Daily Papers

Recent advances in Large Language Model (LLM) compression, such as quantization and pruning, have achieved notable success. However, as these techniques gradually approach their respective limits, relying on a single method for further compression has become increasingly challenging. In this work, we explore an alternative solution by combining quantization and sparsity. This joint approach, though promising, introduces new difficulties due to the inherently conflicting requirements on weight distributions: quantization favors compact ranges, while pruning benefits from high variance. To attack this problem, we propose Optimal Brain Restoration (OBR), a general and training-free framework that aligns pruning and quantization by error compensation between both. OBR minimizes performance degradation on downstream tasks by building on a second-order Hessian objective, which is then reformulated into a tractable problem through surrogate approximation and ultimately reaches a closed-form solution via group error compensation. Experiments show that OBR enables aggressive W4A4KV4 quantization with 50% sparsity on existing LLMs, and delivers up to 4.72x speedup and 6.4x memory reduction compared to the FP16-dense baseline.

Large-scale text-to-image diffusion models, while powerful, suffer from prohibitive computational cost. Existing one-shot network pruning methods can hardly be directly applied to them due to the iterative denoising nature of diffusion models. To bridge the gap, this paper presents OBS-Diff, a novel one-shot pruning framework that enables accurate and training-free compression of large-scale text-to-image diffusion models. Specifically, (i) OBS-Diff revitalizes the classic Optimal Brain Surgeon (OBS), adapting it to the complex architectures of modern diffusion models and supporting diverse pruning granularity, including unstructured, N:M semi-structured, and structured (MHA heads and FFN neurons) sparsity; (ii) To align the pruning criteria with the iterative dynamics of the diffusion process, by examining the problem from an error-accumulation perspective, we propose a novel timestep-aware Hessian construction that incorporates a logarithmic-decrease weighting scheme, assigning greater importance to earlier timesteps to mitigate potential error accumulation; (iii) Furthermore, a computationally efficient group-wise sequential pruning strategy is proposed to amortize the expensive calibration process. Extensive experiments show that OBS-Diff achieves state-of-the-art one-shot pruning for diffusion models, delivering inference acceleration with minimal degradation in visual quality.

We consider the problem of model compression for deep neural networks (DNNs) in the challenging one-shot/post-training setting, in which we are given an accurate trained model, and must compress it without any retraining, based only on a small amount of calibration input data. This problem has become popular in view of the emerging software and hardware support for executing models compressed via pruning and/or quantization with speedup, and well-performing solutions have been proposed independently for both compression approaches. In this paper, we introduce a new compression framework which covers both weight pruning and quantization in a unified setting, is time- and space-efficient, and considerably improves upon the practical performance of existing post-training methods. At the technical level, our approach is based on an exact and efficient realization of the classical Optimal Brain Surgeon (OBS) framework of [LeCun, Denker, and Solla, 1990] extended to also cover weight quantization at the scale of modern DNNs. From the practical perspective, our experimental results show that it can improve significantly upon the compression-accuracy trade-offs of existing post-training methods, and that it can enable the accurate compound application of both pruning and quantization in a post-training setting.

The increasing complexity and parameter count of Convolutional Neural Networks (CNNs) and Transformers pose challenges in terms of computational efficiency and resource demands. Pruning has been identified as an effective strategy to address these challenges by removing redundant elements such as neurons, channels, or connections, thereby enhancing computational efficiency without heavily compromising performance. This paper builds on the foundational work of Optimal Brain Damage (OBD) by advancing the methodology of parameter importance estimation using the Hessian matrix. Unlike previous approaches that rely on approximations, we introduce Optimal Brain Apoptosis (OBA), a novel pruning method that calculates the Hessian-vector product value directly for each parameter. By decomposing the Hessian matrix across network layers and identifying conditions under which inter-layer Hessian submatrices are non-zero, we propose a highly efficient technique for computing the second-order Taylor expansion of parameters. This approach allows for a more precise pruning process, particularly in the context of CNNs and Transformers, as validated in our experiments including VGG19, ResNet32, ResNet50, and ViT-B/16 on CIFAR10, CIFAR100 and Imagenet datasets. Our code is available at https://github.com/NEU-REAL/OBA.

With the discovery of Wasserstein GANs, Optimal Transport (OT) has become a powerful tool for large-scale generative modeling tasks. In these tasks, OT cost is typically used as the loss for training GANs. In contrast to this approach, we show that the OT map itself can be used as a generative model, providing comparable performance. Previous analogous approaches consider OT maps as generative models only in the latent spaces due to their poor performance in the original high-dimensional ambient space. In contrast, we apply OT maps directly in the ambient space, e.g., a space of high-dimensional images. First, we derive a min-max optimization algorithm to efficiently compute OT maps for the quadratic cost (Wasserstein-2 distance). Next, we extend the approach to the case when the input and output distributions are located in the spaces of different dimensions and derive error bounds for the computed OT map. We evaluate the algorithm on image generation and unpaired image restoration tasks. In particular, we consider denoising, colorization, and inpainting, where the optimality of the restoration map is a desired attribute, since the output (restored) image is expected to be close to the input (degraded) one.

Photo-realistic image restoration algorithms are typically evaluated by distortion measures (e.g., PSNR, SSIM) and by perceptual quality measures (e.g., FID, NIQE), where the desire is to attain the lowest possible distortion without compromising on perceptual quality. To achieve this goal, current methods typically attempt to sample from the posterior distribution, or to optimize a weighted sum of a distortion loss (e.g., MSE) and a perceptual quality loss (e.g., GAN). Unlike previous works, this paper is concerned specifically with the optimal estimator that minimizes the MSE under a constraint of perfect perceptual index, namely where the distribution of the reconstructed images is equal to that of the ground-truth ones. A recent theoretical result shows that such an estimator can be constructed by optimally transporting the posterior mean prediction (MMSE estimate) to the distribution of the ground-truth images. Inspired by this result, we introduce Posterior-Mean Rectified Flow (PMRF), a simple yet highly effective algorithm that approximates this optimal estimator. In particular, PMRF first predicts the posterior mean, and then transports the result to a high-quality image using a rectified flow model that approximates the desired optimal transport map. We investigate the theoretical utility of PMRF and demonstrate that it consistently outperforms previous methods on a variety of image restoration tasks.

Objective: To allow efficient learning using the Recurrent Inference Machine (RIM) for image reconstruction whereas not being strictly dependent on the training data distribution so that unseen modalities and pathologies are still accurately recovered. Methods: Theoretically, the RIM learns to solve the inverse problem of accelerated-MRI reconstruction whereas being robust to variable imaging conditions. The efficiency and generalization capabilities with different training datasets were studied, as well as recurrent network units with decreasing complexity: the Gated Recurrent Unit (GRU), the Minimal Gated Unit (MGU), and the Independently Recurrent Neural Network (IndRNN), to reduce inference times. Validation was performed against Compressed Sensing (CS) and further assessed based on data unseen during training. A pathology study was conducted by reconstructing simulated white matter lesions and prospectively undersampled data of a Multiple Sclerosis patient. Results: Training on a single modality of 3T T_1-weighted brain data appeared sufficient to also reconstruct 7T T_{2}^*-weighted brain and 3T T_2-weighted knee data. The IndRNN is an efficient recurrent unit, reducing inference time by 68\% compared to CS, whereas maintaining performance. The RIM was able to reconstruct lesions unseen during training more accurately than CS when trained on T_2-weighted knee data. Training on T_1-weighted brain data and on combined data slightly enhanced the signal compared to CS. Conclusion: The RIM is efficient when decreasing its complexity, which reduces the inference time, whereas still being able to reconstruct data and pathology that was unseen during training.

