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Tolga Çukur

Publications and source records attributed to Tolga Çukur.

At least 19 recordsLinked to original sources
arXiv2026

Stochastic Finite-Transition Learning and Exploration for Accelerated MRI Reconstruction

Generative MRI reconstruction maps an initial source distribution to the target image distribution along a learned recovery trajectory. Common generative methods, such as diffusion and flow, typically learn fine-grained local dynamics whose integration defines this global mapping, hence requiring many network evaluations at inference. Existing few-step sampling approaches can lower computational burden by approximating large transformations from local dynamics, albeit at the expense of reconstruction fidelity. FLEX-MRI instead partitions recovery into a small number of finite intervals between retained states defined by progressive changes in k-space support, and directly learns the reconstruction change across each interval. Because such finite transitions can admit multiple plausible outcomes, FLEX-MRI combines support-relaxed finite-transition learning with stochastic exploration. During training, randomized k-space sampling masks define finite-transition targets with varying support, while the prediction loss remains unrestricted by each individual mask. At inference, FLEX-MRI perturbs a random subset of currently estimated k-space coefficients, allowing the learned predictor to stochastically explore alternative transition paths. Each predicted state is then reconciled with the acquired measurements through data consistency. We theoretically show that this stochastic exploration induces nonzero transition-level variation through the learned recovery map and data consistency without requiring an auxiliary generative sampler. Experiments on multi-coil MRI datasets show that FLEX-MRI outperforms competing methods while maintaining computational efficiency comparable to few-step baselines.

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arXiv2026

ACE-LoRA: Graph-Attentive Context Enhancement for Parameter-Efficient Adaptation of Medical Vision-Language Models

The success of CLIP-like vision-language models (VLMs) on natural images has inspired medical counterparts, yet existing approaches largely fall into two extremes: specialist models trained on single-domain data, which capture domain-specific details but generalize poorly, and generalist medical VLMs trained on multi-domain data, which retain broad semantics but dilute fine-grained diagnostic cues. Bridging this specialization-generalization trade-off remains challenging. To address this problem, we propose ACE-LoRA, a parameter-efficient adaptation framework for generalist medical VLMs that maintains robust zero-shot generalization. ACE-LoRA integrates Low-Rank Adaptation (LoRA) modules into frozen image-text encoders and introduces an Attention-based Context Enhancement Hypergraph Neural Network (ACE-HGNN) module that captures higher-order contextual interactions beyond pairwise similarity to enrich global representations with localized diagnostic cues, addressing a key limitation of prior Parameter-Efficient Fine-Tuning (PEFT) methods that overlook fine-grained details. To further enhance cross-modal alignment, we formulate a label-guided InfoNCE loss to effectively suppress false negatives between semantically related image-text pairs. Despite adding only 0.95M trainable parameters, ACE-LoRA consistently outperforms state-of-the-art medical VLMs and PEFT baselines across zero-shot classification, segmentation, and detection benchmarks spanning multiple domains. Our code is available at https://github.com/icon-lab/ACE-LoRA.

cs.CV↗
arXiv2026

NeuroSSM: Multiscale Differential State-Space Modeling for Context-Aware fMRI Analysis

Accurate fMRI analysis requires sensitivity to temporal structure across multiple scales, as BOLD signals encode cognitive processes that emerge from fast transient dynamics to slower, large-scale fluctuations. Existing deep learning (DL) approaches to temporal modeling face challenges in jointly capturing these dynamics over long fMRI time series. Among current DL models, transformers address long-range dependencies by explicitly modeling pairwise interactions through attention, but the associated quadratic computational cost limits effective integration of temporal dependencies across long fMRI sequences. Selective state-space models (SSMs) instead model long-range temporal dependencies implicitly through latent state evolution in a dynamical system, enabling efficient propagation of dependencies over time. However, recent SSM-based approaches for fMRI commonly operate on derived functional connectivity representations and employ single-scale temporal processing. These design choices constrain the ability to jointly represent fast transient dynamics and slower global trends within a single model. We propose NeuroSSM, a selective state-space architecture designed for end-to-end analysis of raw BOLD signals in fMRI time series. NeuroSSM addresses the above limitations through two complementary design components: a multiscale state-space backbone that captures fast and slow dynamics concurrently, and a parallel differencing branch that increases sensitivity to transient state changes. Experiments on clinical and non-clinical datasets demonstrate that NeuroSSM achieves competitive performance and efficiency against state-of-the-art fMRI analysis methods.

