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Abstract The purpose of the current study was to introduce a Deep learning‐based Accelerated and Noise‐Suppressed Estimation (DANSE) method for reconstructing quantitative maps of biological tissue cellular‐specific,R2t*, and hemodynamic‐specific,R2’, metrics of quantitative gradient‐recalled echo (qGRE) MRI. The DANSE method adapts a supervised learning paradigm to train a convolutional neural network for robust estimation ofR2t*andR2’maps with significantly reduced sensitivity to noise and the adverse effects of macroscopic (B₀) magnetic field inhomogeneities directly from the gradient‐recalled echo (GRE) magnitude images. TheR2t*andR2’maps for training were generated by means of a voxel‐by‐voxel fitting of a previously developed biophysical quantitative qGRE model accounting for tissue, hemodynamic, and B₀‐inhomogeneities contributions to multigradient‐echo GRE signal using a nonlinear least squares (NLLS) algorithm. We show that the DANSE model efficiently estimates the aforementioned qGRE maps and preserves all the features of the NLLS approach with significant improvements including noise suppression and computation speed (from many hours to seconds). The noise‐suppression feature of DANSE is especially prominent for data with low signal‐to‐noise ratio (SNR ~ 50–100), where DANSE‐generatedR2t*andR2’maps had up to three times smaller errors than that of the NLLS method. The DANSE method enables fast reconstruction of qGRE maps with significantly reduced sensitivity to noise and magnetic field inhomogeneities. The DANSE method does not require any information about field inhomogeneities during application. It exploits spatial and gradient echo time‐dependent patterns in the GRE data and previously gained knowledge from the biophysical model, thus producing high quality qGRE maps, even in environments with high noise levels. These features along with fast computational speed can lead to broad qGRE clinical and research applications. 

Posterior sampling has been shown to be a powerful Bayesian approach for solving imaging inverse problems. The recent plug-and-play unadjusted Langevin algorithm (PnP-ULA) has emerged as a promising method for Monte Carlo sampling and minimum mean squared error (MMSE) estimation by combining physical measurement models with deep-learning priors specified using image denoisers. However, the intricate relationship between the sampling distribution of PnP-ULA and the mismatched data-fidelity and denoiser has not been theoretically analyzed. We address this gap by proposing a posterior-L2 pseudometric and using it to quantify an explicit error bound for PnP-ULA under mismatched posterior distribution. We numerically validate our theory on several inverse problems such as sampling from Gaussian mixture models and image deblurring. Our results suggest that the sensitivity of the sampling distribution of PnP-ULA to a mismatch in the measurement model and the denoiser can be precisely characterized. 

Deformable image registration (DIR) is an active research topic in biomedical imaging. There is a growing interest in developing DIR methods based on deep learning (DL). A traditional DL approach to DIR is based on training a convolutional neural network (CNN) to estimate the registration field between two input images. While conceptually simple, this approach comes with a limitation that it exclusively relies on a pre-trained CNN without explicitly enforcing fidelity between the registered image and the reference. We present plug-and-play image registration network (PIRATE) as a new DIR method that addresses this issue by integrating an explicit data-fidelity penalty and a CNN prior. PIRATE pre-trains a CNN denoiser on the registration field and "plugs" it into an iterative method as a regularizer. We additionally present PIRATE+ that fine-tunes the CNN prior in PIRATE using deep equilibrium models (DEQ). PIRATE+ interprets the fixed-point iteration of PIRATE as a network with effectively infinite layers and then trains the resulting network end-to-end, enabling it to learn more task-specific information and boosting its performance. Our numerical results on OASIS and CANDI datasets show that our methods achieve state-of-the-art performance on DIR. 

Regularization by Denoising (RED) is a well-known method for solving image restoration problems by using learned image denoisers as priors. Since the regularization parameter in the traditional RED does not have any physical interpretation, it does not provide an approach for automatic parameter selection. This letter addresses this issue by introducing the Constrained Regularization by Denoising (CRED) method that reformulates RED as a constrained optimization problem where the regularization parameter corresponds directly to the amount of noise in the measurements. The solution to the constrained problem is solved by designing an efficient method based on alternating direction method of multipliers (ADMM). Our experiments show that CRED outperforms the competing methods in terms of stability and robustness, while also achieving competitive performances in terms of image quality. 

Deep learning-based methods deliver state-of-the-art performance for solving inverse problems that arise in computational imaging. These methods can be broadly divided into two groups: (1) learn a network to map measurements to the signal estimate, which is known to be fragile; (2) learn a prior for the signal to use in an optimization-based recovery. Despite the impressive results from the latter approach, many of these methods also lack robustness to shifts in data distribution, measurements, and noise levels. Such domain shifts result in a performance gap and in some cases introduce undesired artifacts in the estimated signal. In this paper, we explore the qualitative and quantitative effects of various domain shifts and propose a flexible and parameter efficient framework that adapts pretrained networks to such shifts. We demonstrate the effectiveness of our method for a number of reconstruction tasks that involve natural image, MRI, and CT imaging domains under distribution, measurement model, and noise level shifts. Our experiments demonstrate that our method achieves competitive performance compared to independently fully trained networks, while requiring significantly fewer additional parameters, and outperforms several domain adaptation techniques. 