Neural network pruning serves as a critical technique for enhancing the efficiency of deep learning models. Unlike unstructured pruning, which only sets specific parameters to zero, structured pruning eliminates entire channels, thus yielding direct computational and storage benefits. However, the diverse patterns for coupling parameters, such as residual connections and group convolutions, the diverse deep learning frameworks, and the various time stages at which pruning can be performed make existing pruning methods less adaptable to different architectures, frameworks, and pruning criteria. To address this, we introduce Structurally Prune Anything (SPA), a versatile structured pruning framework that can prune neural networks with any architecture, from any framework, and at any stage of training. SPA leverages a standardized computational graph and ONNX representation to prune diverse neural network architectures without the need for manual intervention. SPA employs a group-level importance estimation method, which groups dependent computational operators, estimates their importance, and prunes unimportant coupled channels. This enables the transfer of various existing pruning criteria into a structured group style. As a result, SPA supports pruning at any time, either before training, after training with fine-tuning, or after training without fine-tuning. In the context of the latter, we introduce Optimal Brain SPA (OBSPA), an algorithm that achieves state-of-the-art pruning results needing neither fine-tuning nor calibration data. In extensive experiments, SPA shows competitive to state-of-the-art pruning performance across various architectures, from popular frameworks, at different pruning times.

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation regularization. The experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise.

Machine Learning methods can learn how to reconstruct Magnetic Resonance Images and thereby accelerate acquisition, which is of paramount importance to the clinical workflow. Physics-informed networks incorporate the forward model of accelerated MRI reconstruction in the learning process. With increasing network complexity, robustness is not ensured when reconstructing data unseen during training. We aim to embed data consistency (DC) in deep networks while balancing the degree of network complexity. While doing so, we will assess whether either explicit or implicit enforcement of DC in varying network architectures is preferred to optimize performance. We propose a scheme called Cascades of Independently Recurrent Inference Machines (CIRIM) to assess DC through unrolled optimization. Herein we assess DC both implicitly by gradient descent and explicitly by a designed term. Extensive comparison of the CIRIM to CS as well as to other methods is performed: the E2EVN, CascadeNet, KIKINet, LPDNet, RIM, IRIM, and UNet. Models were trained and evaluated on T1-weighted and FLAIR contrast brain data, and T2-weighted knee data. Both 1D and 2D undersampling patterns were evaluated. Robustness was tested by reconstructing 7.5x prospectively undersampled 3D FLAIR MRI data of Multiple Sclerosis (MS) patients with white matter lesions. The CIRIM performed best when implicitly enforcing DC, while the E2EVN required an explicit DC formulation. In reconstructing MS patient data, prospectively acquired with a sampling pattern unseen during model training, the CIRIM maintained lesion contrast while efficiently denoising the images. The CIRIM showed highly promising generalization capabilities maintaining a very fair trade-off between reconstructed image quality and fast reconstruction times, which is crucial in the clinical workflow.

Deep-learning-based brain magnetic resonance imaging (MRI) reconstruction methods have the potential to accelerate the MRI acquisition process. Nevertheless, the scientific community lacks appropriate benchmarks to assess MRI reconstruction quality of high-resolution brain images, and evaluate how these proposed algorithms will behave in the presence of small, but expected data distribution shifts. The Multi-Coil Magnetic Resonance Image (MC-MRI) Reconstruction Challenge provides a benchmark that aims at addressing these issues, using a large dataset of high-resolution, three-dimensional, T1-weighted MRI scans. The challenge has two primary goals: 1) to compare different MRI reconstruction models on this dataset and 2) to assess the generalizability of these models to data acquired with a different number of receiver coils. In this paper, we describe the challenge experimental design, and summarize the results of a set of baseline and state of the art brain MRI reconstruction models. We provide relevant comparative information on the current MRI reconstruction state-of-the-art and highlight the challenges of obtaining generalizable models that are required prior to broader clinical adoption. The MC-MRI benchmark data, evaluation code and current challenge leaderboard are publicly available. They provide an objective performance assessment for future developments in the field of brain MRI reconstruction.

Optimal transport (OT) aims to find a map T that transports mass from one probability measure to another while minimizing a cost function. Recently, neural OT solvers have gained popularity in high dimensional biological applications such as drug perturbation, due to their superior computational and memory efficiency compared to traditional exact Sinkhorn solvers. However, the overly complex high dimensional maps learned by neural OT solvers often suffer from poor interpretability. Prior work addressed this issue in the context of exact OT solvers by introducing displacement-sparse maps via designed elastic cost, but such method failed to be applied to neural OT settings. In this work, we propose an intuitive and theoretically grounded approach to learning displacement-sparse maps within neural OT solvers. Building on our new formulation, we introduce a novel smoothed ell_0 regularizer that outperforms the ell_1 based alternative from prior work. Leveraging Input Convex Neural Network's flexibility, we further develop a heuristic framework for adaptively controlling sparsity intensity, an approach uniquely enabled by the neural OT paradigm. We demonstrate the necessity of this adaptive framework in large-scale, high-dimensional training, showing not only improved accuracy but also practical ease of use for downstream applications.

Off-resonance artifacts in magnetic resonance imaging (MRI) are visual distortions that occur when the actual resonant frequencies of spins within the imaging volume differ from the expected frequencies used to encode spatial information. These discrepancies can be caused by a variety of factors, including magnetic field inhomogeneities, chemical shifts, or susceptibility differences within the tissues. Such artifacts can manifest as blurring, ghosting, or misregistration of the reconstructed image, and they often compromise its diagnostic quality. We propose to resolve these artifacts by lifting the 2D MRI reconstruction problem to 3D, introducing an additional "spectral" dimension to model this off-resonance. Our approach is inspired by recent progress in modeling radiance fields, and is capable of reconstructing both static and dynamic MR images as well as separating fat and water, which is of independent clinical interest. We demonstrate our approach in the context of PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) MRI acquisitions, which are popular for their robustness to motion artifacts. Our method operates in a few minutes on a single GPU, and to our knowledge is the first to correct for chemical shift in gradient echo PROPELLER MRI reconstruction without additional measurements or pretraining data.

The field of image generation has made significant progress thanks to the introduction of Diffusion Models, which learn to progressively reverse a given image corruption. Recently, a few studies introduced alternative ways of corrupting images in Diffusion Models, with an emphasis on blurring. However, these studies are purely empirical and it remains unclear what is the optimal procedure for corrupting an image. In this work, we hypothesize that the optimal procedure minimizes the length of the path taken when corrupting an image towards a given final state. We propose the Fisher metric for the path length, measured in the space of probability distributions. We compute the shortest path according to this metric, and we show that it corresponds to a combination of image sharpening, rather than blurring, and noise deblurring. While the corruption was chosen arbitrarily in previous work, our Shortest Path Diffusion (SPD) determines uniquely the entire spatiotemporal structure of the corruption. We show that SPD improves on strong baselines without any hyperparameter tuning, and outperforms all previous Diffusion Models based on image blurring. Furthermore, any small deviation from the shortest path leads to worse performance, suggesting that SPD provides the optimal procedure to corrupt images. Our work sheds new light on observations made in recent works and provides a new approach to improve diffusion models on images and other types of data.

