arXiv subjects

Mehmet Akçakaya

Publications and source records attributed to Mehmet Akçakaya.

At least 19 recordsLinked to original sources

arXiv2026

Consistency Models for Fast MRI Reconstruction Using Regularization by Denoising

Diffusion models (DMs) have emerged as powerful generative priors for MRI reconstruction with promising results. Yet DM-based methods require extensive iterative refinement, limiting their practical deployment. Consistency models (CMs) provide a compelling alternative, aiming to map out the diffusion trajectory in a single pass, enabling faster generation. In this work, we propose CM-RED, a novel MRI reconstruction method that integrates a pretrained CM into the regularization by denoising (RED) scheme. Our method builds on accelerated proximal gradient RED (RED-APG), and further incorporates controlled noise injection during the update steps to enhance generative diversity and accelerate convergence. Extensive experiments on the fastMRI knee and brain datasets demonstrate that CM-RED achieves high-quality reconstructions across multiple anatomies, contrast weights, acceleration factors, and undersampling patterns, using only 4 network function evaluations (NFEs). The proposed method consistently outperforms existing DM- and CM-based approaches in both quantitative metrics and visual fidelity, and exhibits strong robustness to hyperparameter variations, highlighting CM-RED as an efficient and effective generative framework for accelerated MRI reconstruction. The source code and pretrained models are publicly available at https://github.com/MerveGulle/CM-RED.

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arXiv2026

Harnessing Magnitude-Only and Complex Measurements for Improved Dynamic MRI Reconstruction with Learned Priors

MRI reconstruction methods for undersampled k-space data naturally utilize complex-valued measurements. Parallel developments in sparse phase retrieval have shown that magnitude-only measurements may provide complementary information for signal recovery. However, their use in MRI reconstruction remains largely unexplored, due to lack of practical settings where informative magnitude measurements can be obtained without additional scan time. In this work, we investigate the use of auxiliary k-space magnitude information for accelerated steady-state dynamic MRI reconstruction, and demonstrate strong consistency of k-space magnitudes across time-frames. Building on this observation, we propose $\mathbb{C}+\text{Mag}$, a magnitude-informed physics-driven deep learning reconstruction method. The proposed method employs an ADMM-based unrolling framework with a novel magnitude-aware data-fidelity formulation, where quadratically smoothed optimization and momentum-based updates are introduced to address the non-differentiability and non-convexity of the magnitude constraints. Experiments on retrospectively undersampled cine MRI and phase-contrast flow MRI datasets, as well as prospectively undersampled real-time cine MRI acquisitions, demonstrate improved artifact suppression, sharper anatomical recovery, and better preservation of phase information compared to conventional PD-DL methods, which is further supported through blinded expert reader evaluations.

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arXiv2026

UMPIRE-Net: Unrolled Magnitude-Phase Regularization Network for Accelerated MRI

MRI reconstruction from undersampled k-space measurements is an ill-posed inverse problem. Physics-driven deep learning (PD-DL) methods have shown strong performance for this task by combining the MRI forward model with learned image regularization within algorithm-unrolling frameworks. However, most existing PD-DL methods reconstruct complex-valued images directly, thereby implicitly coupling magnitude and phase within a single learned representation. This coupled regularization may be suboptimal in reconstruction settings where accurate phase modeling plays an important role, such as partial Fourier (PF) imaging, where recovery of the omitted asymmetric k-space measurements depends on the underlying image phase. In such scenarios, explicit modeling of magnitude and phase as separate components may reduce the reliance on externally estimated or predefined phase information. To this end, we propose UMPIRE-Net (Unrolled Magnitude-Phase In REgularization Network), a PD-DL method that introduces separate learned regularizers for magnitude and phase components, together with a novel data-fidelity formulation that enforces measurements consistency. We evaluate UMPIRE-Net for accelerated MRI with PF across different datasets and acceleration factors. Experimental results demonstrate that our proposed method improves reconstruction quality compared with a conventional complex-valued PD-DL baseline, yielding sharper images and reduced artifacts. Code available at: https://github.com/MahdiSaberii/UMPIRE-Net