Plug-and-Play Priors (PnP) is a well-known class of methods for solving inverse problems in computational imaging. PnP methods combine physical forward models with learned prior models specified as image denoisers. A common issue with the learned models is that of a performance drop when there is a distribution shift between the training and testing data. Test-time training (TTT) was recently proposed as a general strategy for improving the performance of learned models when training and testing data come from different distributions. In this paper, we propose PnP-Ttt as a new method for overcoming distribution shifts in PnP. PnP-TTT uses deep equilibrium learning (DEQ) for optimizing a self-supervised loss at the fixed points of PnP iterations. PnP-TTT can be directly applied on a single test sample to improve the generalization of PnP. We show through simulations that given a sufficient number of measurements, PnP-TTT enables the use of image priors trained on natural images for image reconstruction in magnetic resonance imaging (MRI). 

Plug-and-Play Alternating Direction Method of Multipliers (PnP-ADMM) is a widely-used algorithm for solving inverse problems by integrating physical measurement models and convolutional neural network (CNN) priors. PnP-ADMM has been theoretically proven to converge for convex data-fidelity terms and nonexpansive CNNs. It has however been observed that PnP-ADMM often empirically converges even for expansive CNNs. This paper presents a theoretical explanation for the observed stability of PnP-ADMM based on the interpretation of the CNN prior as a minimum mean-squared error (MMSE) denoiser. Our explanation parallels a similar argument recently made for the iterative shrinkage/thresholding algorithm variant of PnP (PnP-ISTA) and relies on the connection between MMSE denoisers and proximal operators. We also numerically evaluate the performance gap between PnP-ADMM using a nonexpan-sive DnCNN denoiser and expansive DRUNet denoiser, thus motivating the use of expansive CNNs. 

Plug-and-play (PnP) prior is a well-known class of methods for solving imaging inverse problems by computing fixed-points of operators combining physical measurement models and learned image denoisers. While PnP methods have been extensively used for image recovery with known measurement operators, there is little work on PnP for solving blind inverse problems. We address this gap by presenting a new block-coordinate PnP (BC-PnP) method that efficiently solves this joint estimation problem by introducing learned denoisers as priors on both the unknown image and the unknown measurement operator. We present a new convergence theory for BC-PnP compatible with blind inverse problems by considering nonconvex data-fidelity terms and expansive denoisers. Our theory analyzes the convergence of BC-PnP to a stationary point of an implicit function associated with an approximate minimum mean-squared error (MMSE) denoiser. We numerically validate our method on two blind inverse problems: automatic coil sensitivity estimation in magnetic resonance imaging (MRI) and blind image deblurring. Our results show that BC-PnP provides an efficient and principled framework for using denoisers as PnP priors for jointly estimating measurement operators and images. 

Plug-and-Play (PnP) methods are efficient iterative algorithms for solving ill-posed image inverse problems. PnP methods are obtained by using deep Gaussian denoisers instead of the proximal operator or the gradient-descent step within proximal algorithms. Current PnP schemes rely on data-fidelity terms that have either Lipschitz gradients or closed-form proximal operators, which is not applicable to Poisson inverse problems. Based on the observation that the Gaussian noise is not the adequate noise model in this setting, we propose to generalize PnP using the Bregman Proximal Gradient (BPG) method. BPG replaces the Euclidean distance with a Bregman divergence that can better capture the smoothness properties of the problem. We introduce the Bregman Score Denoiser specifically parametrized and trained for the new Bregman geometry and prove that it corresponds to the proximal operator of a nonconvex potential. We propose two PnP algorithms based on the Bregman Score Denoiser for solving Poisson inverse problems. Extending the convergence results of BPG in the nonconvex settings, we show that the proposed methods converge, targeting stationary points of an explicit global functional. Experimental evaluations conducted on various Poisson inverse problems validate the convergence results and showcase effective restoration performance. 

Limited-Angle Computed Tomography (LACT) is a nondestructive 3D imaging technique used in a variety of applications ranging from security to medicine. The limited angle coverage in LACT is often a dominant source of severe artifacts in the reconstructed images, making it a challenging imaging inverse problem. Diffusion models are a recent class of deep generative models for synthesizing realistic images using image denoisers. In this work, we present DOLCE as the first framework for integrating conditionally-trained diffusion models and explicit physical measurement models for solving imaging inverse problems. DOLCE achieves the SOTA performance in highly ill-posed LACT by alternating between the data-fidelity and sampling updates of a diffusion model conditioned on the transformed sinogram. We show through extensive experimentation that unlike existing methods, DOLCE can synthesize high-quality and structurally coherent 3D volumes by using only 2D conditionally pre-trained diffusion models. We further show on several challenging real LACT datasets that the same pretrained DOLCE model achieves the SOTA performance on drastically different types of images.