Image restoration networks are usually comprised of an encoder and a decoder, responsible for aggregating image content from noisy, distorted data and to restore clean, undistorted images, respectively. Data aggregation as well as high-resolution image generation both usually come at the risk of involving aliases, i.e.~standard architectures put their ability to reconstruct the model input in jeopardy to reach high PSNR values on validation data. The price to be paid is low model robustness. In this work, we show that simply providing alias-free paths in state-of-the-art reconstruction transformers supports improved model robustness at low costs on the restoration performance. We do so by proposing BOA-Restormer, a transformer-based image restoration model that executes downsampling and upsampling operations partly in the frequency domain to ensure alias-free paths along the entire model while potentially preserving all relevant high-frequency information.

In this study, we propose an enhanced image restoration model, SUPIR, based on the integration of two low-rank adaptive (LoRA) modules with the Stable Diffusion XL (SDXL) framework. Our method leverages the advantages of LoRA to fine-tune SDXL models, thereby significantly improving image restoration quality and efficiency. We collect 2600 high-quality real-world images, each with detailed descriptive text, for training the model. The proposed method is evaluated on standard benchmarks and achieves excellent performance, demonstrated by higher peak signal-to-noise ratio (PSNR), lower learned perceptual image patch similarity (LPIPS), and higher structural similarity index measurement (SSIM) scores. These results underscore the effectiveness of combining LoRA with SDXL for advanced image restoration tasks, highlighting the potential of our approach in generating high-fidelity restored images.

The purpose of this study is to present and compare three denoising diffusion probabilistic models (DDPMs) that generate 3D T_1-weighted MRI human brain images. Three DDPMs were trained using 80,675 image volumes from 42,406 subjects spanning 38 publicly available brain MRI datasets. These images had approximately 1 mm isotropic resolution and were manually inspected by three human experts to exclude those with poor quality, field-of-view issues, and excessive pathology. The images were minimally preprocessed to preserve the visual variability of the data. Furthermore, to enable the DDPMs to produce images with natural orientation variations and inhomogeneity, the images were neither registered to a common coordinate system nor bias field corrected. Evaluations included segmentation, Frechet Inception Distance (FID), and qualitative inspection. Regarding results, all three DDPMs generated coherent MR brain volumes. The velocity and flow prediction models achieved lower FIDs than the sample prediction model. However, all three models had higher FIDs compared to real images across multiple cohorts. In a permutation experiment, the generated brain regional volume distributions differed statistically from real data. However, the velocity and flow prediction models had fewer statistically different volume distributions in the thalamus and putamen. In conclusion this work presents and releases the first 3D non-latent diffusion model for brain data without skullstripping or registration. Despite the negative results in statistical testing, the presented DDPMs are capable of generating high-resolution 3D T_1-weighted brain images. All model weights and corresponding inference code are publicly available at https://github.com/piksl-research/medforj .

We present a super-fast convergence approach to reconstructing the per-scene radiance field from a set of images that capture the scene with known poses. This task, which is often applied to novel view synthesis, is recently revolutionized by Neural Radiance Field (NeRF) for its state-of-the-art quality and flexibility. However, NeRF and its variants require a lengthy training time ranging from hours to days for a single scene. In contrast, our approach achieves NeRF-comparable quality and converges rapidly from scratch in less than 15 minutes with a single GPU. We adopt a representation consisting of a density voxel grid for scene geometry and a feature voxel grid with a shallow network for complex view-dependent appearance. Modeling with explicit and discretized volume representations is not new, but we propose two simple yet non-trivial techniques that contribute to fast convergence speed and high-quality output. First, we introduce the post-activation interpolation on voxel density, which is capable of producing sharp surfaces in lower grid resolution. Second, direct voxel density optimization is prone to suboptimal geometry solutions, so we robustify the optimization process by imposing several priors. Finally, evaluation on five inward-facing benchmarks shows that our method matches, if not surpasses, NeRF's quality, yet it only takes about 15 minutes to train from scratch for a new scene.

Image restoration is a challenging and ill-posed problem which also has been a long-standing issue. However, most of learning based restoration methods are proposed to target one degradation type which means they are lack of generalization. In this paper, we proposed a multi-branch restoration model inspired from the Human Visual System (i.e., Retinal Ganglion Cells) which can achieve multiple restoration tasks in a general framework. The experiments show that the proposed multi-branch architecture, called CMFNet, has competitive performance results on four datasets, including image dehazing, deraindrop, and deblurring, which are very common applications for autonomous cars. The source code and pretrained models of three restoration tasks are available at https://github.com/FanChiMao/CMFNet.

Despite the significant progress made by deep models in various image restoration tasks, existing image restoration networks still face challenges in terms of task generality. An intuitive manifestation is that networks which excel in certain tasks often fail to deliver satisfactory results in others. To illustrate this point, we select five representative networks and conduct a comparative study on five classic image restoration tasks. First, we provide a detailed explanation of the characteristics of different image restoration tasks and backbone networks. Following this, we present the benchmark results and analyze the reasons behind the performance disparity of different models across various tasks. Drawing from this comparative study, we propose that a general image restoration backbone network needs to meet the functional requirements of diverse tasks. Based on this principle, we design a new general image restoration backbone network, X-Restormer. Extensive experiments demonstrate that X-Restormer possesses good task generality and achieves state-of-the-art performance across a variety of tasks.

Image registration is an essential step in many medical image analysis tasks. Traditional methods for image registration are primarily optimization-driven, finding the optimal deformations that maximize the similarity between two images. Recent learning-based methods, trained to directly predict transformations between two images, run much faster, but suffer from performance deficiencies due to model generalization and the inefficiency in handling individual image specific deformations. Here we present a new neural net based image registration framework, called NIR (Neural Image Registration), which is based on optimization but utilizes deep neural nets to model deformations between image pairs. NIR represents the transformation between two images with a continuous function implemented via neural fields, receiving a 3D coordinate as input and outputting the corresponding deformation vector. NIR provides two ways of generating deformation field: directly output a displacement vector field for general deformable registration, or output a velocity vector field and integrate the velocity field to derive the deformation field for diffeomorphic image registration. The optimal registration is discovered by updating the parameters of the neural field via stochastic gradient descent. We describe several design choices that facilitate model optimization, including coordinate encoding, sinusoidal activation, coordinate sampling, and intensity sampling. Experiments on two 3D MR brain scan datasets demonstrate that NIR yields state-of-the-art performance in terms of both registration accuracy and regularity, while running significantly faster than traditional optimization-based methods.

Modern applications such as self-driving cars and drones rely heavily upon robust object detection techniques. However, weather corruptions can hinder the object detectability and pose a serious threat to their navigation and reliability. Thus, there is a need for efficient denoising, deraining, and restoration techniques. Generative adversarial networks and transformers have been widely adopted for image restoration. However, the training of these methods is often unstable and time-consuming. Furthermore, when used for object detection (OD), the output images generated by these methods may provide unsatisfactory results despite image clarity. In this work, we propose a contrastive approach towards mitigating this problem, by evaluating images generated by restoration models during and post training. This approach leverages OD scores combined with attention maps for predicting the usefulness of restored images for the OD task. We conduct experiments using two novel use-cases of conditional GANs and two transformer methods that probe the robustness of the proposed approach on multi-weather corruptions in the OD task. Our approach achieves an averaged 178 percent increase in mAP between the input and restored images under adverse weather conditions like dust tornadoes and snowfall. We report unique cases where greater denoising does not improve OD performance and conversely where noisy generated images demonstrate good results. We conclude the need for explainability frameworks to bridge the gap between human and machine perception, especially in the context of robust object detection for autonomous vehicles.

