arXiv subjects

Mathews Jacob

Publications and source records attributed to Mathews Jacob.

At least 19 recordsLinked to original sources

arXiv2026

Regularized joint reconstruction and slab combination for accelerated three-dimensional multi-slab diffusion-weighted imaging using multi-scale energy models

This work presents Energy-based Profile Encoding, EPEN, a joint reconstruction framework for high-resolution diffusion-weighted MRI from undersampled 3D multi-slab k-space acquisitions, designed to suppress slab-boundary artifacts while preserving fine anatomical detail. EPEN formulates the multi-slab acquisition process using a bilinear forward model in which both the diffusion-weighted image volume and slab excitation profiles are treated as unknown variables. Reconstruction is posed as a maximum a posteriori optimization problem with three components: a Gaussian data-fidelity term enforcing consistency with the acquired k-space measurements, a CNN-based deep energy prior that represents the negative log distribution of clean diffusion-weighted images, and a quadratic regularization term that constrains the estimated slab profiles toward an initial profile estimate. The gradient of the learned energy prior guides accelerated reconstruction toward an artifact-free image distribution. The resulting nonconvex objective is solved using alternating minimization, with image-volume updates performed through a majorize-minimize scheme using conjugate-gradient optimization and slab-profile updates estimated by regularized least squares. Across multiple acceleration factors and slab configurations, EPEN substantially reduced slab-boundary artifacts compared with conventional slab-boundary correction methods, while improving structural consistency and preserving diffusion-weighted contrast. These results demonstrate that EPEN enables robust joint 3D multi-slab diffusion MRI reconstruction and slab-profile correction within a unified optimization framework supported by deep energy-based image priors.

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arXiv2026

Annealed Langevin Posterior Sampling (ALPS): A Rapid Algorithm for Image Restoration with Multiscale Energy Models

Solving inverse problems in imaging requires models that support efficient inference, uncertainty quantification, and principled probabilistic reasoning. Energy-Based Models (EBMs), with their interpretable energy landscapes and compositional structure, are well-suited for this task but have historically suffered from high computational costs and training instability. To overcome the historical shortcomings of EBMs, we introduce a fast distillation strategy to transfer the strengths of pre-trained diffusion models into multi-scale EBMs. These distilled EBMs enable efficient sampling and preserve the interpretability and compositionality inherent to potential-based frameworks. Leveraging EBM compositionality, we propose Annealed Langevin Posterior Sampling (ALPS) algorithm for Maximum-A-Posteriori (MAP), Minimum Mean Square Error (MMSE), and uncertainty estimates for inverse problems in imaging. Unlike diffusion models that use complex guidance strategies for latent variables, we perform annealing on static posterior distributions that are well-defined and composable. Experiments on image inpainting and MRI reconstruction demonstrate that our method matches or surpasses diffusion-based baselines in both accuracy and efficiency, while also supporting MAP recovery. Overall, our framework offers a scalable and principled solution for inverse problems in imaging, with potential for practical deployment in scientific and clinical settings. ALPS code is available at the GitHub repository \href{https://github.com/JyoChand/ALPS}{ALPS}.

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arXiv2025

Motion-compensated cardiac MRI using low-rank diffeomorphic flow (DMoCo)

We introduce an unsupervised motion-compensated image reconstruction algorithm for free-breathing and ungated 3D cardiac magnetic resonance imaging (MRI). We express the image volume corresponding to each specific motion phase as the deformation of a single static image template. The main contribution of the work is the low-rank model for the compact joint representation of the family of diffeomorphisms, parameterized by the motion phases. The diffeomorphism at a specific motion phase is obtained by integrating a parametric velocity field along a path connecting the reference template phase to the motion phase. The velocity field at different phases is represented using a low-rank model. The static template and the low-rank motion model parameters are learned directly from the k-space data in an unsupervised fashion. The more constrained motion model is observed to offer improved recovery compared to current motion-resolved and motion-compensated algorithms for free-breathing 3D cine MRI.

