arXiv subjects

Yamin Arefeen

Publications and source records attributed to Yamin Arefeen.

14 recordsLinked to original sources

arXiv2026

Accelerating Stroke MRI with Diffusion Probabilistic Models through Large-Scale Pre-training and Target-Specific Fine-Tuning

Purpose: To develop a data-efficient strategy for accelerated MRI reconstruction with Diffusion Probabilistic Generative Models (DPMs) that enables faster scan times in clinical stroke MRI when only limited fully-sampled data samples are available. Methods: Our simple training strategy, inspired by the foundation model paradigm, first trains a DPM on a large, diverse collection of publicly available brain MRI data in fastMRI and then fine-tunes on a small dataset from the target application using carefully selected learning rates and fine-tuning durations. The approach is evaluated on controlled fastMRI experiments and on clinical stroke MRI data with a blinded clinical reader study. Results: DPMs pre-trained on approximately 4000 subjects with non-FLAIR contrasts and fine-tuned on FLAIR data from only 20 target subjects achieve reconstruction performance comparable to models trained with substantially more target-domain FLAIR data across multiple acceleration factors. Experiments reveal that moderate fine-tuning with a reduced learning rate yields improved performance, while insufficient or excessive fine-tuning degrades reconstruction quality. When applied to clinical stroke MRI, a blinded reader study involving two neuroradiologists indicates that images reconstructed using the proposed approach from $2 \times$ accelerated data are non-inferior to standard-of-care in terms of image quality and structural delineation. Conclusion: Large-scale pre-training combined with targeted fine-tuning enables DPM-based MRI reconstruction in data-constrained, accelerated clinical stroke MRI. The proposed approach substantially reduces the need for large application-specific datasets while maintaining clinically acceptable image quality, supporting the use of foundation-inspired diffusion models for accelerated MRI in targeted applications.

eess.IV↗

arXiv2026

Theoretical Bounds on Parallel Imaging Implicit Data Crimes in an MRI Reproducing Kernel Hilbert Space

Magnetic Resonance Imaging (MRI) diagnoses and manages a wide range of diseases, yet long scan times drive high costs and limit accessibility. AI methods have demonstrated substantial potential for reducing scan times, but despite rapid progress, clinical translation of AI often fails. One particular class of failure modes, referred to as implicit data crimes, are a result of hidden biases introduced when MRI datasets incompletely model the MRI physics of the acquisition. Previous work identified data crimes resulting from algorithmic completion of k-space with parallel imaging and drew on simulation to demonstrate the resulting downstream biases. This work proposes a mathematical framework to re-characterize the problem as one of error reduction during interpolation between sets of evaluation coordinates. We establish a generalized matrix-based definition of the reconstruction error upper bound as a function of the input sampling pattern. Experiments on relevant sampling pattern structures demonstrate the relevance of the framework and suggest future directions for analysis of data crimes.

eess.SP↗

arXiv2026

Optimizing Sampling Patterns for Compressed Sensing MRI with Diffusion Generative Models

Magnetic resonance imaging (MRI) is a powerful medical imaging modality, but long acquisition times limit throughput, patient comfort, and clinical accessibility. Diffusion-based generative models serve as strong image priors for reducing scan-time with accelerated MRI reconstruction and offer robustness across variations in the acquisition model. However, most existing diffusion-based approaches do not exploit the unique ability in MRI to jointly design both the sampling pattern and the reconstruction method. While prior learning-based approaches have optimized sampling patterns for end-to-end unrolled networks, analogous methods for diffusion-based reconstruction have not been established due to the computational burden of posterior sampling. In this work, we propose a method to optimize k-space sampling patterns for accelerated multi-coil MRI reconstruction using diffusion models as priors. We introduce a training objective based on a single-step posterior mean estimate that avoids backpropagation through an expensive iterative reconstruction process. Then we present a greedy strategy for learning Cartesian sampling patterns that selects informative k-space locations using gradient information from a pre-trained diffusion model while enforcing spatial diversity among samples. Experimental results across multiple anatomies and acceleration factors demonstrate that diffusion models using the optimized sampling patterns achieve higher-quality reconstructions in comparison to using fixed and learned baseline patterns.

cs.LG↗

arXiv2025

A Generative Diffusion Model to Solve Inverse Problems for Robust in-NICU Neonatal MRI

