Weapons is monitored through nuclear safeguards. The Passive Gamma Emission Tomography (PGET) system is a novel instrument developed within the framework of the International Atomic Energy Agency (IAEA) project JNT 1510, which included the European Commission, Finland, Hungary and Sweden. The PGET is used for the verification of spent nuclear fuel stored in water pools. Advanced image reconstruction techniques are crucial for obtaining high-quality cross-sectional images of the spent-fuel bundle to allow inspectors of the IAEA to monitor nuclear material and promptly identify its diversion. In this work, we have developed a software suite to accurately reconstruct the spent-fuel cross sectional image, automatically identify present fuel rods, and estimate their activity. Unique image reconstruction challenges are posed by the measurement of spent fuel, due to its high activity and the self-attenuation. While the former is mitigated by detector physical collimation, we implemented a linear forward model to model the detector responses to the fuel rods inside the PGET, to account for the latter. The image reconstruction is performed by solving a regularized linear inverse problem using the fast-iterative shrinkage-thresholding algorithm. We have also implemented the traditional filtered back projection (FBP) method based on the inverse Radon transform for comparison and applied both methods to reconstruct images of simulated mockup fuel assemblies. Higher image resolution and fewer reconstruction artifacts were obtained with the inverse-problem approach, with the mean-square-error reduced by 50%, and the structural-similarity improved by 200%. We then used a convolutional neural network (CNN) to automatically identify the bundle type and extract the pin locations from the images; the estimated activity levels finally being compared with the ground truth. The proposed computational methods accurately estimated the activity levels of the present pins, with an associated uncertainty of approximately 5%.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

AI-enabled high-resolution scanning coherent diffraction imaging

Ptychographic imaging is a powerful means of imaging beyond the resolution limits of typical x-ray optics. Capturing recovered images from raw ptychographic data, however, requires the solution of an inverse problem, namely, phase retrieval. Phase retrieval algorithms are computationally expensive, which precludes real-time imaging. In this work, we propose PtychoNN, an approach to solve the ptychography data inversion problem based on a deep convolutional neural network. We demonstrate how the proposed method can be used to predict real-space structure and phase at each scan point solely from the corresponding far-field diffraction data. Our results demonstrate the practical application of machine learning to recover high fidelity amplitude and phase contrast images of a real sample hundreds of times faster than current ptychography reconstruction packages. Furthermore, by overcoming the constraints of iterative model-based methods, we can significantly relax sampling constraints on data acquisition while still producing an excellent image of the sample. Besides drastically accelerating acquisition and analysis, this capability has profound implications for the imaging of dose sensitive, dynamic, and extremely voluminous samples.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

New approaches to Bayesian uncertainty quantification for Nuclear Science (Final Technical Report)

Inverse problems play a central role in experimentation and theory/data comparisons for many areas of modern Nuclear Physics (NP) and High-Energy Physics (HEP). Bayes’s Theorem is a powerful tool for solving Inverse Problems, providing conceptually transparent and unbiased constraints on theoretical parameters and their uncertainties (“Bayesian Inference”) and enabling the quantification of agreement or tension between models and data. However, analyses based on Bayesian Inference are often challenging for NP and HEP applications, either because of the large number of parameters in the problem, the high computational cost, or both. We propose a multi-institutional collaboration to develop and deploy novel Bayesian analysis tools that advance the scientific scope of a broad range of current and future NP experiments. This project brings together NP domain scientists working on several high-profile NP projects for which new, high-performance Bayesian Uncertainty Quantification (“Bayesian UQ”) methods are essential to carry out the science, and data scientists who are developing state-of-the-art methods applicable to these problems. The NP projects in this proposal comprise measurements of the mass and fundamental nature of the neutrino; study of the Quark-Gluon Plasma that filled the early universe; and mapping of natural and anthropogenic radiation environments. While these NP projects have very different scientific goals, with datasets and analysis approaches that differ significantly, they share common requirements for improving computationally intensive Bayesian analyses using advanced Machine Learning algorithms and will benefit strongly from a coherent effort to develop general solutions. This proposal brings together these projects and forefront ML-based data science algorithms to develop such general solutions. The methods developed in this project will also be more widely applicable, thereby advancing science in the larger Nuclear Physics portfolio.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Drive-pressure optimization in ramp-wave compression experiments through differential evolution