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arXiv2025

Deep End-to-End Posterior ENergy (DEEPEN) for image recovery

Current end-to-end (E2E) and plug-and-play (PnP) image reconstruction algorithms approximate the maximum a posteriori (MAP) estimate but cannot offer sampling from the posterior distribution, like diffusion models. By contrast, it is challenging for diffusion models to be trained in an E2E fashion. This paper introduces a Deep End-to-End Posterior ENergy (DEEPEN) framework, which enables MAP estimation as well as sampling. We learn the parameters of the posterior, which is the sum of the data consistency error and the negative log-prior distribution, using maximum likelihood optimization in an E2E fashion. The proposed approach does not require algorithm unrolling, and hence has a smaller computational and memory footprint than current E2E methods, while it does not require contraction constraints typically needed by current PnP methods. Our results demonstrate that DEEPEN offers improved performance than current E2E and PnP models in the MAP setting, while it also offers faster sampling compared to diffusion models. In addition, the learned energy-based model is observed to be more robust to changes in image acquisition settings.

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arXiv2025

Accelerating Quantitative MRI using Subspace Multiscale Energy Model (SS-MuSE)

Multi-contrast MRI methods acquire multiple images with different contrast weightings, which are used for the differentiation of the tissue types or quantitative mapping. However, the scan time needed to acquire multiple contrasts is prohibitively long for 3D acquisition schemes, which can offer isotropic image resolution. While deep learning-based methods have been extensively used to accelerate 2D and 2D + time problems, the high memory demand, computation time, and need for large training data sets make them challenging for large-scale volumes. To address these challenges, we generalize the plug-and-play multi-scale energy-based model (MuSE) to a regularized subspace recovery setting, where we jointly regularize the 3D multi-contrast spatial factors in a subspace formulation. The explicit energy-based formulation allows us to use variable splitting optimization methods for computationally efficient recovery.

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arXiv2025

MAP Image Recovery with Guarantees using Locally Convex Multi-Scale Energy (LC-MUSE) Model

We propose a multi-scale deep energy model that is strongly convex in the local neighbourhood around the data manifold to represent its probability density, with application in inverse problems. In particular, we represent the negative log-prior as a multi-scale energy model parameterized by a Convolutional Neural Network (CNN). We restrict the gradient of the CNN to be locally monotone, which constrains the model as a Locally Convex Multi-Scale Energy (LC-MuSE). We use the learned energy model in image-based inverse problems, where the formulation offers several desirable properties: i) uniqueness of the solution, ii) convergence guarantees to a minimum of the inverse problem, and iii) robustness to input perturbations. In the context of parallel Magnetic Resonance (MR) image reconstruction, we show that the proposed method performs better than the state-of-the-art convex regularizers, while the performance is comparable to plug-and-play regularizers and end-to-end trained methods.

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arXiv2025

Three-Dimensional Diffusion-Weighted Multi-Slab MRI With Slice Profile Compensation Using Deep Energy Model

Three-dimensional (3D) multi-slab acquisition is a technique frequently employed in high-resolution diffusion-weighted MRI in order to achieve the best signal-to-noise ratio (SNR) efficiency. However, this technique is limited by slab boundary artifacts that cause intensity fluctuations and aliasing between slabs which reduces the accuracy of anatomical imaging. Addressing this issue is crucial for advancing diffusion MRI quality and making high-resolution imaging more feasible for clinical and research applications. In this work, we propose a regularized slab profile encoding (PEN) method within a Plug-and-Play ADMM framework, incorporating multi-scale energy (MuSE) regularization to effectively improve the slab combined reconstruction. Experimental results demonstrate that the proposed method significantly improves image quality compared to non-regularized and TV-regularized PEN approaches. The regularized PEN framework provides a more robust and efficient solution for high-resolution 3D diffusion MRI, potentially enabling clearer, more reliable anatomical imaging across various applications.

