Learning Patient-Specific Disease Dynamics with Latent Flow Matching for Longitudinal Imaging Generation

Understanding disease progression is a central clinical challenge with direct implications for early diagnosis and personalized treatment. While recent generative approaches have attempted to model progression, key mismatches remain: disease dynamics are inherently continuous and monotonic, yet latent representations are often scattered, lacking semantic structure, and diffusion-based models disrupt continuity with random denoising process. In this work, we propose to treat the disease dynamic as a velocity field and leverage Flow Matching (FM) to align the temporal evolution of patient data. Unlike prior methods, it captures the intrinsic dynamic of disease, making the progression more interpretable. However, a key challenge remains: in latent space, Auto-Encoders (AEs) do not guarantee alignment across patients or correlation with clinical-severity indicators (e.g., age and disease conditions). To address this, we propose to learn patient-specific latent alignment, which enforces patient trajectories to lie along a specific axis, with magnitude increasing monotonically with disease severity. This leads to a consistent and semantically meaningful latent space. Together, we present $Δ$-LFM, a framework for modeling patient-specific latent progression with flow matching. Across three longitudinal MRI benchmarks, $Δ$-LFM demonstrates strong empirical performance and, more importantly, offers a new framework for interpreting and visualizing disease dynamics.

MRIQT: Physics-Aware Diffusion Model for Image Quality Transfer in Neonatal Ultra-Low-Field MRI

Portable ultra-low-field MRI (uLF-MRI, 0.064 T) offers accessible neuroimaging for neonatal care but suffers from low signal-to-noise ratio and poor diagnostic quality compared to high-field (HF) MRI. We propose MRIQT, a 3D conditional diffusion framework for image quality transfer (IQT) from uLF to HF MRI. MRIQT combines realistic K-space degradation for physics-consistent uLF simulation, v-prediction with classifier-free guidance for stable image-to-image generation, and an SNR-weighted 3D perceptual loss for anatomical fidelity. The model denoises from a noised uLF input conditioned on the same scan, leveraging volumetric attention-UNet architecture for structure-preserving translation. Trained on a neonatal cohort with diverse pathologies, MRIQT surpasses recent GAN and CNN baselines in PSNR 15.3% with 1.78% over the state of the art, while physicians rated 85% of its outputs as good quality with clear pathology present. MRIQT enables high-fidelity, diffusion-based enhancement of portable ultra-low-field (uLF) MRI for deliable neonatal brain assessment.

Noisy MRI Reconstruction via MAP Estimation with an Implicit Deep-Denoiser Prior

Accelerating magnetic resonance imaging (MRI) remains challenging, particularly under realistic acquisition noise. While diffusion models have recently shown promise for reconstructing undersampled MRI data, many approaches lack an explicit link to the underlying MRI physics, and their parameters are sensitive to measurement noise, limiting their reliability in practice. We introduce Implicit-MAP (ImMAP), a diffusion-based reconstruction framework that integrates the acquisition noise model directly into a maximum a posteriori (MAP) formulation. Specifically, we build on the stochastic ascent method of Kadkhodaie et al. and generalize it to handle MRI encoding operators and realistic measurement noise. Across both simulated and real noisy datasets, ImMAP consistently outperforms state-of-the-art deep learning (LPDSNet) and diffusion-based (DDS) methods. By clarifying the practical behavior and limitations of diffusion models under realistic noise conditions, ImMAP establishes a more reliable and interpretable

Diffusing the Blind Spot: Uterine MRI Synthesis with Diffusion Models

Despite significant progress in generative modelling, existing diffusion models often struggle to produce anatomically precise female pelvic images, limiting their application in gynaecological imaging, where data scarcity and patient privacy concerns are critical. To overcome these barriers, we introduce a novel diffusion-based framework for uterine MRI synthesis, integrating both unconditional and conditioned Denoising Diffusion Probabilistic Models (DDPMs) and Latent Diffusion Models (LDMs) in 2D and 3D. Our approach generates anatomically coherent, high fidelity synthetic images that closely mimic real scans and provide valuable resources for training robust diagnostic models. We evaluate generative quality using advanced perceptual and distributional metrics, benchmarking against standard reconstruction methods, and demonstrate substantial gains in diagnostic accuracy on a key classification task. A blinded expert evaluation further validates the clinical realism of our synthetic images. We release our models with privacy safeguards and a comprehensive synthetic uterine MRI dataset to support reproducible research and advance equitable AI in gynaecology.