We present the first acquisition-agnostic diffusion generative model for Magnetic Resonance Imaging (MRI) in the neonatal intensive care unit (NICU) to solve a range of inverse problems for shortening scan time and improving motion robustness. In-NICU MRI scanners leverage permanent magnets at lower field-strengths (i.e., below 1.5 Tesla) for non-invasive assessment of potential brain abnormalities during the critical phase of early live development, but suffer from long scan times and motion artifacts. In this setting, training data sizes are small and intrinsically suffer from low signal-to-noise ratio (SNR). This work trains a diffusion probabilistic generative model using such a real-world training dataset of clinical neonatal MRI by applying several novel signal processing and machine learning methods to handle the low SNR and low quantity of data. The model is then used as a statistical image prior to solve various inverse problems at inference time without requiring any retraining. Experiments demonstrate the generative model's utility for three real-world applications of neonatal MRI: accelerated reconstruction, motion correction, and super-resolution.

physics.med-ph↗

arXiv2025

Diffusion Probabilistic Generative Models for Accelerated, in-NICU Permanent Magnet Neonatal MRI

Purpose: Magnetic Resonance Imaging (MRI) enables non-invasive assessment of brain abnormalities during early life development. Permanent magnet scanners operating in the neonatal intensive care unit (NICU) facilitate MRI of sick infants, but have long scan times due to lower signal-to-noise ratios (SNR) and limited receive coils. This work accelerates in-NICU MRI with diffusion probabilistic generative models by developing a training pipeline accounting for these challenges. Methods: We establish a novel training dataset of clinical, 1 Tesla neonatal MR images in collaboration with Aspect Imaging and Sha'are Zedek Medical Center. We propose a pipeline to handle the low quantity and SNR of our real-world dataset (1) modifying existing network architectures to support varying resolutions; (2) training a single model on all data with learned class embedding vectors; (3) applying self-supervised denoising before training; and (4) reconstructing by averaging posterior samples. Retrospective under-sampling experiments, accounting for signal decay, evaluated each item of our proposed methodology. A clinical reader study with practicing pediatric neuroradiologists evaluated our proposed images reconstructed from 1.5x under-sampled data. Results: Combining all data, denoising pre-training, and averaging posterior samples yields quantitative improvements in reconstruction. The generative model decouples the learned prior from the measurement model and functions at two acceleration rates without re-training. The reader study suggests that proposed images reconstructed from approximately 1.5x under-sampled data are adequate for clinical use. Conclusion: Diffusion probabilistic generative models applied with the proposed pipeline to handle challenging real-world datasets could reduce scan time of in-NICU neonatal MRI.

eess.IV↗

arXiv2024

INFusion: Diffusion Regularized Implicit Neural Representations for 2D and 3D accelerated MRI reconstruction

Implicit Neural Representations (INRs) are a learning-based approach to accelerate Magnetic Resonance Imaging (MRI) acquisitions, particularly in scan-specific settings when only data from the under-sampled scan itself are available. Previous work demonstrates that INRs improve rapid MRI through inherent regularization imposed by neural network architectures. Typically parameterized by fully-connected neural networks, INRs support continuous image representations by taking a physical coordinate location as input and outputting the intensity at that coordinate. Previous work has applied unlearned regularization priors during INR training and have been limited to 2D or low-resolution 3D acquisitions. Meanwhile, diffusion based generative models have received recent attention as they learn powerful image priors decoupled from the measurement model. This work proposes INFusion, a technique that regularizes the optimization of INRs from under-sampled MR measurements with pre-trained diffusion models for improved image reconstruction. In addition, we propose a hybrid 3D approach with our diffusion regularization that enables INR application on large-scale 3D MR datasets. 2D experiments demonstrate improved INR training with our proposed diffusion regularization, and 3D experiments demonstrate feasibility of INR training with diffusion regularization on 3D matrix sizes of 256 by 256 by 80.

eess.IV↗

arXiv2024

Zero-DeepSub: Zero-Shot Deep Subspace Reconstruction for Rapid Multiparametric Quantitative MRI Using 3D-QALAS

Purpose: To develop and evaluate methods for 1) reconstructing 3D-quantification using an interleaved Look-Locker acquisition sequence with T2 preparation pulse (3D-QALAS) time-series images using a low-rank subspace method, which enables accurate and rapid T1 and T2 mapping, and 2) improving the fidelity of subspace QALAS by combining scan-specific deep-learning-based reconstruction and subspace modeling. Methods: A low-rank subspace method for 3D-QALAS (i.e., subspace QALAS) and zero-shot deep-learning subspace method (i.e., Zero-DeepSub) were proposed for rapid and high fidelity T1 and T2 mapping and time-resolved imaging using 3D-QALAS. Using an ISMRM/NIST system phantom, the accuracy and reproducibility of the T1 and T2 maps estimated using the proposed methods were evaluated by comparing them with reference techniques. The reconstruction performance of the proposed subspace QALAS using Zero-DeepSub was evaluated in vivo and compared with conventional QALAS at high reduction factors of up to 9-fold. Results: Phantom experiments showed that subspace QALAS had good linearity with respect to the reference methods while reducing biases and improving precision compared to conventional QALAS, especially for T2 maps. Moreover, in vivo results demonstrated that subspace QALAS had better g-factor maps and could reduce voxel blurring, noise, and artifacts compared to conventional QALAS and showed robust performance at up to 9-fold acceleration with Zero-DeepSub, which enabled whole-brain T1, T2, and PD mapping at 1 mm isotropic resolution within 2 min of scan time. Conclusion: The proposed subspace QALAS along with Zero-DeepSub enabled high fidelity and rapid whole-brain multiparametric quantification and time-resolved imaging.