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arXiv2025

Fast multi-contrast MRI using joint multiscale energy model

The acquisition of 3D multicontrast MRI data with good isotropic spatial resolution is challenged by lengthy scan times. In this work, we introduce a CNN-based multiscale energy model to learn the joint probability distribution of the multi-contrast images. The joint recovery of the contrasts from undersampled data is posed as a maximum a posteriori estimation scheme, where the learned energy serves as the prior. We use a majorize-minimize algorithm to solve the optimization scheme. The proposed model leverages the redundancies across different contrasts to improve image fidelity. The proposed scheme is observed to preserve fine details and contrast, offering sharper reconstructions compared to reconstruction methods that independently recover the contrasts. While we focus on 3D MPNRAGE acquisitions in this work, the proposed approach is generalizable to arbitrary multi-contrast settings.

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arXiv2024

Latent Diffusion for Medical Image Segmentation: End to end learning for fast sampling and accuracy

Diffusion Probabilistic Models (DPMs) suffer from inefficient inference due to their slow sampling and high memory consumption, which limits their applicability to various medical imaging applications. In this work, we propose a novel conditional diffusion modeling framework (LDSeg) for medical image segmentation, utilizing the learned inherent low-dimensional latent shape manifolds of the target objects and the embeddings of the source image with an end-to-end framework. Conditional diffusion in latent space not only ensures accurate image segmentation for multiple interacting objects, but also tackles the fundamental issues of traditional DPM-based segmentation methods: (1) high memory consumption, (2) time-consuming sampling process, and (3) unnatural noise injection in the forward and reverse processes. The end-to-end training strategy enables robust representation learning in the latent space related to segmentation features, ensuring significantly faster sampling from the posterior distribution for segmentation generation in the inference phase. Our experiments demonstrate that LDSeg achieved state-of-the-art segmentation accuracy on three medical image datasets with different imaging modalities. In addition, we showed that our proposed model was significantly more robust to noise compared to traditional deterministic segmentation models. The code is available at https://github.com/FahimZaman/LDSeg.git.

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arXiv2024

Deep Learning for Accelerated and Robust MRI Reconstruction: a Review

Deep learning (DL) has recently emerged as a pivotal technology for enhancing magnetic resonance imaging (MRI), a critical tool in diagnostic radiology. This review paper provides a comprehensive overview of recent advances in DL for MRI reconstruction. It focuses on DL approaches and architectures designed to improve image quality, accelerate scans, and address data-related challenges. These include end-to-end neural networks, pre-trained networks, generative models, and self-supervised methods. The paper also discusses the role of DL in optimizing acquisition protocols, enhancing robustness against distribution shifts, and tackling subtle bias. Drawing on the extensive literature and practical insights, it outlines current successes, limitations, and future directions for leveraging DL in MRI reconstruction, while emphasizing the potential of DL to significantly impact clinical imaging practices.

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arXiv2024

Memory-efficient deep end-to-end posterior network (DEEPEN) for inverse problems

End-to-End (E2E) unrolled optimization frameworks show promise for Magnetic Resonance (MR) image recovery, but suffer from high memory usage during training. In addition, these deterministic approaches do not offer opportunities for sampling from the posterior distribution. In this paper, we introduce a memory-efficient approach for E2E learning of the posterior distribution. We represent this distribution as the combination of a data-consistency-induced likelihood term and an energy model for the prior, parameterized by a Convolutional Neural Network (CNN). The CNN weights are learned from training data in an E2E fashion using maximum likelihood optimization. The learned model enables the recovery of images from undersampled measurements using the Maximum A Posteriori (MAP) optimization. In addition, the posterior model can be sampled to derive uncertainty maps about the reconstruction. Experiments on parallel MR image reconstruction show that our approach performs comparable to the memory-intensive E2E unrolled algorithm, performs better than its memory-efficient counterpart, and can provide uncertainty maps. Our framework paves the way towards MR image reconstruction in 3D and higher dimensions