Ramp-wave dynamic-compression experiments are used to examine quasi-isentropic loading paths in materials. The gradual and continuous increase in pressure created by ramp waves make these types of experiments ideal for studying nonequilibrium material behavior, such as solidification kinetics. In ramp-wave compression experiments, the input drive pressure to the experimental setup may be exerted through one of a number of different mechanisms (e.g., magnetic fields, gas-gun-driven impactors, or high-energy lasers) and is generally required for simulating such experiments. Yet, regardless of the specific mechanism, this drive pressure cannot be measured directly (measurements are generally taken at a location near the back of the experimental setup through a transparent window), leading to an inverse problem where one must determine the drive pressure at the front of the experimental setup (i.e., the input) that corresponds to the particle velocity (the output) measured near the back of the experimental setup. Furthermore, we solve this inverse problem using a heuristic optimization algorithm, known as differential evolution, coupled with a multiphysics, hydrodynamics code that simulates the compression of the experimental setup. By running many rounds of forward simulations of the experimental setup, our optimization process iteratively searches for a drive pressure that is optimized to closely reproduce the experimentally measured particle velocity near the back of the experimental setup. While our optimization methodology requires a significant number of hydrodynamics simulations to be conducted, many of these can be performed in parallel, which greatly reduces the time cost of our methodology. One novel aspect of our method for determining the drive pressure is that it does not require physical modeling of the drive mechanism and can thus be broadly applied to many types of ramp-compression experiments, regardless of the drive mechanism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Ensemble Kalman inversion of induced polarization data

SUMMARY This paper explores the applicability of ensemble Kalman inversion (EKI) with level-set parametrization for solving geophysical inverse problems. In particular, we focus on its extension to induced polarization (IP) data with uncertainty quantification. IP data may provide rich information on characteristics of geological materials due to its sensitivity to characteristics of the pore–grain interface. In many IP studies, different geological units are juxtaposed and the goal is to delineate these units and obtain estimates of unit properties with uncertainty bounds. Conventional inversion of IP data does not resolve well sharp interfaces and tends to reduce and smooth resistivity variations, while not readily providing uncertainty estimates. Recently, it has been shown for DC resistivity that EKI is an efficient solver for inverse problems which provides uncertainty quantification, and its combination with level set parametrization can delineate arbitrary interfaces well. In this contribution, we demonstrate the extension of EKI to IP data using a sequential approach, where the mean field obtained from DC resistivity inversion is used as input for a separate phase angle inversion. We illustrate our workflow using a series of synthetic and field examples. Variations with uncertainty bounds in both DC resistivity and phase angles are recovered by EKI, which provides useful information for hydrogeological site characterization. Although phase angles are less well-resolved than DC resistivity, partly due to their smaller range and higher percentage data errors, it complements DC resistivity for site characterization. Overall, EKI with level set parametrization provides a practical approach forward for efficient hydrogeophysical imaging under uncertainty.

Geochemistry & Geophysics↗

DOE OSTI2020

Integrated Biophysical Modeling and Image Analysis: Application to Neuro-Oncology

Central nervous system (CNS) tumors come with vastly heterogeneous histologic, molecular, and radiographic landscapes, rendering their precise characterization challenging. The rapidly growing fields of biophysical modeling and radiomics have shown promise in better characterizing the molecular, spatial, and temporal heterogeneity of tumors. Integrative analysis of CNS tumors, including clinically acquired multi-parametric magnetic resonance imaging (mpMRI) and the inverse problem of calibrating biophysical models to mpMRI data, assists in identifying macroscopic quantifiable tumor patterns of invasion and proliferation, potentially leading to improved (a) detection/segmentation of tumor subregions and (b) computer-aided diagnostic/prognostic/predictive modeling. This article presents a summary of (a) biophysical growth modeling and simulation,(b) inverse problems for model calibration, (c) these models' integration with imaging workflows, and (d) their application to clinically relevant studies. We anticipate that such quantitative integrative analysis may even be beneficial in a future revision of the World Health Organization (WHO) classification for CNS tumors, ultimately improving patient survival prospects.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Conditional diffusion machine-learning framework for mapping valence electron distribution from convergent beam electron diffraction