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arXiv2025

Generative Autoregressive Transformers for Model-Agnostic Federated MRI Reconstruction

While learning-based models hold great promise for MRI reconstruction, single-site models trained on limited local datasets often show poor generalization. This has motivated collaborative training across institutions via federated learning (FL)-a privacy-preserving framework that aggregates model updates instead of sharing raw data. Conventional FL requires architectural homogeneity, restricting sites from using models tailored to their resources or needs. To address this limitation, we propose FedGAT, a model-agnostic FL technique that first collaboratively trains a global generative prior for MR images, adapted from a natural image foundation model composed of a variational autoencoder (VAE) and a transformer that generates images via spatial-scale autoregression. We fine-tune the transformer module after injecting it with a lightweight site-specific prompting mechanism, keeping the VAE frozen, to efficiently adapt the model to multi-site MRI data. In a second tier, each site independently trains its preferred reconstruction model by augmenting local data with synthetic MRI data from other sites, generated by site-prompting the tuned prior. This decentralized augmentation improves generalization while preserving privacy. Experiments on multi-institutional datasets show that FedGAT outperforms state-of-the-art FL baselines in both within- and cross-site reconstruction performance under model-heterogeneous settings.

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arXiv2025

I2I-Mamba: Multi-modal medical image synthesis via selective state space modeling

Multi-modal medical image synthesis involves nonlinear transformation of tissue signals between source and target modalities, where tissues exhibit contextual interactions across diverse spatial distances. As such, the utility of a network architecture in synthesis depends on its ability to express the broad set of contextual features in medical images. Convolutional neural networks (CNNs) offer high local precision at the expense of poor sensitivity to long-range context. While transformers promise to alleviate this issue, they suffer from an unfavorable trade-off between sensitivity to long- versus short-range context due to the intrinsic complexity of attention filters. To effectively capture contextual features while avoiding the complexitydriven trade-offs, here we introduce a novel multi-modal synthesis method, I2I-Mamba, based on the state space modeling (SSM) framework. Focusing on high-level representations across a hybrid residual architecture, I2I-Mamba leverages novel dual-domain Mamba (ddMamba) blocks for complementary contextual modeling in image and Fourier domains, while maintaining spatial precision with convolutional layers. Diverting from conventional raster-scan trajectories, ddMamba leverages novel SSM operators based on a spiral-scan trajectory to learn context with enhanced angular isotropy and radial coverage, and a channel-mixing layer to aggregate context across the channel dimension. Comprehensive demonstrations on multi-contrast MRI and MRI-CT protocols indicate that I2I-Mamba outperforms state-of-the-art CNNs, transformers and SSMs.

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arXiv2025

A Tutorial on MRI Reconstruction: From Modern Methods to Clinical Implications

MRI is an indispensable clinical tool, offering a rich variety of tissue contrasts to support broad diagnostic and research applications. Clinical exams routinely acquire multiple structural sequences that provide complementary information for differential diagnosis, while research protocols often incorporate advanced functional, diffusion, spectroscopic, and relaxometry sequences to capture multidimensional insights into tissue structure and composition. However, these capabilities come at the cost of prolonged scan times, which reduce patient throughput, increase susceptibility to motion artifacts, and may require trade-offs in image quality or diagnostic scope. Over the last two decades, advances in image reconstruction algorithms--alongside improvements in hardware and pulse sequence design--have made it possible to accelerate acquisitions while preserving diagnostic quality. Central to this progress is the ability to incorporate prior information to regularize the solutions to the reconstruction problem. In this tutorial, we overview the basics of MRI reconstruction and highlight state-of-the-art approaches, beginning with classical methods that rely on explicit hand-crafted priors, and then turning to deep learning methods that leverage a combination of learned and crafted priors to further push the performance envelope. We also explore the translational aspects and eventual clinical implications of these methods. We conclude by discussing future directions to address remaining challenges in MRI reconstruction. The tutorial is accompanied by a Python toolbox (https://github.com/tutorial-MRI-recon/tutorial) to demonstrate select methods discussed in the article.