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arXiv2026

UDT: Reconciling U-Nets and Diffusion Transformers with Data-Adaptive Token Reduction

Diffusion Transformers (DiTs) have emerged as a core architecture in generative modeling due to their scalability and adaptability to multimodal tasks. DiTs comprise isotropic transformer blocks, and learn representations progressively across depth, where the denoising objective drives later layers to focus on fine-detail reconstruction. This results in degraded representation quality and an imbalanced encoder-decoder behavior. Prior approaches such as representation alignment (REPA) mitigate this by encouraging stronger early representations via training regularization. Alternatively, U-Net-style DiT architectures introduce explicit multi-scale encoder-decoder structures for improved convergence. But they build on standard U-Net wisdom via learnable operators for spatial downsampling, which are not well-suited to transformer architectures, introducing inefficiencies and compatibility issues with components such as cross-attention and representation regularization. In this work, we propose UDT, a U-Net diffusion transformer that combines the representation power of DiTs with the encoding-decoding benefits of U-Nets, through data-adaptive token merging for downsampling and upsampling, while preserving the DiT token dimension. Our baseline UDT architecture outperforms existing U-Net DiTs and achieves performance comparable to REPA across all model sizes. Furthermore, using architectural optimization and REPA, UDT outperforms SiT's 7.9 FID at 1400 epochs (w/o CFG) within 40 epochs (~ 40x faster convergence) for XL model size on 256x256 ImageNet. Finally, it achieves strong image generation performance with CFG, reaching FID of 1.38 (320 epochs) with SD-VAE and 1.35 (500 epochs) with VA-VAE, providing a new backbone for DiTs with strong empirical benefits.

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arXiv2026

Training-Free Adversarial Robustness in Computational MRI

Deep learning (DL) methods have become the state-of-the-art for reconstructing sub-sampled magnetic resonance imaging (MRI) data. However, studies have shown that these methods are susceptible to small adversarial input perturbations, resulting in major distortions in the output images. Various strategies have been proposed to reduce the effects of these attacks, but they require retraining. In this work, we propose a novel approach for mitigating adversarial attacks on MRI reconstruction models without any retraining. Based on the idea of cyclic measurement consistency, we devise a novel mitigation objective that is minimized in a small ball around the attack input. Results show that our method substantially reduces the impact of adversarial perturbations across different datasets, attack types/strengths and PD-DL networks, and qualitatively and quantitatively outperforms conventional mitigation methods. We also introduce a practically relevant scenario for small adversarial perturbations that models impulse noise in raw data, which relates to herringbone artifacts, and show the applicability of our approach in this setting. Finally, we show our mitigation approach remains effective in two realistic extension scenarios: a blind setup, where the attack strength or algorithm is not known to the user; and an adaptive attack setup, where the attacker has full knowledge of the defense strategy.

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arXiv2026

PnP-CM: Consistency Models as Plug-and-Play Priors for Inverse Problems

Diffusion models have found extensive use in solving inverse problems, by sampling from an approximate posterior distribution of data given the measurements. Recently, consistency models (CMs) have been proposed to directly predict the final output from any point on the diffusion ODE trajectory, enabling high-quality sampling in just a few neural function evaluations (NFEs). CMs have also been utilized for inverse problems, but existing CM-based solvers either require additional task-specific training or utilize data fidelity operations with slow convergence, limiting their applicability to large-scale problems and making them difficult to extend to nonlinear settings. In this work, we reinterpret CMs as proximal operators of a prior, enabling their integration into plug-and-play (PnP) frameworks. Specifically, we propose PnP-CM, an ADMM-based PnP solver that provides a unified framework for solving a wide range of inverse problems, and incorporates noise perturbations and momentum-based updates to improve performance in the low-NFE regime. We evaluate our approach on a diverse set of linear and nonlinear inverse problems. We also train and apply CMs to MRI data for the first time. Our results show that PnP-CM achieves high-quality reconstructions in as few as 4 NFEs, and produces meaningful results in 2 steps, highlighting its effectiveness in real-world inverse problems while outperforming existing CM-based approaches.