Bayesian optimisation (BO) uses probabilistic surrogate models - usually Gaussian processes (GPs) - for the optimisation of expensive black-box functions. At each BO iteration, the GP hyperparameters are fit to previously-evaluated data by maximising the marginal likelihood. However, this fails to account for uncertainty in the hyperparameters themselves, leading to overconfident model predictions. This uncertainty can be accounted for by taking the Bayesian approach of marginalising out the model hyperparameters. We investigate whether a fully-Bayesian treatment of the Gaussian process hyperparameters in BO (FBBO) leads to improved optimisation performance. Since an analytic approach is intractable, we compare FBBO using three approximate inference schemes to the maximum likelihood approach, using the Expected Improvement (EI) and Upper Confidence Bound (UCB) acquisition functions paired with ARD and isotropic Matern kernels, across 15 well-known benchmark problems for 4 observational noise settings. FBBO using EI with an ARD kernel leads to the best performance in the noise-free setting, with much less difference between combinations of BO components when the noise is increased. FBBO leads to over-exploration with UCB, but is not detrimental with EI. Therefore, we recommend that FBBO using EI with an ARD kernel as the default choice for BO.

Survival prediction using whole slide images (WSIs) can be formulated as a multiple instance learning (MIL) problem. However, existing MIL methods often fail to explicitly capture pathological heterogeneity within WSIs, both globally -- through long-tailed morphological distributions, and locally through -- tile-level prediction uncertainty. Optimal transport (OT) provides a principled way of modeling such heterogeneity by incorporating marginal distribution constraints. Building on this insight, we propose OTSurv, a novel MIL framework from an optimal transport perspective. Specifically, OTSurv formulates survival predictions as a heterogeneity-aware OT problem with two constraints: (1) global long-tail constraint that models prior morphological distributions to avert both mode collapse and excessive uniformity by regulating transport mass allocation, and (2) local uncertainty-aware constraint that prioritizes high-confidence patches while suppressing noise by progressively raising the total transport mass. We then recast the initial OT problem, augmented by these constraints, into an unbalanced OT formulation that can be solved with an efficient, hardware-friendly matrix scaling algorithm. Empirically, OTSurv sets new state-of-the-art results across six popular benchmarks, achieving an absolute 3.6% improvement in average C-index. In addition, OTSurv achieves statistical significance in log-rank tests and offers high interpretability, making it a powerful tool for survival prediction in digital pathology. Our codes are available at https://github.com/Y-Research-SBU/OTSurv.

MRI is an inherently slow process, which leads to long scan time for high-resolution imaging. The speed of acquisition can be increased by ignoring parts of the data (undersampling). Consequently, this leads to the degradation of image quality, such as loss of resolution or introduction of image artefacts. This work aims to reconstruct highly undersampled Cartesian or radial MR acquisitions, with better resolution and with less to no artefact compared to conventional techniques like compressed sensing. In recent times, deep learning has emerged as a very important area of research and has shown immense potential in solving inverse problems, e.g. MR image reconstruction. In this paper, a deep learning based MR image reconstruction framework is proposed, which includes a modified regularised version of ResNet as the network backbone to remove artefacts from the undersampled image, followed by data consistency steps that fusions the network output with the data already available from undersampled k-space in order to further improve reconstruction quality. The performance of this framework for various undersampling patterns has also been tested, and it has been observed that the framework is robust to deal with various sampling patterns, even when mixed together while training, and results in very high quality reconstruction, in terms of high SSIM (highest being 0.990pm0.006 for acceleration factor of 3.5), while being compared with the fully sampled reconstruction. It has been shown that the proposed framework can successfully reconstruct even for an acceleration factor of 20 for Cartesian (0.968pm0.005) and 17 for radially (0.962pm0.012) sampled data. Furthermore, it has been shown that the framework preserves brain pathology during reconstruction while being trained on healthy subjects.

We propose an image restoration algorithm that can control the perceptual quality and/or the mean square error (MSE) of any pre-trained model, trading one over the other at test time. Our algorithm is few-shot: Given about a dozen images restored by the model, it can significantly improve the perceptual quality and/or the MSE of the model for newly restored images without further training. Our approach is motivated by a recent theoretical result that links between the minimum MSE (MMSE) predictor and the predictor that minimizes the MSE under a perfect perceptual quality constraint. Specifically, it has been shown that the latter can be obtained by optimally transporting the output of the former, such that its distribution matches the source data. Thus, to improve the perceptual quality of a predictor that was originally trained to minimize MSE, we approximate the optimal transport by a linear transformation in the latent space of a variational auto-encoder, which we compute in closed-form using empirical means and covariances. Going beyond the theory, we find that applying the same procedure on models that were initially trained to achieve high perceptual quality, typically improves their perceptual quality even further. And by interpolating the results with the original output of the model, we can improve their MSE on the expense of perceptual quality. We illustrate our method on a variety of degradations applied to general content images of arbitrary dimensions.

Image denoisers have been shown to be powerful priors for solving inverse problems in imaging. In this work, we introduce a generalization of these methods that allows any image restoration network to be used as an implicit prior. The proposed method uses priors specified by deep neural networks pre-trained as general restoration operators. The method provides a principled approach for adapting state-of-the-art restoration models for other inverse problems. Our theoretical result analyzes its convergence to a stationary point of a global functional associated with the restoration operator. Numerical results show that the method using a super-resolution prior achieves state-of-the-art performance both quantitatively and qualitatively. Overall, this work offers a step forward for solving inverse problems by enabling the use of powerful pre-trained restoration models as priors.

Diffusion models are promising for joint trajectory prediction and controllable generation in autonomous driving, but they face challenges of inefficient inference steps and high computational demands. To tackle these challenges, we introduce Optimal Gaussian Diffusion (OGD) and Estimated Clean Manifold (ECM) Guidance. OGD optimizes the prior distribution for a small diffusion time T and starts the reverse diffusion process from it. ECM directly injects guidance gradients to the estimated clean manifold, eliminating extensive gradient backpropagation throughout the network. Our methodology streamlines the generative process, enabling practical applications with reduced computational overhead. Experimental validation on the large-scale Argoverse 2 dataset demonstrates our approach's superior performance, offering a viable solution for computationally efficient, high-quality joint trajectory prediction and controllable generation for autonomous driving. Our project webpage is at https://yixiaowang7.github.io/OptTrajDiff_Page/.

Computed tomography and magnetic resonance imaging are two widely used clinical imaging modalities for non-invasive diagnosis. However, both of these modalities come with certain problems. CT uses harmful ionising radiation, and MRI suffers from slow acquisition speed. Both problems can be tackled by undersampling, such as sparse sampling. However, such undersampled data leads to lower resolution and introduces artefacts. Several techniques, including deep learning based methods, have been proposed to reconstruct such data. However, the undersampled reconstruction problem for these two modalities was always considered as two different problems and tackled separately by different research works. This paper proposes a unified solution for both sparse CT and undersampled radial MRI reconstruction, achieved by applying Fourier transform-based pre-processing on the radial MRI and then finally reconstructing both modalities using sinogram upsampling combined with filtered back-projection. The Primal-Dual network is a deep learning based method for reconstructing sparsely-sampled CT data. This paper introduces Primal-Dual UNet, which improves the Primal-Dual network in terms of accuracy and reconstruction speed. The proposed method resulted in an average SSIM of 0.932\textpm0.021 while performing sparse CT reconstruction for fan-beam geometry with a sparsity level of 16, achieving a statistically significant improvement over the previous model, which resulted in 0.919\textpm0.016. Furthermore, the proposed model resulted in 0.903\textpm0.019 and 0.957\textpm0.023 average SSIM while reconstructing undersampled brain and abdominal MRI data with an acceleration factor of 16, respectively - statistically significant improvements over the original model, which resulted in 0.867\textpm0.025 and 0.949\textpm0.025.