MoEDiff-SR: Mixture of Experts-Guided Diffusion Model for Region-Adaptive MRI Super-Resolution

Magnetic Resonance Imaging (MRI) at lower field strengths (e.g., 3T) suffers from limited spatial resolution, making it challenging to capture fine anatomical details essential for clinical diagnosis and neuroimaging research. To overcome this limitation, we propose MoEDiff-SR, a Mixture of Experts (MoE)-guided diffusion model for region-adaptive MRI Super-Resolution (SR). Unlike conventional diffusion-based SR models that apply a uniform denoising process across the entire image, MoEDiff-SR dynamically selects specialized denoising experts at a fine-grained token level, ensuring region-specific adaptation and enhanced SR performance. Specifically, our approach first employs a Transformer-based feature extractor to compute multi-scale patch embeddings, capturing both global structural information and local texture details. The extracted feature embeddings are then fed into an MoE gating network, which assigns adaptive weights to multiple diffusion-based denoisers, each specializing in different brain MRI characteristics, such as centrum semiovale, sulcal and gyral cortex, and grey-white matter junction. The final output is produced by aggregating the denoised results from these specialized experts according to dynamically assigned gating probabilities. Experimental results demonstrate that MoEDiff-SR outperforms existing state-of-the-art methods in terms of quantitative image quality metrics, perceptual fidelity, and computational efficiency. Difference maps from each expert further highlight their distinct specializations, confirming the effective region-specific denoising capability and the interpretability of expert contributions. Additionally, clinical evaluation validates its superior diagnostic capability in identifying subtle pathological features, emphasizing its practical relevance in clinical neuroimaging. Our code is available at https://github.com/ZWang78/MoEDiff-SR.

Regression is all you need for medical image translation

The acquisition of information-rich images within a limited time budget is crucial in medical imaging. Medical image translation (MIT) can help enhance and supplement existing datasets by generating synthetic images from acquired data. While Generative Adversarial Nets (GANs) and Diffusion Models (DMs) have achieved remarkable success in natural image generation, their benefits - creativity and image realism - do not necessarily transfer to medical applications where highly accurate anatomical information is required. In fact, the imitation of acquisition noise or content hallucination hinder clinical utility. Here, we introduce YODA (You Only Denoise once - or Average), a novel 2.5D diffusion-based framework for volumetric MIT. YODA unites diffusion and regression paradigms to produce realistic or noise-free outputs. Furthermore, we propose Expectation-Approximation (ExpA) DM sampling, which draws inspiration from MRI signal averaging. ExpA-sampling suppresses generated noise and, thus, eliminates noise from biasing the evaluation of image quality. Through extensive experiments on four diverse multi-modal datasets - comprising multi-contrast brain MRI and pelvic MRI-CT - we show that diffusion and regression sampling yield similar results in practice. As such, the computational overhead of diffusion sampling does not provide systematic benefits in medical information translation. Building on these insights, we demonstrate that YODA outperforms several state-of-the-art GAN and DM methods. Notably, YODA-generated images are shown to be interchangeable with, or even superior to, physical acquisitions for several downstream tasks. Our findings challenge the presumed advantages of DMs in MIT and pave the way for the practical application of MIT in medical imaging.

Regression s all you need for medical image translation

The acquisition of information-rich images within a limited time budget is crucial in medical imaging. Medical image translation (MIT) can help enhance and supplement existing datasets by generating synthetic images from acquired data. While Generative Adversarial Nets (GANs) and Diffusion Models (DMs) have achieved remarkable success in natural image generation, their benefits - creativity and image realism - do not necessarily transfer to medical applications where highly accurate anatomical information is required. In fact, the imitation of acquisition noise or content hallucination hinder clinical utility. Here, we introduce YODA (You Only Denoise once - or Average), a novel 2.5D diffusion-based framework for volumetric MIT. YODA unites diffusion and regression paradigms to produce realistic or noise-free outputs. Furthermore, we propose Expectation-Approximation (ExpA) DM sampling, which draws inspiration from MRI signal averaging. ExpA-sampling suppresses generated noise and, thus, eliminates noise from biasing the evaluation of image quality. Through extensive experiments on four diverse multi-modal datasets - comprising multi-contrast brain MRI and pelvic MRI-CT - we show that diffusion and regression sampling yield similar results in practice. As such, the computational overhead of diffusion sampling does not provide systematic benefits in medical information translation. Building on these insights, we demonstrate that YODA outperforms several state-of-the-art GAN and DM methods. Notably, YODA-generated images are shown to be interchangeable with, or even superior to, physical acquisitions for several downstream tasks. Our findings challenge the presumed advantages of DMs in MIT and pave the way for the practical application of MIT in medical imaging.