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arXiv2025

Fast MRI for All: Bridging Access Gaps by Training without Raw Data

Physics-driven deep learning (PD-DL) approaches have become popular for improved reconstruction of fast magnetic resonance imaging (MRI) scans. Though PD-DL offers higher acceleration rates than existing clinical fast MRI techniques, their use has been limited outside specialized MRI centers. A key challenge is generalization to rare pathologies or different populations, noted in multiple studies, with fine-tuning on target populations suggested for improvement. However, current approaches for PD-DL training require access to raw k-space measurements, which is typically only available at specialized MRI centers that have research agreements for such data access. This is especially an issue for rural and under-resourced areas, where commercial MRI scanners only provide access to a final reconstructed image. To tackle these challenges, we propose Compressibility-inspired Unsupervised Learning via Parallel Imaging Fidelity (CUPID) for high-quality PD-DL training using only routine clinical reconstructed images exported from an MRI scanner. CUPID evaluates output quality with a compressibility-based approach while ensuring that the output stays consistent with the clinical parallel imaging reconstruction through well-designed perturbations. Our results show CUPID achieves similar quality to established PD-DL training that requires k-space data while outperforming compressed sensing (CS) and diffusion-based generative methods. We further demonstrate its effectiveness in a zero-shot training setup for retrospectively and prospectively sub-sampled acquisitions, attesting to its minimal training burden. As an approach that radically deviates from existing strategies, CUPID presents an opportunity to provide broader access to fast MRI for remote and rural populations in an attempt to reduce the obstacles associated with this expensive imaging modality.

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arXiv2025

Time-Embedded Algorithm Unrolling for Computational MRI

Algorithm unrolling methods have proven powerful for solving the regularized least squares problem in computational magnetic resonance imaging (MRI). These approaches unfold an iterative algorithm with a fixed number of iterations, typically alternating between a neural network-based proximal operator for regularization, a data fidelity operation and auxiliary updates with learnable parameters. While the connection to optimization methods dictate that the proximal operator network should be shared across unrolls, this can introduce artifacts or blurring. Heuristically, practitioners have shown that using distinct networks may be beneficial, but this significantly increases the number of learnable parameters, making it challenging to prevent overfitting. To address these shortcomings, by taking inspirations from proximal operators with varying thresholds in approximate message passing (AMP) and the success of time-embedding in diffusion models, we propose a time-embedded algorithm unrolling scheme for inverse problems. Specifically, we introduce a novel perspective on the iteration-dependent proximal operation in vector AMP (VAMP) and the subsequent Onsager correction in the context of algorithm unrolling, framing them as a time-embedded neural network. Similarly, the scalar weights in the data fidelity operation and its associated Onsager correction are cast as time-dependent learnable parameters. Our extensive experiments on the fastMRI dataset, spanning various acceleration rates and datasets, demonstrate that our method effectively reduces aliasing artifacts and mitigates noise amplification, achieving state-of-the-art performance. Furthermore, we show that our time-embedding strategy extends to existing algorithm unrolling approaches, enhancing reconstruction quality without increasing the computational complexity significantly.

