DiffGEPCI: 3D MRI Synthesis from mGRE Signals using 2.5D Diffusion Model

We introduce a new framework called DiffGEPCI for cross-modality generation in magnetic resonance imaging (MRI) using a 2.5D conditional diffusion model. DiffGEPCI can synthesize high-quality Fluid Attenuated Inversion Recovery (FLAIR) and Magnetization Prepared-Rapid Gradient Echo (MPRAGE) images, without acquiring corresponding measurements, by leveraging multi-Gradient-Recalled Echo (mGRE) MRI signals as conditional inputs. DiffGEPCI operates in a two-step fashion: it initially estimates a 3D volume slice-by-slice using the axial plane and subsequently applies a refinement algorithm (referred to as 2.5D) to enhance the quality of the coronal and sagittal planes. Experimental validation on real mGRE data shows that DiffGEPCI achieves excellent performance, surpassing generative adversarial networks (GANs) and traditional diffusion models.

A Structured Pruning Algorithm for Model-based Deep Learning

There is a growing interest in model-based deep learning (MBDL) for solving imaging inverse problems. MBDL networks can be seen as iterative algorithms that estimate the desired image using a physical measurement model and a learned image prior specified using a convolutional neural net (CNNs). The iterative nature of MBDL networks increases the test-time computational complexity, which limits their applicability in certain large-scale applications. We address this issue by presenting structured pruning algorithm for model-based deep learning (SPADE) as the first structured pruning algorithm for MBDL networks. SPADE reduces the computational complexity of CNNs used within MBDL networks by pruning its non-essential weights. We propose three distinct strategies to fine-tune the pruned MBDL networks to minimize the performance loss. Each fine-tuning strategy has a unique benefit that depends on the presence of a pre-trained model and a high-quality ground truth. We validate SPADE on two distinct inverse problems, namely compressed sensing MRI and image super-resolution. Our results highlight that MBDL models pruned by SPADE can achieve substantial speed up in testing time while maintaining competitive performance.

A Restoration Network as an Implicit Prior

Image denoisers have been shown to be powerful priors for solving inverse problems in imaging. In this work, we introduce a generalization of these methods that allows any image restoration network to be used as an implicit prior. The proposed method uses priors specified by deep neural networks pre-trained as general restoration operators. The method provides a principled approach for adapting state-of-the-art restoration models for other inverse problems. Our theoretical result analyzes its convergence to a stationary point of a global functional associated with the restoration operator. Numerical results show that the method using a super-resolution prior achieves state-of-the-art performance both quantitatively and qualitatively. Overall, this work offers a step forward for solving inverse problems by enabling the use of powerful pre-trained restoration models as priors.

Block Coordinate Plug-and-Play Methods for Blind Inverse Problems

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.

Self-Supervised Deep Equilibrium Models for Inverse Problems with Theoretical Guarantees

Deep equilibrium models (DEQ) have emerged as a powerful alternative to deep unfolding (DU) for image reconstruction. DEQ models-implicit neural networks with effectively infinite number of layers-were shown to achieve state-of-the-art image reconstruction without the memory complexity associated with DU. While the performance of DEQ has been widely investigated, the existing work has primarily focused on the settings where groundtruth data is available for training. We present self-supervised deep equilibrium model (SelfDEQ) as the first self-supervised reconstruction framework for training model-based implicit networks from undersampled and noisy MRI measurements. Our theoretical results show that SelfDEQ can compensate for unbalanced sampling across multiple acquisitions and match the performance of fully supervised DEQ. Our numerical results on in-vivo MRI data show that SelfDEQ leads to state-of-the-art performance using only undersampled and noisy training data.