MRI super-resolution reconstruction using efficient diffusion probabilistic model with residual shifting

Objective:This study introduces a residual error-shifting mechanism that drastically reduces sampling steps while preserving critical anatomical details, thus accelerating MRI reconstruction. Approach:We propose a novel diffusion-based SR framework called Res-SRDiff, which integrates residual error shifting into the forward diffusion process. This enables efficient HR image reconstruction by aligning the degraded HR and LR distributions.We evaluated Res-SRDiff on ultra-high-field brain T1 MP2RAGE maps and T2-weighted prostate images, comparing it with Bicubic, Pix2pix, CycleGAN, and a conventional denoising diffusion probabilistic model with vision transformer backbone (TM-DDPM), using quantitative metrics such as peak signal-to-noise ratio (PSNR), structural similarity index (SSIM), gradient magnitude similarity deviation (GMSD), and learned perceptual image patch similarity (LPIPS). Main results: Res-SRDiff significantly outperformed all comparative methods in terms of PSNR, SSIM, and GMSD across both datasets, with statistically significant improvements (p-values<<0.05). The model achieved high-fidelity image restoration with only four sampling steps, drastically reducing computational time to under one second per slice, which is substantially faster than conventional TM-DDPM with around 20 seconds per slice. Qualitative analyses further demonstrated that Res-SRDiff effectively preserved fine anatomical details and lesion morphology in both brain and pelvic MRI images. Significance: Our findings show that Res-SRDiff is an efficient and accurate MRI SR method, markedly improving computational efficiency and image quality. Integrating residual error shifting into the diffusion process allows for rapid and robust HR image reconstruction, enhancing clinical MRI workflows and advancing medical imaging research. The source at:https://github.com/mosaf/Res-SRDiff

The R2D2 Deep Neural Network Series for Scalable Non-Cartesian Magnetic Resonance Imaging

We introduce the R2D2 Deep Neural Network (DNN) series paradigm for fast and scalable image reconstruction from highly-accelerated non-Cartesian k-space acquisitions in Magnetic Resonance Imaging (MRI). While unrolled DNN architectures provide a robust image formation approach via data-consistency layers, embedding non-uniform fast Fourier transform operators in a DNN can become impractical to train at large scale, e.g in 2D MRI with a large number of coils, or for higher-dimensional imaging. Plug-and-play approaches that alternate a learned denoiser blind to the measurement setting with a data-consistency step are not affected by this limitation but their highly iterative nature implies slow reconstruction. To address this scalability challenge, we leverage the R2D2 paradigm that was recently introduced to enable ultra-fast reconstruction for large-scale Fourier imaging in radio astronomy. R2D2's reconstruction is formed as a series of residual images iteratively estimated as outputs of DNN modules taking the previous iteration's data residual as input. The method can be interpreted as a learned version of the Matching Pursuit algorithm. A series of R2D2 DNN modules were sequentially trained in a supervised manner on the fastMRI dataset and validated for 2D multi-coil MRI in simulation and on real data, targeting highly under-sampled radial k-space sampling. Results suggest that a series with only few DNNs achieves superior reconstruction quality over its unrolled incarnation R2D2-Net (whose training is also much less scalable), and over the state-of-the-art diffusion-based "Decomposed Diffusion Sampler" approach (also characterised by a slower reconstruction process).

MedEdit: Counterfactual Diffusion-based Image Editing on Brain MRI

Denoising diffusion probabilistic models enable high-fidelity image synthesis and editing. In biomedicine, these models facilitate counterfactual image editing, producing pairs of images where one is edited to simulate hypothetical conditions. For example, they can model the progression of specific diseases, such as stroke lesions. However, current image editing techniques often fail to generate realistic biomedical counterfactuals, either by inadequately modeling indirect pathological effects like brain atrophy or by excessively altering the scan, which disrupts correspondence to the original images. Here, we propose MedEdit, a conditional diffusion model for medical image editing. MedEdit induces pathology in specific areas while balancing the modeling of disease effects and preserving the integrity of the original scan. We evaluated MedEdit on the Atlas v2.0 stroke dataset using Frechet Inception Distance and Dice scores, outperforming state-of-the-art diffusion-based methods such as Palette (by 45%) and SDEdit (by 61%). Additionally, clinical evaluations by a board-certified neuroradiologist confirmed that MedEdit generated realistic stroke scans indistinguishable from real ones. We believe this work will enable counterfactual image editing research to further advance the development of realistic and clinically useful imaging tools.