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arXiv2025

No Alignment Needed for Generation: Learning Linearly Separable Representations in Diffusion Models

Efficient training strategies for large-scale diffusion models have recently emphasized the importance of improving discriminative feature representations in these models. A central line of work in this direction is representation alignment with features obtained from powerful external encoders, which improves the representation quality as assessed through linear probing. Alignment-based approaches show promise but depend on large pretrained encoders, which are computationally expensive to obtain. In this work, we propose an alternative regularization for training, based on promoting the Linear SEParability (LSEP) of intermediate layer representations. LSEP eliminates the need for an auxiliary encoder and representation alignment, while incorporating linear probing directly into the network's learning dynamics rather than treating it as a simple post-hoc evaluation tool. Our results demonstrate substantial improvements in both training efficiency and generation quality on flow-based transformer architectures such as SiTs, achieving an FID of 1.46 on $256 \times 256$ ImageNet dataset.

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arXiv2025

Automated Tuning for Diffusion Inverse Problem Solvers without Generative Prior Retraining

Diffusion/score-based models have recently emerged as powerful generative priors for solving inverse problems, including accelerated MRI reconstruction. While their flexibility allows decoupling the measurement model from the learned prior, their performance heavily depends on carefully tuned data fidelity weights, especially under fast sampling schedules with few denoising steps. Existing approaches often rely on heuristics or fixed weights, which fail to generalize across varying measurement conditions and irregular timestep schedules. In this work, we propose Zero-shot Adaptive Diffusion Sampling (ZADS), a test-time optimization method that adaptively tunes fidelity weights across arbitrary noise schedules without requiring retraining of the diffusion prior. ZADS treats the denoising process as a fixed unrolled sampler and optimizes fidelity weights in a self-supervised manner using only undersampled measurements. Experiments on the fastMRI knee dataset demonstrate that ZADS consistently outperforms both traditional compressed sensing and recent diffusion-based methods, showcasing its ability to deliver high-fidelity reconstructions across varying noise schedules and acquisition settings.

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arXiv2025

Deploying AI for Signal Processing education: Selected challenges and intriguing opportunities

Powerful artificial intelligence (AI) tools that have emerged in recent years -- including large language models, automated coding assistants, and advanced image and speech generation technologies -- are the result of monumental human achievements. These breakthroughs reflect mastery across multiple technical disciplines and the resolution of significant technological challenges. However, some of the most profound challenges may still lie ahead. These challenges are not purely technical but pertain to the fair and responsible use of AI in ways that genuinely improve the global human condition. This article explores one promising application aligned with that vision: the use of AI tools to facilitate and enhance education, with a specific focus on signal processing (SP). It presents two interrelated perspectives: identifying and addressing technical limitations, and applying AI tools in practice to improve educational experiences. Primers are provided on several core technical issues that arise when using AI in educational settings, including how to ensure fairness and inclusivity, handle hallucinated outputs, and achieve efficient use of resources. These and other considerations -- such as transparency, explainability, and trustworthiness -- are illustrated through the development of an immersive, structured, and reliable "smart textbook." The article serves as a resource for researchers and educators seeking to advance AI's role in engineering education.

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arXiv2025

Edge Computing for Physics-Driven AI in Computational MRI: A Feasibility Study

Physics-driven artificial intelligence (PD-AI) reconstruction methods have emerged as the state-of-the-art for accelerating MRI scans, enabling higher spatial and temporal resolutions. However, the high resolution of these scans generates massive data volumes, leading to challenges in transmission, storage, and real-time processing. This is particularly pronounced in functional MRI, where hundreds of volumetric acquisitions further exacerbate these demands. Edge computing with FPGAs presents a promising solution for enabling PD-AI reconstruction near the MRI sensors, reducing data transfer and storage bottlenecks. However, this requires optimization of PD-AI models for hardware efficiency through quantization and bypassing traditional FFT-based approaches, which can be a limitation due to their computational demands. In this work, we propose a novel PD-AI computational MRI approach optimized for FPGA-based edge computing devices, leveraging 8-bit complex data quantization and eliminating redundant FFT/IFFT operations. Our results show that this strategy improves computational efficiency while maintaining reconstruction quality comparable to conventional PD-AI methods, and outperforms standard clinical methods. Our approach presents an opportunity for high-resolution MRI reconstruction on resource-constrained devices, highlighting its potential for real-world deployment.