Brain decoding, a pivotal field in neuroscience, aims to reconstruct stimuli from acquired brain signals, primarily utilizing functional magnetic resonance imaging (fMRI). Currently, brain decoding is confined to a per-subject-per-model paradigm, limiting its applicability to the same individual for whom the decoding model is trained. This constraint stems from three key challenges: 1) the inherent variability in input dimensions across subjects due to differences in brain size; 2) the unique intrinsic neural patterns, influencing how different individuals perceive and process sensory information; 3) limited data availability for new subjects in real-world scenarios hampers the performance of decoding models. In this paper, we present a novel approach, MindBridge, that achieves cross-subject brain decoding by employing only one model. Our proposed framework establishes a generic paradigm capable of addressing these challenges by introducing biological-inspired aggregation function and novel cyclic fMRI reconstruction mechanism for subject-invariant representation learning. Notably, by cycle reconstruction of fMRI, MindBridge can enable novel fMRI synthesis, which also can serve as pseudo data augmentation. Within the framework, we also devise a novel reset-tuning method for adapting a pretrained model to a new subject. Experimental results demonstrate MindBridge's ability to reconstruct images for multiple subjects, which is competitive with dedicated subject-specific models. Furthermore, with limited data for a new subject, we achieve a high level of decoding accuracy, surpassing that of subject-specific models. This advancement in cross-subject brain decoding suggests promising directions for wider applications in neuroscience and indicates potential for more efficient utilization of limited fMRI data in real-world scenarios. Project page: https://littlepure2333.github.io/MindBridge

Brain tumor growth is unique to each glioma patient and extends beyond what is visible in imaging scans, infiltrating surrounding brain tissue. Understanding these hidden patient-specific progressions is essential for effective therapies. Current treatment plans for brain tumors, such as radiotherapy, typically involve delineating a uniform margin around the visible tumor on pre-treatment scans to target this invisible tumor growth. This "one size fits all" approach is derived from population studies and often fails to account for the nuances of individual patient conditions. We present the GliODIL framework, which infers the full spatial distribution of tumor cell concentration from available multi-modal imaging, leveraging a Fisher-Kolmogorov type physics model to describe tumor growth. This is achieved through the newly introduced method of Optimizing the Discrete Loss (ODIL), where both data and physics-based constraints are softly assimilated into the solution. Our test dataset comprises 152 glioblastoma patients with pre-treatment imaging and post-treatment follow-ups for tumor recurrence monitoring. By blending data-driven techniques with physics-based constraints, GliODIL enhances recurrence prediction in radiotherapy planning, challenging traditional uniform margins and strict adherence to the Fisher-Kolmogorov partial differential equation (PDE) model, which is adapted for complex cases.

Diffusion-based image restoration (IR) methods aim to use diffusion models to recover high-quality (HQ) images from degraded images and achieve promising performance. Due to the inherent property of diffusion models, most of these methods need long serial sampling chains to restore HQ images step-by-step. As a result, it leads to expensive sampling time and high computation costs. Moreover, such long sampling chains hinder understanding the relationship between the restoration results and the inputs since it is hard to compute the gradients in the whole chains. In this work, we aim to rethink the diffusion-based IR models through a different perspective, i.e., a deep equilibrium (DEQ) fixed point system. Specifically, we derive an analytical solution by modeling the entire sampling chain in diffusion-based IR models as a joint multivariate fixed point system. With the help of the analytical solution, we are able to conduct single-image sampling in a parallel way and restore HQ images without training. Furthermore, we compute fast gradients in DEQ and found that initialization optimization can boost performance and control the generation direction. Extensive experiments on benchmarks demonstrate the effectiveness of our proposed method on typical IR tasks and real-world settings. The code and models will be made publicly available.

Diffusion model-based inverse problem solvers have demonstrated state-of-the-art performance in cases where the forward operator is known (i.e. non-blind). However, the applicability of the method to blind inverse problems has yet to be explored. In this work, we show that we can indeed solve a family of blind inverse problems by constructing another diffusion prior for the forward operator. Specifically, parallel reverse diffusion guided by gradients from the intermediate stages enables joint optimization of both the forward operator parameters as well as the image, such that both are jointly estimated at the end of the parallel reverse diffusion procedure. We show the efficacy of our method on two representative tasks -- blind deblurring, and imaging through turbulence -- and show that our method yields state-of-the-art performance, while also being flexible to be applicable to general blind inverse problems when we know the functional forms.

Energy-based models (EBMs) are known in the Machine Learning community for decades. Since the seminal works devoted to EBMs dating back to the noughties, there have been a lot of efficient methods which solve the generative modelling problem by means of energy potentials (unnormalized likelihood functions). In contrast, the realm of Optimal Transport (OT) and, in particular, neural OT solvers is much less explored and limited by few recent works (excluding WGAN-based approaches which utilize OT as a loss function and do not model OT maps themselves). In our work, we bridge the gap between EBMs and Entropy-regularized OT. We present a novel methodology which allows utilizing the recent developments and technical improvements of the former in order to enrich the latter. From the theoretical perspective, we prove generalization bounds for our technique. In practice, we validate its applicability in toy 2D and image domains. To showcase the scalability, we empower our method with a pre-trained StyleGAN and apply it to high-res AFHQ 512times 512 unpaired I2I translation. For simplicity, we choose simple short- and long-run EBMs as a backbone of our Energy-guided Entropic OT approach, leaving the application of more sophisticated EBMs for future research. Our code is available at: https://github.com/PetrMokrov/Energy-guided-Entropic-OT

The removal of non-brain signal from magnetic resonance imaging (MRI) data, known as skull-stripping, is an integral component of many neuroimage analysis streams. Despite their abundance, popular classical skull-stripping methods are usually tailored to images with specific acquisition properties, namely near-isotropic resolution and T1-weighted (T1w) MRI contrast, which are prevalent in research settings. As a result, existing tools tend to adapt poorly to other image types, such as stacks of thick slices acquired with fast spin-echo (FSE) MRI that are common in the clinic. While learning-based approaches for brain extraction have gained traction in recent years, these methods face a similar burden, as they are only effective for image types seen during the training procedure. To achieve robust skull-stripping across a landscape of imaging protocols, we introduce SynthStrip, a rapid, learning-based brain-extraction tool. By leveraging anatomical segmentations to generate an entirely synthetic training dataset with anatomies, intensity distributions, and artifacts that far exceed the realistic range of medical images, SynthStrip learns to successfully generalize to a variety of real acquired brain images, removing the need for training data with target contrasts. We demonstrate the efficacy of SynthStrip for a diverse set of image acquisitions and resolutions across subject populations, ranging from newborn to adult. We show substantial improvements in accuracy over popular skull-stripping baselines -- all with a single trained model. Our method and labeled evaluation data are available at https://w3id.org/synthstrip.

Transformers have revolutionized medical image restoration, but the quadratic complexity still poses limitations for their application to high-resolution medical images. The recent advent of the Receptance Weighted Key Value (RWKV) model in the natural language processing field has attracted much attention due to its ability to process long sequences efficiently. To leverage its advanced design, we propose Restore-RWKV, the first RWKV-based model for medical image restoration. Since the original RWKV model is designed for 1D sequences, we make two necessary modifications for modeling spatial relations in 2D medical images. First, we present a recurrent WKV (Re-WKV) attention mechanism that captures global dependencies with linear computational complexity. Re-WKV incorporates bidirectional attention as basic for a global receptive field and recurrent attention to effectively model 2D dependencies from various scan directions. Second, we develop an omnidirectional token shift (Omni-Shift) layer that enhances local dependencies by shifting tokens from all directions and across a wide context range. These adaptations make the proposed Restore-RWKV an efficient and effective model for medical image restoration. Even a lightweight variant of Restore-RWKV, with only 1.16 million parameters, achieves comparable or even superior results compared to existing state-of-the-art (SOTA) methods. Extensive experiments demonstrate that the resulting Restore-RWKV achieves SOTA performance across a range of medical image restoration tasks, including PET image synthesis, CT image denoising, MRI image super-resolution, and all-in-one medical image restoration. Code is available at: https://github.com/Yaziwel/Restore-RWKV.

