arXiv subjects

Jeffrey A. Fessler

Publications and source records attributed to Jeffrey A. Fessler.

At least 37 records · Page 2Linked to original sources

arXiv2024

Imaging 3D Chemistry at 1 nm Resolution with Fused Multi-Modal Electron Tomography

Measuring the three-dimensional (3D) distribution of chemistry in nanoscale matter is a longstanding challenge for metrological science. The inelastic scattering events required for 3D chemical imaging are too rare, requiring high beam exposure that destroys the specimen before an experiment completes. Even larger doses are required to achieve high resolution. Thus, chemical mapping in 3D has been unachievable except at lower resolution with the most radiation-hard materials. Here, high-resolution 3D chemical imaging is achieved near or below one nanometer resolution in a Au-Fe$_3$O$_4$ metamaterial, Co$_3$O$_4$ - Mn$_3$O$_4$ core-shell nanocrystals, and ZnS-Cu$_{0.64}$S$_{0.36}$ nanomaterial using fused multi-modal electron tomography. Multi-modal data fusion enables high-resolution chemical tomography often with 99\% less dose by linking information encoded within both elastic (HAADF) and inelastic (EDX / EELS) signals. Now sub-nanometer 3D resolution of chemistry is measurable for a broad class of geometrically and compositionally complex materials.

physics.comp-ph↗

arXiv2024

DiffusionBlend: Learning 3D Image Prior through Position-aware Diffusion Score Blending for 3D Computed Tomography Reconstruction

Diffusion models face significant challenges when employed for large-scale medical image reconstruction in real practice such as 3D Computed Tomography (CT). Due to the demanding memory, time, and data requirements, it is difficult to train a diffusion model directly on the entire volume of high-dimensional data to obtain an efficient 3D diffusion prior. Existing works utilizing diffusion priors on single 2D image slice with hand-crafted cross-slice regularization would sacrifice the z-axis consistency, which results in severe artifacts along the z-axis. In this work, we propose a novel framework that enables learning the 3D image prior through position-aware 3D-patch diffusion score blending for reconstructing large-scale 3D medical images. To the best of our knowledge, we are the first to utilize a 3D-patch diffusion prior for 3D medical image reconstruction. Extensive experiments on sparse view and limited angle CT reconstruction show that our DiffusionBlend method significantly outperforms previous methods and achieves state-of-the-art performance on real-world CT reconstruction problems with high-dimensional 3D image (i.e., $256 \times 256 \times 500$). Our algorithm also comes with better or comparable computational efficiency than previous state-of-the-art methods.

cs.CV↗

arXiv2024

A Complex Quasi-Newton Proximal Method for Image Reconstruction in Compressed Sensing MRI

Model-based methods are widely used for reconstruction in compressed sensing (CS) magnetic resonance imaging (MRI), using regularizers to describe the images of interest. The reconstruction process is equivalent to solving a composite optimization problem. Accelerated proximal methods (APMs) are very popular approaches for such problems. This paper proposes a complex quasi-Newton proximal method (CQNPM) for the wavelet and total variation based CS MRI reconstruction. Compared with APMs, CQNPM requires fewer iterations to converge but needs to compute a more challenging proximal mapping called weighted proximal mapping (WPM). To make CQNPM more practical, we propose efficient methods to solve the related WPM. Numerical experiments on reconstructing non-Cartesian MRI data demonstrate the effectiveness and efficiency of CQNPM.

math.OC↗

arXiv2023

ALPCAH: Sample-wise Heteroscedastic PCA with Tail Singular Value Regularization

Principal component analysis (PCA) is a key tool in the field of data dimensionality reduction that is useful for various data science problems. However, many applications involve heterogeneous data that varies in quality due to noise characteristics associated with different sources of the data. Methods that deal with this mixed dataset are known as heteroscedastic methods. Current methods like HePPCAT make Gaussian assumptions of the basis coefficients that may not hold in practice. Other methods such as Weighted PCA (WPCA) assume the noise variances are known, which may be difficult to know in practice. This paper develops a PCA method that can estimate the sample-wise noise variances and use this information in the model to improve the estimate of the subspace basis associated with the low-rank structure of the data. This is done without distributional assumptions of the low-rank component and without assuming the noise variances are known. Simulations show the effectiveness of accounting for such heteroscedasticity in the data, the benefits of using such a method with all of the data versus retaining only good data, and comparisons are made against other PCA methods established in the literature like PCA, Robust PCA (RPCA), and HePPCAT. Code available at https://github.com/javiersc1/ALPCAH