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arXiv2025

Sparsity-Driven Parallel Imaging Consistency for Improved Self-Supervised MRI Reconstruction

Physics-driven deep learning (PD-DL) models have proven to be a powerful approach for improved reconstruction of rapid MRI scans. In order to train these models in scenarios where fully-sampled reference data is unavailable, self-supervised learning has gained prominence. However, its application at high acceleration rates frequently introduces artifacts, compromising image fidelity. To mitigate this shortcoming, we propose a novel way to train PD-DL networks via carefully-designed perturbations. In particular, we enhance the k-space masking idea of conventional self-supervised learning with a novel consistency term that assesses the model's ability to accurately predict the added perturbations in a sparse domain, leading to more reliable and artifact-free reconstructions. The results obtained from the fastMRI knee and brain datasets show that the proposed training strategy effectively reduces aliasing artifacts and mitigates noise amplification at high acceleration rates, outperforming state-of-the-art self-supervised methods both visually and quantitatively.

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arXiv2025

Deep Learning Assisted Outer Volume Removal for Highly-Accelerated Real-Time Dynamic MRI

Real-time (RT) dynamic MRI plays a vital role in capturing rapid physiological processes, offering unique insights into organ motion and function. Among these applications, RT cine MRI is particularly important for functional assessment of the heart with high temporal resolution. RT imaging enables free-breathing, ungated imaging of cardiac motion, making it a crucial alternative for patients who cannot tolerate conventional breath-hold, ECG-gated acquisitions. However, achieving high acceleration rates in RT cine MRI is challenging due to aliasing artifacts from extra-cardiac tissues, particularly at high undersampling factors. In this study, we propose a novel outer volume removal (OVR) method to address this challenge by eliminating aliasing contributions from non-cardiac regions in a post-processing framework. Our approach estimates the outer volume signal for each timeframe using composite temporal images from time-interleaved undersampling patterns, which inherently contain pseudo-periodic ghosting artifacts. A deep learning (DL) model is trained to identify and remove these artifacts, producing a clean outer volume estimate that is subsequently subtracted from the corresponding k-space data. The final reconstruction is performed with a physics-driven DL (PD-DL) method trained using an OVR-specific loss function to restore high spatio-temporal resolution images. Experimental results show that the proposed method at high accelerations achieves image quality that is visually comparable to clinical baseline images, while outperforming conventional reconstruction techniques, both qualitatively and quantitatively. The proposed approach provides a practical and effective solution for artifact reduction in RT cine MRI without requiring acquisition modifications, offering a pathway to higher acceleration rates while preserving diagnostic quality.

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arXiv2024

Generative Model-Based Fusion for Improved Few-Shot Semantic Segmentation of Infrared Images

Infrared (IR) imaging is commonly used in various scenarios, including autonomous driving, fire safety and defense applications. Thus, semantic segmentation of such images is of great interest. However, this task faces several challenges, including data scarcity, differing contrast and input channel number compared to natural images, and emergence of classes not represented in databases in certain scenarios, such as defense applications. Few-shot segmentation (FSS) provides a framework to overcome these issues by segmenting query images using a few labeled support samples. However, existing FSS models for IR images require paired visible RGB images, which is a major limitation since acquiring such paired data is difficult or impossible in some applications. In this work, we develop new strategies for FSS of IR images by using generative modeling and fusion techniques. To this end, we propose to synthesize auxiliary data to provide additional channel information to complement the limited contrast in the IR images, as well as IR data synthesis for data augmentation. Here, the former helps the FSS model to better capture the relationship between the support and query sets, while the latter addresses the issue of data scarcity. Finally, to further improve the former aspect, we propose a novel fusion ensemble module for integrating the two different modalities. Our methods are evaluated on different IR datasets, and improve upon the state-of-the-art (SOTA) FSS models.