SPICE: Self-Supervised Learning for MRI with Automatic Coil Sensitivity Estimation

Deep model-based architectures (DMBAs) integrating physical measurement models and learned image regularizers are widely used in parallel magnetic resonance imaging (PMRI). Traditional DMBAs for PMRI rely on pre-estimated coil sensitivity maps (CSMs) as a component of the measurement model. However, estimation of accurate CSMs is a challenging problem when measurements are highly undersampled. Additionally, traditional training of DMBAs requires high-quality groundtruth images, limiting their use in applications where groundtruth is difficult to obtain. This paper addresses these issues by presenting SPICE as a new method that integrates self-supervised learning and automatic coil sensitivity estimation. Instead of using pre-estimated CSMs, SPICE simultaneously reconstructs accurate MR images and estimates high-quality CSMs. SPICE also enables learning from undersampled noisy measurements without any groundtruth. We validate SPICE on experimentally collected data, showing that it can achieve state-of-the-art performance in highly accelerated data acquisition settings (up to 10x).

Deep Model-Based Architectures for Inverse Problems under Mismatched Priors

There is a growing interest in deep model-based architectures (DMBAs) for solving imaging inverse problems by combining physical measurement models and learned image priors specified using convolutional neural nets (CNNs). For example, well-known frameworks for systematically designing DMBAs include plug-and-play priors (PnP), deep unfolding (DU), and deep equilibrium models (DEQ). While the empirical performance and theoretical properties of DMBAs have been widely investigated, the existing work in the area has primarily focused on their performance when the desired image prior is known exactly. This work addresses the gap in the prior work by providing new theoretical and numerical insights into DMBAs under mismatched CNN priors. Mismatched priors arise naturally when there is a distribution shift between training and testing data, for example, due to test images being from a different distribution than images used for training the CNN prior. They also arise when the CNN prior used for inference is an approximation of some desired statistical estimator (MAP or MMSE). Our theoretical analysis provides explicit error bounds on the solution due to the mismatched CNN priors under a set of clearly specified assumptions. Our numerical results compare the empirical performance of DMBAs under realistic distribution shifts and approximate statistical estimators.

Monotonically Convergent Regularization by Denoising

Regularization by denoising (RED) is a widely-used framework for solving inverse problems by leveraging image denoisers as image priors. Recent work has reported the state-of-the-art performance of RED in a number of imaging applications using pre-trained deep neural nets as denoisers. Despite the recent progress, the stable convergence of RED algorithms remains an open problem. The existing RED theory only guarantees stability for convex data-fidelity terms and nonexpansive denoisers. This work addresses this issue by developing a new monotone RED (MRED) algorithm, whose convergence does not require nonexpansiveness of the deep denoising prior. Simulations on image deblurring and compressive sensing recovery from random matrices show the stability of MRED even when the traditional RED algorithm diverges.

Fine-Grained Classification of Cervical Cells Using Morphological and Appearance Based Convolutional Neural Networks

Fine-grained classification of cervical cells into different abnormality levels is of great clinical importance but remains very challenging. Contrary to traditional classification methods that rely on hand-crafted or engineered features, convolution neural network (CNN) can classify cervical cells based on automatically learned deep features. However, CNN in previous studies do not involve cell morphological information, and it is unknown whether morphological features can be directly modeled by CNN to classify cervical cells. This paper presents a CNN-based method that combines cell image appearance with cell morphology for classification of cervical cells in Pap smear. The training cervical cell dataset consists of adaptively re-sampled image patches coarsely centered on the nuclei. Several CNN models (AlexNet, GoogleNet, ResNet and DenseNet) pre-trained on ImageNet dataset were fine-tuned on the cervical dataset for comparison. The proposed method is evaluated on the Herlev cervical dataset by five-fold cross-validation at patient level splitting. Results show that by adding cytoplasm and nucleus masks as raw morphological information into appearance-based CNN learning, higher classification accuracies can be achieved in general. Among the four CNN models, GoogleNet fed with both morphological and appearance information obtains the highest classification accuracies of 94.5% for 2-class classification task and 64.5% for 7-class classification task. Our method demonstrates that combining cervical cell morphology with appearance information can provide improved classification performance, which is clinically important for early diagnosis of cervical dysplastic changes.