stat.ML↗

arXiv2023

Imaging Atomic-Scale Chemistry from Fused Multi-Modal Electron Microscopy

Efforts to map atomic-scale chemistry at low doses with minimal noise using electron microscopes are fundamentally limited by inelastic interactions. Here, fused multi-modal electron microscopy offers high signal-to-noise ratio (SNR) recovery of material chemistry at nano- and atomic- resolution by coupling correlated information encoded within both elastic scattering (high-angle annular dark field (HAADF)) and inelastic spectroscopic signals (electron energy loss (EELS) or energy-dispersive x-ray (EDX)). By linking these simultaneously acquired signals, or modalities, the chemical distribution within nanomaterials can be imaged at significantly lower doses with existing detector hardware. In many cases, the dose requirements can be reduced by over one order of magnitude. This high SNR recovery of chemistry is tested against simulated and experimental atomic resolution data of heterogeneous nanomaterials.

physics.comp-ph↗

arXiv2023

Poisson-Gaussian Holographic Phase Retrieval with Score-based Image Prior

Phase retrieval (PR) is a crucial problem in many imaging applications. This study focuses on resolving the holographic phase retrieval problem in situations where the measurements are affected by a combination of Poisson and Gaussian noise, which commonly occurs in optical imaging systems. To address this problem, we propose a new algorithm called "AWFS" that uses the accelerated Wirtinger flow (AWF) with a score function as generative prior. Specifically, we formulate the PR problem as an optimization problem that incorporates both data fidelity and regularization terms. We calculate the gradient of the log-likelihood function for PR and determine its corresponding Lipschitz constant. Additionally, we introduce a generative prior in our regularization framework by using score matching to capture information about the gradient of image prior distributions. We provide theoretical analysis that establishes a critical-point convergence guarantee for the proposed algorithm. The results of our simulation experiments on three different datasets show the following: 1) By using the PG likelihood model, the proposed algorithm improves reconstruction compared to algorithms based solely on Gaussian or Poisson likelihood. 2) The proposed score-based image prior method, performs better than the method based on denoising diffusion probabilistic model (DDPM), as well as plug-and-play alternating direction method of multipliers (PnP-ADMM) and regularization by denoising (RED).

eess.SP↗

arXiv2023

Dynamic Subspace Estimation with Grassmannian Geodesics

Dynamic subspace estimation, or subspace tracking, is a fundamental problem in statistical signal processing and machine learning. This paper considers a geodesic model for time-varying subspaces. The natural objective function for this model is non-convex. We propose a novel algorithm for minimizing this objective and estimating the parameters of the model from data with Grassmannian-constrained optimization. We show that with this algorithm, the objective is monotonically non-increasing. We demonstrate the performance of this model and our algorithm on synthetic data, video data, and dynamic fMRI data.

eess.SP↗

arXiv2023

Adaptive Sampling for Linear Sensing Systems via Langevin Dynamics

Adaptive or dynamic signal sampling in sensing systems can adapt subsequent sampling strategies based on acquired signals, thereby potentially improving image quality and speed. This paper proposes a Bayesian method for adaptive sampling based on greedy variance reduction and stochastic gradient Langevin dynamics (SGLD). The image priors involved can be either analytical or neural network-based. Notably, the learned image priors generalize well to out-of-distribution test cases that have different statistics than the training dataset. As a real-world validation, the method is applied to accelerate the acquisition of magnetic resonance imaging (MRI). Compared to non-adaptive sampling, the proposed method effectively improved the image quality by 2-3 dB in PSNR, and improved the restoration of subtle details.

eess.SP↗

arXiv2023

HeMPPCAT: Mixtures of Probabilistic Principal Component Analysers for Data with Heteroscedastic Noise