eess.IV↗

arXiv2023

SubZero: Subspace Zero-Shot MRI Reconstruction

Recently introduced zero-shot self-supervised learning (ZS-SSL) has shown potential in accelerated MRI in a scan-specific scenario, which enabled high-quality reconstructions without access to a large training dataset. ZS-SSL has been further combined with the subspace model to accelerate 2D T2-shuffling acquisitions. In this work, we propose a parallel network framework and introduce an attention mechanism to improve subspace-based zero-shot self-supervised learning and enable higher acceleration factors. We name our method SubZero and demonstrate that it can achieve improved performance compared with current methods in T1 and T2 mapping acquisitions.

eess.IV↗

arXiv2023

Zero-Shot Self-Supervised Joint Temporal Image and Sensitivity Map Reconstruction via Linear Latent Space

Fast spin-echo (FSE) pulse sequences for Magnetic Resonance Imaging (MRI) offer important imaging contrast in clinically feasible scan times. T2-shuffling is widely used to resolve temporal signal dynamics in FSE acquisitions by exploiting temporal correlations via linear latent space and a predefined regularizer. However, predefined regularizers fail to exploit the incoherence especially for 2D acquisitions.Recent self-supervised learning methods achieve high-fidelity reconstructions by learning a regularizer from undersampled data without a standard supervised training data set. In this work, we propose a novel approach that utilizes a self supervised learning framework to learn a regularizer constrained on a linear latent space which improves time-resolved FSE images reconstruction quality. Additionally, in regimes without groundtruth sensitivity maps, we propose joint estimation of coil-sensitivity maps using an iterative reconstruction technique. Our technique functions is in a zero-shot fashion, as it only utilizes data from a single scan of highly undersampled time series images. We perform experiments on simulated and retrospective in-vivo data to evaluate the performance of the proposed zero-shot learning method for temporal FSE reconstruction. The results demonstrate the success of our proposed method where NMSE and SSIM are significantly increased and the artifacts are reduced.

eess.IV↗

arXiv2022

Latent Signal Models: Learning Compact Representations of Signal Evolution for Improved Time-Resolved, Multi-contrast MRI

Purpose: Training auto-encoders on simulated signal evolution and inserting the decoder into the forward model improves reconstructions through more compact, Bloch-equation-based representations of signal in comparison to linear subspaces. Methods: Building on model-based nonlinear and linear subspace techniques that enable reconstruction of signal dynamics, we train auto-encoders on dictionaries of simulated signal evolution to learn more compact, non-linear, latent representations. The proposed Latent Signal Model framework inserts the decoder portion of the auto-encoder into the forward model and directly reconstructs the latent representation. Latent Signal Models essentially serve as a proxy for fast and feasible differentiation through the Bloch-equations used to simulate signal. This work performs experiments in the context of T2-shuffling, gradient echo EPTI, and MPRAGE-shuffling. We compare how efficiently auto-encoders represent signal evolution in comparison to linear subspaces. Simulation and in-vivo experiments then evaluate if reducing degrees of freedom by inserting the decoder into the forward model improves reconstructions in comparison to subspace constraints. Results: An auto-encoder with one real latent variable represents FSE, EPTI, and MPRAGE signal evolution as well as linear subspaces characterized by four basis vectors. In simulated/in-vivo T2-shuffling and in-vivo EPTI experiments, the proposed framework achieves consistent quantitative NRMSE and qualitative improvement over linear approaches. From qualitative evaluation, the proposed approach yields images with reduced blurring and noise amplification in MPRAGE shuffling experiments. Conclusion: Directly solving for non-linear latent representations of signal evolution improves time-resolved MRI reconstructions through reduced degrees of freedom.

eess.SP↗

arXiv2022

Scan Specific Artifact Reduction in K-space (SPARK) Neural Networks Synergize with Physics-based Reconstruction to Accelerate MRI