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arXiv2024

Zero-Shot Adaptation for Approximate Posterior Sampling of Diffusion Models in Inverse Problems

Diffusion models have emerged as powerful generative techniques for solving inverse problems. Despite their success in a variety of inverse problems in imaging, these models require many steps to converge, leading to slow inference time. Recently, there has been a trend in diffusion models for employing sophisticated noise schedules that involve more frequent iterations of timesteps at lower noise levels, thereby improving image generation and convergence speed. However, application of these ideas for solving inverse problems with diffusion models remain challenging, as these noise schedules do not perform well when using empirical tuning for the forward model log-likelihood term weights. To tackle these challenges, we propose zero-shot approximate posterior sampling (ZAPS) that leverages connections to zero-shot physics-driven deep learning. ZAPS fixes the number of sampling steps, and uses zero-shot training with a physics-guided loss function to learn log-likelihood weights at each irregular timestep. We apply ZAPS to the recently proposed diffusion posterior sampling method as baseline, though ZAPS can also be used with other posterior sampling diffusion models. We further approximate the Hessian of the logarithm of the prior using a diagonalization approach with learnable diagonal entries for computational efficiency. These parameters are optimized over a fixed number of epochs with a given computational budget. Our results for various noisy inverse problems, including Gaussian and motion deblurring, inpainting, and super-resolution show that ZAPS reduces inference time, provides robustness to irregular noise schedules and improves reconstruction quality. Code is available at https://github.com/ualcalar17/ZAPS

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arXiv2023

Non-Cartesian Self-Supervised Physics-Driven Deep Learning Reconstruction for Highly-Accelerated Multi-Echo Spiral fMRI

Functional MRI (fMRI) is an important tool for non-invasive studies of brain function. Over the past decade, multi-echo fMRI methods that sample multiple echo times has become popular with potential to improve quantification. While these acquisitions are typically performed with Cartesian trajectories, non-Cartesian trajectories, in particular spiral acquisitions, hold promise for denser sampling of echo times. However, such acquisitions require very high acceleration rates for sufficient spatiotemporal resolutions. In this work, we propose to use a physics-driven deep learning (PD-DL) reconstruction to accelerate multi-echo spiral fMRI by 10-fold. We modify a self-supervised learning algorithm for optimized training with non-Cartesian trajectories and use it to train the PD-DL network. Results show that the proposed self-supervised PD-DL reconstruction achieves high spatio-temporal resolution with meaningful BOLD analysis.

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arXiv2023

Zero-Shot Self-Supervised Learning for MRI Reconstruction

Deep learning (DL) has emerged as a powerful tool for accelerated MRI reconstruction, but often necessitates a database of fully-sampled measurements for training. Recent self-supervised and unsupervised learning approaches enable training without fully-sampled data. However, a database of undersampled measurements may not be available in many scenarios, especially for scans involving contrast or translational acquisitions in development. Moreover, recent studies show that database-trained models may not generalize well when the unseen measurements differ in terms of sampling pattern, acceleration rate, SNR, image contrast, and anatomy. Such challenges necessitate a new methodology to enable subject-specific DL MRI reconstruction without external training datasets, since it is clinically imperative to provide high-quality reconstructions that can be used to identify lesions/disease for \emph{every individual}. In this work, we propose a zero-shot self-supervised learning approach to perform subject-specific accelerated DL MRI reconstruction to tackle these issues. The proposed approach partitions the available measurements from a single scan into three disjoint sets. Two of these sets are used to enforce data consistency and define loss during training for self-supervision, while the last set serves to self-validate, establishing an early stopping criterion. In the presence of models pre-trained on a database with different image characteristics, we show that the proposed approach can be combined with transfer learning for faster convergence time and reduced computational complexity. The code is available at \url{https://github.com/byaman14/ZS-SSL}.

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