Mixtures of probabilistic principal component analysis (MPPCA) is a well-known mixture model extension of principal component analysis (PCA). Similar to PCA, MPPCA assumes the data samples in each mixture contain homoscedastic noise. However, datasets with heterogeneous noise across samples are becoming increasingly common, as larger datasets are generated by collecting samples from several sources with varying noise profiles. The performance of MPPCA is suboptimal for data with heteroscedastic noise across samples. This paper proposes a heteroscedastic mixtures of probabilistic PCA technique (HeMPPCAT) that uses a generalized expectation-maximization (GEM) algorithm to jointly estimate the unknown underlying factors, means, and noise variances under a heteroscedastic noise setting. Simulation results illustrate the improved factor estimates and clustering accuracies of HeMPPCAT compared to MPPCA.

stat.ME↗

arXiv2023

Training End-to-End Unrolled Iterative Neural Networks for SPECT Image Reconstruction

Training end-to-end unrolled iterative neural networks for SPECT image reconstruction requires a memory-efficient forward-backward projector for efficient backpropagation. This paper describes an open-source, high performance Julia implementation of a SPECT forward-backward projector that supports memory-efficient backpropagation with an exact adjoint. Our Julia projector uses only ~5% of the memory of an existing Matlab-based projector. We compare unrolling a CNN-regularized expectation-maximization (EM) algorithm with end-to-end training using our Julia projector with other training methods such as gradient truncation (ignoring gradients involving the projector) and sequential training, using XCAT phantoms and virtual patient (VP) phantoms generated from SIMIND Monte Carlo (MC) simulations. Simulation results with two different radionuclides (90Y and 177Lu) show that: 1) For 177Lu XCAT phantoms and 90Y VP phantoms, training unrolled EM algorithm in end-to-end fashion with our Julia projector yields the best reconstruction quality compared to other training methods and OSEM, both qualitatively and quantitatively. For VP phantoms with 177Lu radionuclide, the reconstructed images using end-to-end training are in higher quality than using sequential training and OSEM, but are comparable with using gradient truncation. We also find there exists a trade-off between computational cost and reconstruction accuracy for different training methods. End-to-end training has the highest accuracy because the correct gradient is used in backpropagation; sequential training yields worse reconstruction accuracy, but is significantly faster and uses much less memory.

eess.SP↗

arXiv2022

Efficient approximation of Jacobian matrices involving a non-uniform fast Fourier transform (NUFFT)

There is growing interest in learning Fourier domain sampling strategies (particularly for magnetic resonance imaging, MRI) using optimization approaches. For non-Cartesian sampling patterns, the system models typically involve non-uniform FFT (NUFFT) operations. Commonly used NUFFT algorithms contain frequency domain interpolation, which is not differentiable with respect to the sampling pattern, complicating the use of gradient methods. This paper describes an efficient and accurate approach for computing approximate gradients involving NUFFTs. Multiple numerical experiments validated the improved accuracy and efficiency of the proposed approximation. As an application to computational imaging, the NUFFT Jacobians were used to optimize non-Cartesian MRI sampling trajectories via data-driven stochastic optimization. Specifically, the sampling patterns were learned with respect to various model-based reconstruction algorithms, including quadratic regularized reconstruction and compressed sensing-based reconstruction. The proposed approach enables sampling optimization for image sizes that are infeasible with standard auto-differentiation methods due to memory limits. The synergistic acquisition and reconstruction lead to remarkably improved image quality. In fact, we show that model-based image reconstruction (MBIR) methods with suitably optimized imaging parameters can perform nearly as well as CNN-based methods.

eess.IV↗

arXiv2022

Poisson Phase Retrieval in Very Low-count Regimes

This paper discusses phase retrieval algorithms for maximum likelihood (ML) estimation from measurements following independent Poisson distributions in very low-count regimes, e.g., 0.25 photon per pixel. To maximize the log-likelihood of the Poisson ML model, we propose a modified Wirtinger flow (WF) algorithm using a step size based on the observed Fisher information. This approach eliminates all parameter tuning except the number of iterations. We also propose a novel curvature for majorize-minimize (MM) algorithms with a quadratic majorizer. We show theoretically that our proposed curvature is sharper than the curvature derived from the supremum of the second derivative of the Poisson ML cost function. We compare the proposed algorithms (WF, MM) with existing optimization methods, including WF using other step-size schemes, quasi-Newton methods such as LBFGS and alternating direction method of multipliers (ADMM) algorithms, under a variety of experimental settings. Simulation experiments with a random Gaussian matrix, a canonical DFT matrix, a masked DFT matrix and an empirical transmission matrix demonstrate the following. 1) As expected, algorithms based on the Poisson ML model consistently produce higher quality reconstructions than algorithms derived from Gaussian noise ML models when applied to low-count data. 2) For unregularized cases, our proposed WF algorithm with Fisher information for step size converges faster than other WF methods, e.g., WF with empirical step size, backtracking line search, and optimal step size for the Gaussian noise model; it also converges faster than the LBFGS quasi-Newton method. 3) In regularized cases, our proposed WF algorithm converges faster than WF with backtracking line search, LBFGS, MM and ADMM.