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arXiv2025

Physics-Driven Autoregressive State Space Models for Medical Image Reconstruction

Medical image reconstruction from undersampled acquisitions is an ill-posed inverse problem requiring accurate recovery of anatomical structures from incomplete measurements. Physics-driven (PD) network models have gained prominence for this task by integrating data-consistency mechanisms with learned priors, enabling improved performance over purely data-driven approaches. However, reconstruction quality still hinges on the network's ability to disentangle artifacts from true anatomical signals-both of which exhibit complex, multi-scale contextual structure. Convolutional neural networks (CNNs) capture local correlations but often struggle with non-local dependencies. While transformers aim to alleviate this limitation, practical implementations involve design compromises to reduce computational cost by balancing local and non-local sensitivity, occasionally resulting in performance comparable to CNNs. To address these challenges, we propose MambaRoll, a novel physics-driven autoregressive state space model (SSM) for high-fidelity and efficient image reconstruction. MambaRoll employs an unrolled architecture where each cascade autoregressively predicts finer-scale feature maps conditioned on coarser-scale representations, enabling consistent multi-scale context propagation. Each stage is built on a hierarchy of scale-specific PD-SSM modules that capture spatial dependencies while enforcing data consistency through residual correction. To further improve scale-aware learning, we introduce a Deep Multi-Scale Decoding (DMSD) loss, which provides supervision at intermediate spatial scales in alignment with the autoregressive design. Demonstrations on accelerated MRI and sparse-view CT reconstructions show that MambaRoll consistently outperforms state-of-the-art CNN-, transformer-, and SSM-based methods.

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arXiv2025

Efficient Noise Calculation in Deep Learning-based MRI Reconstructions

Accelerated MRI reconstruction involves solving an ill-posed inverse problem where noise in acquired data propagates to the reconstructed images. Noise analyses are central to MRI reconstruction for providing an explicit measure of solution fidelity and for guiding the design and deployment of novel reconstruction methods. However, deep learning (DL)-based reconstruction methods have often overlooked noise propagation due to inherent analytical and computational challenges, despite its critical importance. This work proposes a theoretically grounded, memory-efficient technique to calculate voxel-wise variance for quantifying uncertainty due to acquisition noise in accelerated MRI reconstructions. Our approach approximates noise covariance using the DL network's Jacobian, which is intractable to calculate. To circumvent this, we derive an unbiased estimator for the diagonal of this covariance matrix (voxel-wise variance) and introduce a Jacobian sketching technique to efficiently implement it. We evaluate our method on knee and brain MRI datasets for both data- and physics-driven networks trained in supervised and unsupervised manners. Compared to empirical references obtained via Monte Carlo simulations, our technique achieves near-equivalent performance while reducing computational and memory demands by an order of magnitude or more. Furthermore, our method is robust across varying input noise levels, acceleration factors, and diverse undersampling schemes, highlighting its broad applicability. Our work reintroduces accurate and efficient noise analysis as a central tenet of reconstruction algorithms, holding promise to reshape how we evaluate and deploy DL-based MRI. Our code will be made publicly available upon acceptance.