Quantitative convergent beam electron diffraction (CBED) enables determination of aspherical valence electron distributions through refinement of low-order structure factors, which are highly sensitive to chemical bonding and charge density variations. However, conventional quantitative CBED (QCBED) requires solving a highly nonlinear inverse problem with many coupled parameters, and computationally intensive dynamical diffraction calculations, making it time-consuming and difficult to apply to complex systems. More broadly, reconstructing charge density and orbital electron distribution from diffraction data has long been a central challenge in both x-ray and electron crystallography. Here, in this study, we introduce an artificial-intelligence (AI)-based framework that replaces traditional refinement with a data-driven inverse solver. Using a large synthetic CBED dataset generated by Bloch-wave simulations, we train a conditional diffusion model to directly infer crystal structural parameters and multipole density formalism parameters, and hence valence electron distributions, from CBED patterns alone. By learning from forward simulations across realistic parameter space, the model effectively solves the inverse problem. Compared with direct regression approaches, the diffusion-based framework provides posterior parameter distributions for rigorous uncertainty quantification while preserving quantitative fidelity and reducing analysis time by orders of magnitude. By eliminating the need for external single-crystal x-ray diffraction data and complex nonlinear refinement, this approach enables practical, high-throughput, and in situ quantitative CBED, enabling real-time mapping of valence electron distributions and their correlation with functional responses in quantum and energy materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Optimal Estimation Retrievals and Their Uncertainties: What Every Atmospheric Scientist Should Know

Remote sensing instruments are heavily used to provide observations for both the operational and research communities. These sensors do not provide direct observations of the desired atmospheric variables, but instead, retrieval algorithms are necessary to convert the indirect observations into the variable of interest. It is critical to be aware of the underlying assumptions made by many retrieval algorithms, including that the retrieval problem is often ill posed and that there are various sources of uncertainty that need to be treated properly. In short, the retrieval challenge is to invert a set of noisy observations to obtain estimates of atmospheric quantities. The problem is often complicated by imperfect forward models, by imperfect prior knowledge, and by the existence of nonunique solutions. Optimal estimation (OE) is a widely used physical retrieval method that combines measurements, prior information, and the corresponding uncertainties based on Bayes’s theorem to find an optimal solution for the atmospheric state. Furthermore, OE also allows the relative contributions of the different sources of error to the uncertainty in the final retrieved atmospheric state to be understood. Here, we provide a novel Python library to illustrate the use of OE for inverse problems in the atmospheric sciences. We introduce two example problems: how to retrieve drop size distribution parameters from radar observations and how to retrieve the temperature profile from ground-based microwave sensors. Using these examples, we discuss common pitfalls, how the various error sources impact the retrieval, and how the quality of the retrieval results can be quantified.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Thinking Bayesian for plasma physicists

Bayesian statistics offers a powerful technique for plasma physicists to infer knowledge from the heterogeneous data types encountered. To explain this power, a simple example, Gaussian Process Regression, and the application of Bayesian statistics to inverse problems are explained. The likelihood is the key distribution because it contains the data model, or theoretic predictions, of the desired quantities. By using prior knowledge, the distribution of the inferred quantities of interest based on the data given can be inferred. Because it is a distribution of inferred quantities given the data and not a single prediction, uncertainty quantification is a natural consequence of Bayesian statistics. The benefits of machine learning in developing surrogate models for solving inverse problems are discussed, as well as progress in quantitatively understanding the errors that such a model introduces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Inferring Stochastic Rates from Heterogeneous Snapshots of Particle Positions

Many imaging techniques for biological systems—like fixation of cells coupled with fluorescence microscopy—provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. In this study, these snapshot observations contain no information about individual trajectories, but still encode information about movement and demographic dynamics, especially when combined with a well-motivated biophysical model. The relationship between spatially evolving populations and single-moment representations of their collective locations is well-established with partial differential equations (PDEs) and their inverse problems. However, experimental data is commonly a set of locations whose number is insufficient to approximate a continuous-in-space PDE solution. Here, motivated by popular subcellular imaging data of gene expression, we embrace the stochastic nature of the data and investigate the mathematical foundations of parametrically inferring demographic rates from snapshots of particles undergoing birth, diffusion, and death in a nuclear or cellular domain. Toward inference, we rigorously derive a connection between individual particle paths and their presentation as a Poisson spatial process. Using this framework, we investigate the properties of the resulting inverse problem and study factors that affect quality of inference. One pervasive feature of this experimental regime is the presence of cell-to-cell heterogeneity. Rather than being a hindrance, we show that cell-to-cell geometric heterogeneity can increase the quality of inference on dynamics for certain parameter regimes. Altogether, the results serve as a basis for more detailed investigations of subcellular spatial patterns of RNA molecules and other stochastically evolving populations that can only be observed for single instants in their time evolution.

59 BASIC BIOLOGICAL SCIENCES↗