In the pursuit to understand the intricacies of human brain's visual processing, reconstructing dynamic visual experiences from brain activities emerges as a challenging yet fascinating endeavor. While recent advancements have achieved success in reconstructing static images from non-invasive brain recordings, the domain of translating continuous brain activities into video format remains underexplored. In this work, we introduce NeuroCine, a novel dual-phase framework to targeting the inherent challenges of decoding fMRI data, such as noises, spatial redundancy and temporal lags. This framework proposes spatial masking and temporal interpolation-based augmentation for contrastive learning fMRI representations and a diffusion model enhanced by dependent prior noise for video generation. Tested on a publicly available fMRI dataset, our method shows promising results, outperforming the previous state-of-the-art models by a notable margin of {20.97%}, {31.00%} and {12.30%} respectively on decoding the brain activities of three subjects in the fMRI dataset, as measured by SSIM. Additionally, our attention analysis suggests that the model aligns with existing brain structures and functions, indicating its biological plausibility and interpretability.

We introduce SUPIR (Scaling-UP Image Restoration), a groundbreaking image restoration method that harnesses generative prior and the power of model scaling up. Leveraging multi-modal techniques and advanced generative prior, SUPIR marks a significant advance in intelligent and realistic image restoration. As a pivotal catalyst within SUPIR, model scaling dramatically enhances its capabilities and demonstrates new potential for image restoration. We collect a dataset comprising 20 million high-resolution, high-quality images for model training, each enriched with descriptive text annotations. SUPIR provides the capability to restore images guided by textual prompts, broadening its application scope and potential. Moreover, we introduce negative-quality prompts to further improve perceptual quality. We also develop a restoration-guided sampling method to suppress the fidelity issue encountered in generative-based restoration. Experiments demonstrate SUPIR's exceptional restoration effects and its novel capacity to manipulate restoration through textual prompts.

MRI super-resolution (SR) and denoising tasks are fundamental challenges in the field of deep learning, which have traditionally been treated as distinct tasks with separate paired training data. In this paper, we propose an innovative method that addresses both tasks simultaneously using a single deep learning model, eliminating the need for explicitly paired noisy and clean images during training. Our proposed model is primarily trained for SR, but also exhibits remarkable noise-cleaning capabilities in the super-resolved images. Instead of conventional approaches that introduce frequency-related operations into the generative process, our novel approach involves the use of a GAN model guided by a frequency-informed discriminator. To achieve this, we harness the power of the 3D Discrete Wavelet Transform (DWT) operation as a frequency constraint within the GAN framework for the SR task on magnetic resonance imaging (MRI) data. Specifically, our contributions include: 1) a 3D generator based on residual-in-residual connected blocks; 2) the integration of the 3D DWT with 1times 1 convolution into a DWT+conv unit within a 3D Unet for the discriminator; 3) the use of the trained model for high-quality image SR, accompanied by an intrinsic denoising process. We dub the model "Denoising Induced Super-resolution GAN (DISGAN)" due to its dual effects of SR image generation and simultaneous denoising. Departing from the traditional approach of training SR and denoising tasks as separate models, our proposed DISGAN is trained only on the SR task, but also achieves exceptional performance in denoising. The model is trained on 3D MRI data from dozens of subjects from the Human Connectome Project (HCP) and further evaluated on previously unseen MRI data from subjects with brain tumours and epilepsy to assess its denoising and SR performance.

Diffusion-weighted magnetic resonance imaging (DW-MRI) can be used to characterise the microstructure of the nervous tissue, e.g. to delineate brain white matter connections in a non-invasive manner via fibre tracking. Magnetic Resonance Imaging (MRI) in high spatial resolution would play an important role in visualising such fibre tracts in a superior manner. However, obtaining an image of such resolution comes at the expense of longer scan time. Longer scan time can be associated with the increase of motion artefacts, due to the patient's psychological and physical conditions. Single Image Super-Resolution (SISR), a technique aimed to obtain high-resolution (HR) details from one single low-resolution (LR) input image, achieved with Deep Learning, is the focus of this study. Compared to interpolation techniques or sparse-coding algorithms, deep learning extracts prior knowledge from big datasets and produces superior MRI images from the low-resolution counterparts. In this research, a deep learning based super-resolution technique is proposed and has been applied for DW-MRI. Images from the IXI dataset have been used as the ground-truth and were artificially downsampled to simulate the low-resolution images. The proposed method has shown statistically significant improvement over the baselines and achieved an SSIM of 0.913pm0.045.

How to decode human vision through neural signals has attracted a long-standing interest in neuroscience and machine learning. Modern contrastive learning and generative models improved the performance of fMRI-based visual decoding and reconstruction. However, the high cost and low temporal resolution of fMRI limit their applications in brain-computer interfaces (BCIs), prompting a high need for EEG-based visual reconstruction. In this study, we present an EEG-based visual reconstruction framework. It consists of a plug-and-play EEG encoder called the Adaptive Thinking Mapper (ATM), which is aligned with image embeddings, and a two-stage EEG guidance image generator that first transforms EEG features into image priors and then reconstructs the visual stimuli with a pre-trained image generator. Our approach allows EEG embeddings to achieve superior performance in image classification and retrieval tasks. Our two-stage image generation strategy vividly reconstructs images seen by humans. Furthermore, we analyzed the impact of signals from different time windows and brain regions on decoding and reconstruction. The versatility of our framework is demonstrated in the magnetoencephalogram (MEG) data modality. We report that EEG-based visual decoding achieves SOTA performance, highlighting the portability, low cost, and high temporal resolution of EEG, enabling a wide range of BCI applications. The code of ATM is available at https://github.com/dongyangli-del/EEG_Image_decode.

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

In real-world scenarios, image impairments often manifest as composite degradations, presenting a complex interplay of elements such as low light, haze, rain, and snow. Despite this reality, existing restoration methods typically target isolated degradation types, thereby falling short in environments where multiple degrading factors coexist. To bridge this gap, our study proposes a versatile imaging model that consolidates four physical corruption paradigms to accurately represent complex, composite degradation scenarios. In this context, we propose OneRestore, a novel transformer-based framework designed for adaptive, controllable scene restoration. The proposed framework leverages a unique cross-attention mechanism, merging degraded scene descriptors with image features, allowing for nuanced restoration. Our model allows versatile input scene descriptors, ranging from manual text embeddings to automatic extractions based on visual attributes. Our methodology is further enhanced through a composite degradation restoration loss, using extra degraded images as negative samples to fortify model constraints. Comparative results on synthetic and real-world datasets demonstrate OneRestore as a superior solution, significantly advancing the state-of-the-art in addressing complex, composite degradations.