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arXiv2025

Meta-Entity Driven Triplet Mining for Aligning Medical Vision-Language Models

Diagnostic imaging relies on interpreting both images and radiology reports, but the growing data volumes place significant pressure on medical experts, yielding increased errors and workflow backlogs. Medical vision-language models (med-VLMs) have emerged as a powerful framework to efficiently process multimodal imaging data, particularly in chest X-ray (CXR) evaluations, albeit their performance hinges on how well image and text representations are aligned. Existing alignment methods, predominantly based on contrastive learning, prioritize separation between disease classes over segregation of fine-grained pathology attributes like location, size or severity, leading to suboptimal representations. Here, we propose MedTrim (Meta-entity-driven Triplet mining), a novel method that enhances image-text alignment through multimodal triplet learning synergistically guided by disease class as well as adjectival and directional pathology descriptors. Unlike common alignment methods that separate broad disease classes, MedTrim leverages structured meta-entity information to preserve subtle but clinically significant intra-class variations. For this purpose, we first introduce an ontology-based entity recognition module that extracts pathology-specific meta-entities from CXR reports, as annotations on pathology attributes are rare in public datasets. For refined sample selection in triplet mining, we then introduce a novel score function that captures an aggregate measure of inter-sample similarity based on disease classes and adjectival/directional descriptors. Lastly, we introduce a multimodal triplet alignment objective for explicit within- and cross-modal alignment between samples sharing detailed pathology characteristics. Our demonstrations indicate that MedTrim improves performance in downstream retrieval and classification tasks compared to state-of-the-art alignment methods.

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arXiv2024

DenoMamba: A fused state-space model for low-dose CT denoising

Low-dose computed tomography (LDCT) lower potential risks linked to radiation exposure while relying on advanced denoising algorithms to maintain diagnostic quality in reconstructed images. The reigning paradigm in LDCT denoising is based on neural network models that learn data-driven image priors to separate noise evoked by dose reduction from underlying tissue signals. Naturally, the fidelity of these priors depend on the model's ability to capture the broad range of contextual features evident in CT images. Earlier convolutional neural networks (CNN) are highly adept at efficiently capturing short-range spatial context, but their limited receptive fields reduce sensitivity to interactions over longer distances. Although transformers based on self-attention mechanisms have recently been posed to increase sensitivity to long-range context, they can suffer from suboptimal performance and efficiency due to elevated model complexity, particularly for high-resolution CT images. For high-quality restoration of LDCT images, here we introduce DenoMamba, a novel denoising method based on state-space modeling (SSM), that efficiently captures short- and long-range context in medical images. Following an hourglass architecture with encoder-decoder stages, DenoMamba employs a spatial SSM module to encode spatial context and a novel channel SSM module equipped with a secondary gated convolution network to encode latent features of channel context at each stage. Feature maps from the two modules are then consolidated with low-level input features via a convolution fusion module (CFM). Comprehensive experiments on LDCT datasets with 25\% and 10\% dose reduction demonstrate that DenoMamba outperforms state-of-the-art denoisers with average improvements of 1.4dB PSNR, 1.1% SSIM, and 1.6% RMSE in recovered image quality.

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arXiv2024

Bayesian Conditioned Diffusion Models for Inverse Problems

Diffusion models have recently been shown to excel in many image reconstruction tasks that involve inverse problems based on a forward measurement operator. A common framework uses task-agnostic unconditional models that are later post-conditioned for reconstruction, an approach that typically suffers from suboptimal task performance. While task-specific conditional models have also been proposed, current methods heuristically inject measured data as a naive input channel that elicits sampling inaccuracies. Here, we address the optimal conditioning of diffusion models for solving challenging inverse problems that arise during image reconstruction. Specifically, we propose a novel Bayesian conditioning technique for diffusion models, BCDM, based on score-functions associated with the conditional distribution of desired images given measured data. We rigorously derive the theory to express and train the conditional score-function. Finally, we show state-of-the-art performance in image dealiasing, deblurring, super-resolution, and inpainting with the proposed technique.

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arXiv2024

Self-Consistent Recursive Diffusion Bridge for Medical Image Translation

Denoising diffusion models (DDM) have gained recent traction in medical image translation given improved training stability over adversarial models. DDMs learn a multi-step denoising transformation to progressively map random Gaussian-noise images onto target-modality images, while receiving stationary guidance from source-modality images. As this denoising transformation diverges significantly from the task-relevant source-to-target transformation, DDMs can suffer from weak source-modality guidance. Here, we propose a novel self-consistent recursive diffusion bridge (SelfRDB) for improved performance in medical image translation. Unlike DDMs, SelfRDB employs a novel forward process with start- and end-points defined based on target and source images, respectively. Intermediate image samples across the process are expressed via a normal distribution with mean taken as a convex combination of start-end points, and variance from additive noise. Unlike regular diffusion bridges that prescribe zero variance at start-end points and high variance at mid-point of the process, we propose a novel noise scheduling with monotonically increasing variance towards the end-point in order to boost generalization performance and facilitate information transfer between the two modalities. To further enhance sampling accuracy in each reverse step, we propose a novel sampling procedure where the network recursively generates a transient-estimate of the target image until convergence onto a self-consistent solution. Comprehensive analyses in multi-contrast MRI and MRI-CT translation indicate that SelfRDB offers superior performance against competing methods.