cs.IT↗

arXiv2022

Stochastic Optimization of 3D Non-Cartesian Sampling Trajectory (SNOPY)

Optimizing 3D k-space sampling trajectories for efficient MRI is important yet challenging. This work proposes a generalized framework for optimizing 3D non-Cartesian sampling patterns via data-driven optimization. We built a differentiable MRI system model to enable gradient-based methods for sampling trajectory optimization. By combining training losses, the algorithm can simultaneously optimize multiple properties of sampling patterns, including image quality, hardware constraints (maximum slew rate and gradient strength), reduced peripheral nerve stimulation (PNS), and parameter-weighted contrast. The proposed method can either optimize the gradient waveform (spline-based freeform optimization) or optimize properties of given sampling trajectories (such as the rotation angle of radial trajectories). Notably, the method optimizes sampling trajectories synergistically with either model-based or learning-based reconstruction methods. We proposed several strategies to alleviate the severe non-convexity and huge computation demand posed by the high-dimensional optimization. The corresponding code is organized as an open-source, easy-to-use toolbox. We applied the optimized trajectory to multiple applications including structural and functional imaging. In the simulation studies, the reconstruction PSNR of a 3D kooshball trajectory was increased by 4 dB with SNOPY optimization. In the prospective studies, by optimizing the rotation angles of a stack-of-stars (SOS) trajectory, SNOPY improved the PSNR by 1.4dB compared to the best empirical method. Optimizing the gradient waveform of a rotational EPI trajectory improved subjects' rating of the PNS effect from 'strong' to 'mild.' In short, SNOPY provides an efficient data-driven and optimization-based method to tailor non-Cartesian sampling trajectories.

eess.SP↗

arXiv2022

Optimally Weighted PCA for High-Dimensional Heteroscedastic Data

Modern data are increasingly both high-dimensional and heteroscedastic. This paper considers the challenge of estimating underlying principal components from high-dimensional data with noise that is heteroscedastic across samples, i.e., some samples are noisier than others. Such heteroscedasticity naturally arises, e.g., when combining data from diverse sources or sensors. A natural way to account for this heteroscedasticity is to give noisier blocks of samples less weight in PCA by using the leading eigenvectors of a weighted sample covariance matrix. We consider the problem of choosing weights to optimally recover the underlying components. In general, one cannot know these optimal weights since they depend on the underlying components we seek to estimate. However, we show that under some natural statistical assumptions the optimal weights converge to a simple function of the signal and noise variances for high-dimensional data. Surprisingly, the optimal weights are not the inverse noise variance weights commonly used in practice. We demonstrate the theoretical results through numerical simulations and comparisons with existing weighting schemes. Finally, we briefly discuss how estimated signal and noise variances can be used when the true variances are unknown, and we illustrate the optimal weights on real data from astronomy.

math.ST↗

arXiv2022

Bilevel methods for image reconstruction

This review discusses methods for learning parameters for image reconstruction problems using bilevel formulations. Image reconstruction typically involves optimizing a cost function to recover a vector of unknown variables that agrees with collected measurements and prior assumptions. State-of-the-art image reconstruction methods learn these prior assumptions from training data using various machine learning techniques, such as bilevel methods. One can view the bilevel problem as formalizing hyperparameter optimization, as bridging machine learning and cost function based optimization methods, or as a method to learn variables best suited to a specific task. More formally, bilevel problems attempt to minimize an upper-level loss function, where variables in the upper-level loss function are themselves minimizers of a lower-level cost function. This review contains a running example problem of learning tuning parameters and the coefficients for sparsifying filters used in a regularizer. Such filters generalize the popular total variation regularization method, and learned filters are closely related to convolutional neural networks approaches that are rapidly gaining in popularity. Here, the lower-level problem is to reconstruct an image using a regularizer with learned sparsifying filters; the corresponding upper-level optimization problem involves a measure of reconstructed image quality based on training data. This review discusses multiple perspectives to motivate the use of bilevel methods and to make them more easily accessible to different audiences. We then turn to ways to optimize the bilevel problem, providing pros and cons of the variety of proposed approaches. Finally we overview bilevel applications in image reconstruction.