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arXiv2023

Surf-CDM: Score-Based Surface Cold-Diffusion Model For Medical Image Segmentation

Diffusion models have shown impressive performance for image generation, often times outperforming other generative models. Since their introduction, researchers have extended the powerful noise-to-image denoising pipeline to discriminative tasks, including image segmentation. In this work we propose a conditional score-based generative modeling framework for medical image segmentation which relies on a parametric surface representation for the segmentation masks. The surface re-parameterization allows the direct application of standard diffusion theory, as opposed to when the mask is represented as a binary mask. Moreover, we adapted an extended variant of the diffusion technique known as the "cold-diffusion" where the diffusion model can be constructed with deterministic perturbations instead of Gaussian noise, which facilitates significantly faster convergence in the reverse diffusion. We evaluated our method on the segmentation of the left ventricle from 65 transthoracic echocardiogram videos (2230 echo image frames) and compared its performance to the most popular and widely used image segmentation models. Our proposed model not only outperformed the compared methods in terms of segmentation accuracy, but also showed potential in estimating segmentation uncertainties for further downstream analyses due to its inherent generative nature.

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arXiv2023

Local monotone operator learning using non-monotone operators: MnM-MOL

The recovery of magnetic resonance (MR) images from undersampled measurements is a key problem that has seen extensive research in recent years. Unrolled approaches, which rely on end-to-end training of convolutional neural network (CNN) blocks within iterative reconstruction algorithms, offer state-of-the-art performance. These algorithms require a large amount of memory during training, making them difficult to employ in high-dimensional applications. Deep equilibrium (DEQ) models and the recent monotone operator learning (MOL) approach were introduced to eliminate the need for unrolling, thus reducing the memory demand during training. Both approaches require a Lipschitz constraint on the network to ensure that the forward and backpropagation iterations converge. Unfortunately, the constraint often results in reduced performance compared to unrolled methods. The main focus of this work is to relax the constraint on the CNN block in two different ways. Inspired by convex-non-convex regularization strategies, we now impose the monotone constraint on the sum of the gradient of the data term and the CNN block, rather than constrain the CNN itself to be a monotone operator. This approach enables the CNN to learn possibly non-monotone score functions, which can translate to improved performance. In addition, we only restrict the operator to be monotone in a local neighborhood around the image manifold. Our theoretical results show that the proposed algorithm is guaranteed to converge to the fixed point and that the solution is robust to input perturbations, provided that it is initialized close to the true solution. Our empirical results show that the relaxed constraints translate to improved performance and that the approach enjoys robustness to input perturbations similar to MOL.

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arXiv2023

Motion Compensated Unsupervised Deep Learning for 5D MRI

We propose an unsupervised deep learning algorithm for the motion-compensated reconstruction of 5D cardiac MRI data from 3D radial acquisitions. Ungated free-breathing 5D MRI simplifies the scan planning, improves patient comfort, and offers several clinical benefits over breath-held 2D exams, including isotropic spatial resolution and the ability to reslice the data to arbitrary views. However, the current reconstruction algorithms for 5D MRI take very long computational time, and their outcome is greatly dependent on the uniformity of the binning of the acquired data into different physiological phases. The proposed algorithm is a more data-efficient alternative to current motion-resolved reconstructions. This motion-compensated approach models the data in each cardiac/respiratory bin as Fourier samples of the deformed version of a 3D image template. The deformation maps are modeled by a convolutional neural network driven by the physiological phase information. The deformation maps and the template are then jointly estimated from the measured data. The cardiac and respiratory phases are estimated from 1D navigators using an auto-encoder. The proposed algorithm is validated on 5D bSSFP datasets acquired from two subjects.