Benefiting from their powerful generative capabilities, pretrained diffusion models have garnered significant attention for real-world image super-resolution (Real-SR). Existing diffusion-based SR approaches typically utilize semantic information from degraded images and restoration prompts to activate prior for producing realistic high-resolution images. However, general-purpose pretrained diffusion models, not designed for restoration tasks, often have suboptimal prior, and manually defined prompts may fail to fully exploit the generated potential. To address these limitations, we introduce RAP-SR, a novel restoration prior enhancement approach in pretrained diffusion models for Real-SR. First, we develop the High-Fidelity Aesthetic Image Dataset (HFAID), curated through a Quality-Driven Aesthetic Image Selection Pipeline (QDAISP). Our dataset not only surpasses existing ones in fidelity but also excels in aesthetic quality. Second, we propose the Restoration Priors Enhancement Framework, which includes Restoration Priors Refinement (RPR) and Restoration-Oriented Prompt Optimization (ROPO) modules. RPR refines the restoration prior using the HFAID, while ROPO optimizes the unique restoration identifier, improving the quality of the resulting images. RAP-SR effectively bridges the gap between general-purpose models and the demands of Real-SR by enhancing restoration prior. Leveraging the plug-and-play nature of RAP-SR, our approach can be seamlessly integrated into existing diffusion-based SR methods, boosting their performance. Extensive experiments demonstrate its broad applicability and state-of-the-art results. Codes and datasets will be available upon acceptance.

Since convolutional neural networks (CNNs) perform well at learning generalizable image priors from large-scale data, these models have been extensively applied to image restoration and related tasks. Recently, another class of neural architectures, Transformers, have shown significant performance gains on natural language and high-level vision tasks. While the Transformer model mitigates the shortcomings of CNNs (i.e., limited receptive field and inadaptability to input content), its computational complexity grows quadratically with the spatial resolution, therefore making it infeasible to apply to most image restoration tasks involving high-resolution images. In this work, we propose an efficient Transformer model by making several key designs in the building blocks (multi-head attention and feed-forward network) such that it can capture long-range pixel interactions, while still remaining applicable to large images. Our model, named Restoration Transformer (Restormer), achieves state-of-the-art results on several image restoration tasks, including image deraining, single-image motion deblurring, defocus deblurring (single-image and dual-pixel data), and image denoising (Gaussian grayscale/color denoising, and real image denoising). The source code and pre-trained models are available at https://github.com/swz30/Restormer.

Compressed Sensing MRI reconstructs images of the body's internal anatomy from undersampled measurements, thereby reducing scan time. Recently, deep learning has shown great potential for reconstructing high-fidelity images from highly undersampled measurements. However, one needs to train multiple models for different undersampling patterns and desired output image resolutions, since most networks operate on a fixed discretization. Such approaches are highly impractical in clinical settings, where undersampling patterns and image resolutions are frequently changed to accommodate different real-time imaging and diagnostic requirements. We propose a unified MRI reconstruction model robust to various measurement undersampling patterns and image resolutions. Our approach uses neural operators, a discretization-agnostic architecture applied in both image and measurement spaces, to capture local and global features. Empirically, our model improves SSIM by 11% and PSNR by 4 dB over a state-of-the-art CNN (End-to-End VarNet), with 600times faster inference than diffusion methods. The resolution-agnostic design also enables zero-shot super-resolution and extended field-of-view reconstruction, offering a versatile and efficient solution for clinical MR imaging. Our unified model offers a versatile solution for MRI, adapting seamlessly to various measurement undersampling and imaging resolutions, making it highly effective for flexible and reliable clinical imaging. Our code is available at https://armeet.ca/nomri.

Image restoration (IR) in real-world scenarios presents significant challenges due to the lack of high-capacity models and comprehensive datasets. To tackle these issues, we present a dual strategy: GenIR, an innovative data curation pipeline, and DreamClear, a cutting-edge Diffusion Transformer (DiT)-based image restoration model. GenIR, our pioneering contribution, is a dual-prompt learning pipeline that overcomes the limitations of existing datasets, which typically comprise only a few thousand images and thus offer limited generalizability for larger models. GenIR streamlines the process into three stages: image-text pair construction, dual-prompt based fine-tuning, and data generation & filtering. This approach circumvents the laborious data crawling process, ensuring copyright compliance and providing a cost-effective, privacy-safe solution for IR dataset construction. The result is a large-scale dataset of one million high-quality images. Our second contribution, DreamClear, is a DiT-based image restoration model. It utilizes the generative priors of text-to-image (T2I) diffusion models and the robust perceptual capabilities of multi-modal large language models (MLLMs) to achieve photorealistic restoration. To boost the model's adaptability to diverse real-world degradations, we introduce the Mixture of Adaptive Modulator (MoAM). It employs token-wise degradation priors to dynamically integrate various restoration experts, thereby expanding the range of degradations the model can address. Our exhaustive experiments confirm DreamClear's superior performance, underlining the efficacy of our dual strategy for real-world image restoration. Code and pre-trained models will be available at: https://github.com/shallowdream204/DreamClear.

The Mamba-based image restoration backbones have recently demonstrated significant potential in balancing global reception and computational efficiency. However, the inherent causal modeling limitation of Mamba, where each token depends solely on its predecessors in the scanned sequence, restricts the full utilization of pixels across the image and thus presents new challenges in image restoration. In this work, we propose MambaIRv2, which equips Mamba with the non-causal modeling ability similar to ViTs to reach the attentive state space restoration model. Specifically, the proposed attentive state-space equation allows to attend beyond the scanned sequence and facilitate image unfolding with just one single scan. Moreover, we further introduce a semantic-guided neighboring mechanism to encourage interaction between distant but similar pixels. Extensive experiments show our MambaIRv2 outperforms SRFormer by even 0.35dB PSNR for lightweight SR even with 9.3\% less parameters and suppresses HAT on classic SR by up to 0.29dB. Code is available at https://github.com/csguoh/MambaIR.

Optimal transport (OT) theory has been been used in machine learning to study and characterize maps that can push-forward efficiently a probability measure onto another. Recent works have drawn inspiration from Brenier's theorem, which states that when the ground cost is the squared-Euclidean distance, the ``best'' map to morph a continuous measure in P(Rd) into another must be the gradient of a convex function. To exploit that result, [Makkuva+ 2020, Korotin+2020] consider maps T=nabla f_theta, where f_theta is an input convex neural network (ICNN), as defined by Amos+2017, and fit theta with SGD using samples. Despite their mathematical elegance, fitting OT maps with ICNNs raises many challenges, due notably to the many constraints imposed on theta; the need to approximate the conjugate of f_theta; or the limitation that they only work for the squared-Euclidean cost. More generally, we question the relevance of using Brenier's result, which only applies to densities, to constrain the architecture of candidate maps fitted on samples. Motivated by these limitations, we propose a radically different approach to estimating OT maps: Given a cost c and a reference measure rho, we introduce a regularizer, the Monge gap M^c_{rho}(T) of a map T. That gap quantifies how far a map T deviates from the ideal properties we expect from a c-OT map. In practice, we drop all architecture requirements for T and simply minimize a distance (e.g., the Sinkhorn divergence) between Tsharpmu and nu, regularized by M^c_rho(T). We study M^c_{rho}, and show how our simple pipeline outperforms significantly other baselines in practice.

Optimal transport (OT) has gained popularity due to its various applications in fields such as machine learning, statistics, and signal processing. However, the balanced mass requirement limits its performance in practical problems. To address these limitations, variants of the OT problem, including unbalanced OT, Optimal partial transport (OPT), and Hellinger Kantorovich (HK), have been proposed. In this paper, we propose the Linear optimal partial transport (LOPT) embedding, which extends the (local) linearization technique on OT and HK to the OPT problem. The proposed embedding allows for faster computation of OPT distance between pairs of positive measures. Besides our theoretical contributions, we demonstrate the LOPT embedding technique in point-cloud interpolation and PCA analysis.