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arXiv2023

Learning Fourier-Constrained Diffusion Bridges for MRI Reconstruction

Deep generative models have gained recent traction in accelerated MRI reconstruction. Diffusion priors are particularly promising given their representational fidelity. Instead of the target transformation from undersampled to fully-sampled data required for MRI reconstruction, common diffusion priors are trained to learn a task-agnostic transformation from an asymptotic start-point of Gaussian noise onto the finite end-point of fully-sampled data. During inference, data-consistency projections are injected in between reverse diffusion steps to reach a compromise solution within the span of both the trained diffusion prior and the imaging operator for an accelerated MRI acquisition. Unfortunately, performance losses can occur due to the discrepancy between target and learned transformations given the asymptotic normality assumption in diffusion priors. To address this discrepancy, here we introduce a novel Fourier-constrained diffusion bridge (FDB) for MRI reconstruction that transforms between a finite start-point of moderately undersampled data and an end-point of fully-sampled data. We derive the theoretical formulation of FDB as a generalized diffusion process based on a stochastic degradation operator that performs random spatial-frequency removal. We propose an enhanced sampling algorithm with a learned correction term for soft dealiasing across reverse diffusion steps. Demonstrations on brain MRI indicate that FDB outperforms state-of-the-art methods including non-diffusion and diffusion priors.

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arXiv2023

HydraViT: Adaptive Multi-Branch Transformer for Multi-Label Disease Classification from Chest X-ray Images

Chest X-ray is an essential diagnostic tool in the identification of chest diseases given its high sensitivity to pathological abnormalities in the lungs. However, image-driven diagnosis is still challenging due to heterogeneity in size and location of pathology, as well as visual similarities and co-occurrence of separate pathology. Since disease-related regions often occupy a relatively small portion of diagnostic images, classification models based on traditional convolutional neural networks (CNNs) are adversely affected given their locality bias. While CNNs were previously augmented with attention maps or spatial masks to guide focus on potentially critical regions, learning localization guidance under heterogeneity in the spatial distribution of pathology is challenging. To improve multi-label classification performance, here we propose a novel method, HydraViT, that synergistically combines a transformer backbone with a multi-branch output module with learned weighting. The transformer backbone enhances sensitivity to long-range context in X-ray images, while using the self-attention mechanism to adaptively focus on task-critical regions. The multi-branch output module dedicates an independent branch to each disease label to attain robust learning across separate disease classes, along with an aggregated branch across labels to maintain sensitivity to co-occurrence relationships among pathology. Experiments demonstrate that, on average, HydraViT outperforms competing attention-guided methods by 1.2%, region-guided methods by 1.4%, and semantic-guided methods by 1.0% in multi-label classification performance.

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arXiv2023

CalibFPA: A Focal Plane Array Imaging System based on Online Deep-Learning Calibration

Compressive focal plane arrays (FPA) enable cost-effective high-resolution (HR) imaging by acquisition of several multiplexed measurements on a low-resolution (LR) sensor. Multiplexed encoding of the visual scene is typically performed via electronically controllable spatial light modulators (SLM). An HR image is then reconstructed from the encoded measurements by solving an inverse problem that involves the forward model of the imaging system. To capture system non-idealities such as optical aberrations, a mainstream approach is to conduct an offline calibration scan to measure the system response for a point source at each spatial location on the imaging grid. However, it is challenging to run calibration scans when using structured SLMs as they cannot encode individual grid locations. In this study, we propose a novel compressive FPA system based on online deep-learning calibration of multiplexed LR measurements (CalibFPA). We introduce a piezo-stage that locomotes a pre-printed fixed coded aperture. A deep neural network is then leveraged to correct for the influences of system non-idealities in multiplexed measurements without the need for offline calibration scans. Finally, a deep plug-and-play algorithm is used to reconstruct images from corrected measurements. On simulated and experimental datasets, we demonstrate that CalibFPA outperforms state-of-the-art compressive FPA methods. We also report analyses to validate the design elements in CalibFPA and assess computational complexity.