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arXiv2023

Multi-Scale Energy (MuSE) plug and play framework for inverse problems

We introduce multi-scale energy models to learn the prior distribution of images, which can be used in inverse problems to derive the Maximum A Posteriori (MAP) estimate and to sample from the posterior distribution. Compared to the traditional single-scale energy models, the multi-scale strategy improves the estimation accuracy and convergence of the MAP algorithm, even when it is initialized far away from the solution. We propose two kinds of multi-scale strategies: a) the explicit (e-MuSE) framework, where we use a sequence of explicit energies, each corresponding to a smooth approximation of the original negative log-prior, and b) the implicit (i-MuSE), where we rely on a single energy function whose gradients at different scales closely match the corresponding e-MuSE gradients. Although both schemes improve convergence and accuracy, the e-MuSE MAP solution depends on the scheduling strategy, including the choice of intermediate scales and exit conditions. In contrast, the i-MuSE formulation is significantly simpler, resulting in faster convergence and improved performance. We compare the performance of the proposed MuSE models in the context of Magnetic Resonance (MR) image recovery. The results demonstrate that the multi-scale framework yields a MAP reconstruction comparable in quality to the End-to-End (E2E) trained models, while being relatively unaffected by the changes in the forward model. In addition, the i-MuSE scheme also allows the generation of samples from the posterior distribution, enabling us to estimate the uncertainty maps.

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arXiv2023

Adapting model-based deep learning to multiple acquisition conditions: Ada-MoDL

Purpose: The aim of this work is to introduce a single model-based deep network that can provide high-quality reconstructions from undersampled parallel MRI data acquired with multiple sequences, acquisition settings and field strengths. Methods: A single unrolled architecture, which offers good reconstructions for multiple acquisition settings, is introduced. The proposed scheme adapts the model to each setting by scaling the CNN features and the regularization parameter with appropriate weights. The scaling weights and regularization parameter are derived using a multi-layer perceptron model from conditional vectors, which represents the specific acquisition setting. The perceptron parameters and the CNN weights are jointly trained using data from multiple acquisition settings, including differences in field strengths, acceleration, and contrasts. The conditional network is validated using datasets acquired with different acquisition settings. Results: The comparison of the adaptive framework, which trains a single model using the data from all the settings, shows that it can offer consistently improved performance for each acquisition condition. The comparison of the proposed scheme with networks that are trained independently for each acquisition setting shows that it requires less training data per acquisition setting to offer good performance. Conclusion: The Ada-MoDL framework enables the use of a single model-based unrolled network for multiple acquisition settings. In addition to eliminating the need to train and store multiple networks for different acquisition settings, this approach reduces the training data needed for each acquisition setting.

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arXiv2023

Accelerated parallel MRI using memory efficient and robust monotone operator learning (MOL)

Model-based deep learning methods that combine imaging physics with learned regularization priors have been emerging as powerful tools for parallel MRI acceleration. The main focus of this paper is to determine the utility of the monotone operator learning (MOL) framework in the parallel MRI setting. The MOL algorithm alternates between a gradient descent step using a monotone convolutional neural network (CNN) and a conjugate gradient algorithm to encourage data consistency. The benefits of this approach include similar guarantees as compressive sensing algorithms including uniqueness, convergence, and stability, while being significantly more memory efficient than unrolled methods. We validate the proposed scheme by comparing it with different unrolled algorithms in the context of accelerated parallel MRI for static and dynamic settings.

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arXiv2023

Deep Factor Model: A Novel Approach for Motion Compensated Multi-Dimensional MRI

Recent quantitative parameter mapping methods including MR fingerprinting (MRF) collect a time series of images that capture the evolution of magnetization. The focus of this work is to introduce a novel approach termed as Deep Factor Model(DFM), which offers an efficient representation of the multi-contrast image time series. The higher efficiency of the representation enables the acquisition of the images in a highly undersampled fashion, which translates to reduced scan time in 3D high-resolution multi-contrast applications. The approach integrates motion estimation and compensation, making the approach robust to subject motion during the scan.

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