math.OC↗

arXiv2022

B-spline Parameterized Joint Optimization of Reconstruction and K-space Trajectories (BJORK) for Accelerated 2D MRI

Optimizing k-space sampling trajectories is a promising yet challenging topic for fast magnetic resonance imaging (MRI). This work proposes to optimize a reconstruction method and sampling trajectories jointly concerning image reconstruction quality in a supervised learning manner. We parameterize trajectories with quadratic B-spline kernels to reduce the number of parameters and apply multi-scale optimization, which may help to avoid sub-optimal local minima. The algorithm includes an efficient non-Cartesian unrolled neural network-based reconstruction and an accurate approximation for backpropagation through the non-uniform fast Fourier transform (NUFFT) operator to accurately reconstruct and back-propagate multi-coil non-Cartesian data. Penalties on slew rate and gradient amplitude enforce hardware constraints. Sampling and reconstruction are trained jointly using large public datasets. To correct for possible eddy-current effects introduced by the curved trajectory, we use a pencil-beam trajectory mapping technique. In both simulations and in-vivo experiments, the learned trajectory demonstrates significantly improved image quality compared to previous model-based and learning-based trajectory optimization methods for 10 times acceleration factors. Though trained with neural network-based reconstruction, the proposed trajectory also leads to improved image quality with compressed sensing-based reconstruction.

eess.SP↗

arXiv2022

Sparse-view Cone Beam CT Reconstruction using Data-consistent Supervised and Adversarial Learning from Scarce Training Data

Reconstruction of CT images from a limited set of projections through an object is important in several applications ranging from medical imaging to industrial settings. As the number of available projections decreases, traditional reconstruction techniques such as the FDK algorithm and model-based iterative reconstruction methods perform poorly. Recently, data-driven methods such as deep learning-based reconstruction have garnered a lot of attention in applications because they yield better performance when enough training data is available. However, even these methods have their limitations when there is a scarcity of available training data. This work focuses on image reconstruction in such settings, i.e., when both the number of available CT projections and the training data is extremely limited. We adopt a sequential reconstruction approach over several stages using an adversarially trained shallow network for 'destreaking' followed by a data-consistency update in each stage. To deal with the challenge of limited data, we use image subvolumes to train our method, and patch aggregation during testing. To deal with the computational challenge of learning on 3D datasets for 3D reconstruction, we use a hybrid 3D-to-2D mapping network for the 'destreaking' part. Comparisons to other methods over several test examples indicate that the proposed method has much potential, when both the number of projections and available training data are highly limited.

cs.CV↗

arXiv2021

HePPCAT: Probabilistic PCA for Data with Heteroscedastic Noise

Principal component analysis (PCA) is a classical and ubiquitous method for reducing data dimensionality, but it is suboptimal for heterogeneous data that are increasingly common in modern applications. PCA treats all samples uniformly so degrades when the noise is heteroscedastic across samples, as occurs, e.g., when samples come from sources of heterogeneous quality. This paper develops a probabilistic PCA variant that estimates and accounts for this heterogeneity by incorporating it in the statistical model. Unlike in the homoscedastic setting, the resulting nonconvex optimization problem is not seemingly solved by singular value decomposition. This paper develops a heteroscedastic probabilistic PCA technique (HePPCAT) that uses efficient alternating maximization algorithms to jointly estimate both the underlying factors and the unknown noise variances. Simulation experiments illustrate the comparative speed of the algorithms, the benefit of accounting for heteroscedasticity, and the seemingly favorable optimization landscape of this problem. Real data experiments on environmental air quality data show that HePPCAT can give a better PCA estimate than techniques that do not account for heteroscedasticity.

math.ST↗