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arXiv2023

Adaptive Diffusion Priors for Accelerated MRI Reconstruction

Deep MRI reconstruction is commonly performed with conditional models that de-alias undersampled acquisitions to recover images consistent with fully-sampled data. Since conditional models are trained with knowledge of the imaging operator, they can show poor generalization across variable operators. Unconditional models instead learn generative image priors decoupled from the operator to improve reliability against domain shifts related to the imaging operator. Recent diffusion models are particularly promising given their high sample fidelity. Nevertheless, inference with a static image prior can perform suboptimally. Here we propose the first adaptive diffusion prior for MRI reconstruction, AdaDiff, to improve performance and reliability against domain shifts. AdaDiff leverages an efficient diffusion prior trained via adversarial mapping over large reverse diffusion steps. A two-phase reconstruction is executed following training: a rapid-diffusion phase that produces an initial reconstruction with the trained prior, and an adaptation phase that further refines the result by updating the prior to minimize data-consistency loss. Demonstrations on multi-contrast brain MRI clearly indicate that AdaDiff outperforms competing conditional and unconditional methods under domain shifts, and achieves superior or on par within-domain performance.

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arXiv2023

DEQ-MPI: A Deep Equilibrium Reconstruction with Learned Consistency for Magnetic Particle Imaging

Magnetic particle imaging (MPI) offers unparalleled contrast and resolution for tracing magnetic nanoparticles. A common imaging procedure calibrates a system matrix (SM) that is used to reconstruct data from subsequent scans. The ill-posed reconstruction problem can be solved by simultaneously enforcing data consistency based on the SM and regularizing the solution based on an image prior. Traditional hand-crafted priors cannot capture the complex attributes of MPI images, whereas recent MPI methods based on learned priors can suffer from extensive inference times or limited generalization performance. Here, we introduce a novel physics-driven method for MPI reconstruction based on a deep equilibrium model with learned data consistency (DEQ-MPI). DEQ-MPI reconstructs images by augmenting neural networks into an iterative optimization, as inspired by unrolling methods in deep learning. Yet, conventional unrolling methods are computationally restricted to few iterations resulting in non-convergent solutions, and they use hand-crafted consistency measures that can yield suboptimal capture of the data distribution. DEQ-MPI instead trains an implicit mapping to maximize the quality of a convergent solution, and it incorporates a learned consistency measure to better account for the data distribution. Demonstrations on simulated and experimental data indicate that DEQ-MPI achieves superior image quality and competitive inference time to state-of-the-art MPI reconstruction methods.

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arXiv2023

DreaMR: Diffusion-driven Counterfactual Explanation for Functional MRI

Deep learning analyses have offered sensitivity leaps in detection of cognitive states from functional MRI (fMRI) measurements across the brain. Yet, as deep models perform hierarchical nonlinear transformations on their input, interpreting the association between brain responses and cognitive states is challenging. Among common explanation approaches for deep fMRI classifiers, attribution methods show poor specificity and perturbation methods show limited plausibility. While counterfactual generation promises to address these limitations, previous methods use variational or adversarial priors that yield suboptimal sample fidelity. Here, we introduce the first diffusion-driven counterfactual method, DreaMR, to enable fMRI interpretation with high specificity, plausibility and fidelity. DreaMR performs diffusion-based resampling of an input fMRI sample to alter the decision of a downstream classifier, and then computes the minimal difference between the original and counterfactual samples for explanation. Unlike conventional diffusion methods, DreaMR leverages a novel fractional multi-phase-distilled diffusion prior to improve sampling efficiency without compromising fidelity, and it employs a transformer architecture to account for long-range spatiotemporal context in fMRI scans. Comprehensive experiments on neuroimaging datasets demonstrate the superior specificity, fidelity and efficiency of DreaMR in sample generation over state-of-the-art counterfactual methods for fMRI interpretation.

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