Purpose: To develop a scan-specific model that estimates and corrects k-space errors made when reconstructing accelerated Magnetic Resonance Imaging (MRI) data. Methods: Scan-Specific Artifact Reduction in k-space (SPARK) trains a convolutional-neural-network to estimate and correct k-space errors made by an input reconstruction technique by back-propagating from the mean-squared-error loss between an auto-calibration signal (ACS) and the input technique's reconstructed ACS. First, SPARK is applied to GRAPPA and demonstrates improved robustness over other scan-specific models, such as RAKI and residual-RAKI. Subsequent experiments demonstrate that SPARK synergizes with residual-RAKI to improve reconstruction performance. SPARK also improves reconstruction quality when applied to advanced acquisition and reconstruction techniques like 2D virtual coil (VC-) GRAPPA, 2D LORAKS, 3D GRAPPA without an integrated ACS region, and 2D/3D wave-encoded images. Results: SPARK yields 1.5x - 2x RMSE reduction when applied to GRAPPA and improves robustness to ACS size for various acceleration rates in comparison to other scan-specific techniques. When applied to advanced reconstruction techniques such as residual-RAKI, 2D VC-GRAPPA and LORAKS, SPARK achieves up to 20% RMSE improvement. SPARK with 3D GRAPPA also improves performance by ~2x and perceived image quality without a fully sampled ACS region. Finally, SPARK synergizes with non-cartesian 2D and 3D wave-encoding imaging by reducing RMSE between 20-25% and providing qualitative improvements. Conclusion: SPARK synergizes with physics-based acquisition and reconstruction techniques to improve accelerated MRI by training scan-specific models to estimate and correct reconstruction errors in k-space.

eess.SP↗

arXiv2021

Predicting Critical Biogeochemistry of the Southern Ocean for Climate Monitoring

The Biogeochemical-Argo (BGC-Argo) program is building a network of globally distributed, sensor-equipped robotic profiling floats, improving our understanding of the climate system and how it is changing. These floats, however, are limited in the number of variables measured. In this study, we train neural networks to predict silicate and phosphate values in the Southern Ocean from temperature, pressure, salinity, oxygen, nitrate, and location and apply these models to earth system model (ESM) and BGC-Argo data to expand the utility of this ocean observation network. We trained our neural networks on observations from the Global Ocean Ship-Based Hydrographic Investigations Program (GO-SHIP) and use dropout regularization to provide uncertainty bounds around our predicted values. Our neural network significantly improves upon linear regression but shows variable levels of uncertainty across the ranges of predicted variables. We explore the generalization of our estimators to test data outside our training distribution from both ESM and BGC-Argo data. Our use of out-of-distribution test data to examine shifts in biogeochemical parameters and calculate uncertainty bounds around estimates advance the state-of-the-art in oceanographic data and climate monitoring. We make our data and code publicly available.

cs.LG↗

arXiv2021

Image2Lego: Customized LEGO Set Generation from Images

Although LEGO sets have entertained generations of children and adults, the challenge of designing customized builds matching the complexity of real-world or imagined scenes remains too great for the average enthusiast. In order to make this feat possible, we implement a system that generates a LEGO brick model from 2D images. We design a novel solution to this problem that uses an octree-structured autoencoder trained on 3D voxelized models to obtain a feasible latent representation for model reconstruction, and a separate network trained to predict this latent representation from 2D images. LEGO models are obtained by algorithmic conversion of the 3D voxelized model to bricks. We demonstrate first-of-its-kind conversion of photographs to 3D LEGO models. An octree architecture enables the flexibility to produce multiple resolutions to best fit a user's creative vision or design needs. In order to demonstrate the broad applicability of our system, we generate step-by-step building instructions and animations for LEGO models of objects and human faces. Finally, we test these automatically generated LEGO sets by constructing physical builds using real LEGO bricks.

cs.CV↗

arXiv2021

eRAKI: Fast Robust Artificial neural networks for K-space Interpolation (RAKI) with Coil Combination and Joint Reconstruction

RAKI can perform database-free MRI reconstruction by training models using only auto-calibration signal (ACS) from each specific scan. As it trains a separate model for each individual coil, learning and inference with RAKI can be computationally prohibitive, particularly for large 3D datasets. In this abstract, we accelerate RAKI more than 200 times by directly learning a coil-combined target and further improve the reconstruction performance using joint reconstruction across multiple echoes together with an elliptical-CAIPI sampling approach. We further deploy these improvements in quantitative imaging and rapidly obtain T2 and T2* parameter maps from a fast EPTI scan.

cs.CV↗