Magnetic resonance imaging (MRI) provides high spatial resolution and excellent soft-tissue contrast without using harmful ionising radiation. Dynamic MRI is an essential tool for interventions to visualise movements or changes of the target organ. However, such MRI acquisition with high temporal resolution suffers from limited spatial resolution - also known as the spatio-temporal trade-off of dynamic MRI. Several approaches, including deep learning based super-resolution approaches, have been proposed to mitigate this trade-off. Nevertheless, such an approach typically aims to super-resolve each time-point separately, treating them as individual volumes. This research addresses the problem by creating a deep learning model which attempts to learn both spatial and temporal relationships. A modified 3D UNet model, DDoS-UNet, is proposed - which takes the low-resolution volume of the current time-point along with a prior image volume. Initially, the network is supplied with a static high-resolution planning scan as the prior image along with the low-resolution input to super-resolve the first time-point. Then it continues step-wise by using the super-resolved time-points as the prior image while super-resolving the subsequent time-points. The model performance was tested with 3D dynamic data that was undersampled to different in-plane levels. The proposed network achieved an average SSIM value of 0.951pm0.017 while reconstructing the lowest resolution data (i.e. only 4\% of the k-space acquired) - which could result in a theoretical acceleration factor of 25. The proposed approach can be used to reduce the required scan-time while achieving high spatial resolution.

This paper contributes to the "BraTS 2024 Brain MR Image Synthesis Challenge" and presents a conditional Wavelet Diffusion Model (cWDM) for directly solving a paired image-to-image translation task on high-resolution volumes. While deep learning-based brain tumor segmentation models have demonstrated clear clinical utility, they typically require MR scans from various modalities (T1, T1ce, T2, FLAIR) as input. However, due to time constraints or imaging artifacts, some of these modalities may be missing, hindering the application of well-performing segmentation algorithms in clinical routine. To address this issue, we propose a method that synthesizes one missing modality image conditioned on three available images, enabling the application of downstream segmentation models. We treat this paired image-to-image translation task as a conditional generation problem and solve it by combining a Wavelet Diffusion Model for high-resolution 3D image synthesis with a simple conditioning strategy. This approach allows us to directly apply our model to full-resolution volumes, avoiding artifacts caused by slice- or patch-wise data processing. While this work focuses on a specific application, the presented method can be applied to all kinds of paired image-to-image translation problems, such as CT leftrightarrow MR and MR leftrightarrow PET translation, or mask-conditioned anatomically guided image generation.

Omnidirectional images (ODIs) are commonly used in real-world visual tasks, and high-resolution ODIs help improve the performance of related visual tasks. Most existing super-resolution methods for ODIs use end-to-end learning strategies, resulting in inferior realness of generated images and a lack of effective out-of-domain generalization capabilities in training methods. Image generation methods represented by diffusion model provide strong priors for visual tasks and have been proven to be effectively applied to image restoration tasks. Leveraging the image priors of the Stable Diffusion (SD) model, we achieve omnidirectional image super-resolution with both fidelity and realness, dubbed as OmniSSR. Firstly, we transform the equirectangular projection (ERP) images into tangent projection (TP) images, whose distribution approximates the planar image domain. Then, we use SD to iteratively sample initial high-resolution results. At each denoising iteration, we further correct and update the initial results using the proposed Octadecaplex Tangent Information Interaction (OTII) and Gradient Decomposition (GD) technique to ensure better consistency. Finally, the TP images are transformed back to obtain the final high-resolution results. Our method is zero-shot, requiring no training or fine-tuning. Experiments of our method on two benchmark datasets demonstrate the effectiveness of our proposed method.

Regularized optimal transport (OT) is now increasingly used as a loss or as a matching layer in neural networks. Entropy-regularized OT can be computed using the Sinkhorn algorithm but it leads to fully-dense transportation plans, meaning that all sources are (fractionally) matched with all targets. To address this issue, several works have investigated quadratic regularization instead. This regularization preserves sparsity and leads to unconstrained and smooth (semi) dual objectives, that can be solved with off-the-shelf gradient methods. Unfortunately, quadratic regularization does not give direct control over the cardinality (number of nonzeros) of the transportation plan. We propose in this paper a new approach for OT with explicit cardinality constraints on the transportation plan. Our work is motivated by an application to sparse mixture of experts, where OT can be used to match input tokens such as image patches with expert models such as neural networks. Cardinality constraints ensure that at most k tokens are matched with an expert, which is crucial for computational performance reasons. Despite the nonconvexity of cardinality constraints, we show that the corresponding (semi) dual problems are tractable and can be solved with first-order gradient methods. Our method can be thought as a middle ground between unregularized OT (recovered in the limit case k=1) and quadratically-regularized OT (recovered when k is large enough). The smoothness of the objectives increases as k increases, giving rise to a trade-off between convergence speed and sparsity of the optimal plan.

Dynamic imaging is a beneficial tool for interventions to assess physiological changes. Nonetheless during dynamic MRI, while achieving a high temporal resolution, the spatial resolution is compromised. To overcome this spatio-temporal trade-off, this research presents a super-resolution (SR) MRI reconstruction with prior knowledge based fine-tuning to maximise spatial information while reducing the required scan-time for dynamic MRIs. An U-Net based network with perceptual loss is trained on a benchmark dataset and fine-tuned using one subject-specific static high resolution MRI as prior knowledge to obtain high resolution dynamic images during the inference stage. 3D dynamic data for three subjects were acquired with different parameters to test the generalisation capabilities of the network. The method was tested for different levels of in-plane undersampling for dynamic MRI. The reconstructed dynamic SR results after fine-tuning showed higher similarity with the high resolution ground-truth, while quantitatively achieving statistically significant improvement. The average SSIM of the lowest resolution experimented during this research (6.25~\% of the k-space) before and after fine-tuning were 0.939 pm 0.008 and 0.957 pm 0.006 respectively. This could theoretically result in an acceleration factor of 16, which can potentially be acquired in less than half a second. The proposed approach shows that the super-resolution MRI reconstruction with prior-information can alleviate the spatio-temporal trade-off in dynamic MRI, even for high acceleration factors.

Image quality is a critical factor in delivering visually appealing content on web platforms. However, images often suffer from degradation due to lossy operations applied by online social networks (OSNs), negatively affecting user experience. Image restoration is the process of recovering a clean high-quality image from a given degraded input. Recently, multi-task (all-in-one) image restoration models have gained significant attention, due to their ability to simultaneously handle different types of image degradations. However, these models often come with an excessively high number of trainable parameters, making them computationally inefficient. In this paper, we propose a strategy for compressing multi-task image restoration models. We aim to discover highly sparse subnetworks within overparameterized deep models that can match or even surpass the performance of their dense counterparts. The proposed model, namely MIR-L, utilizes an iterative pruning strategy that removes low-magnitude weights across multiple rounds, while resetting the remaining weights to their original initialization. This iterative process is important for the multi-task image restoration model's optimization, effectively uncovering "winning tickets" that maintain or exceed state-of-the-art performance at high sparsity levels. Experimental evaluation on benchmark datasets for the deraining, dehazing, and denoising tasks shows that MIR-L retains only 10% of the trainable parameters while maintaining high image restoration performance. Our code, datasets and pre-trained models are made publicly available at https://github.com/Thomkat/MIR-L.

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES'22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model achieved superior ischemic lesion detection and segmentation accuracy on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm's segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model's generalizability. The algorithm's outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm (https://github.com/Tabrisrei/ISLES22_Ensemble) that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)radiologists. Second, we show the potential for biomedical challenge outputs to extend beyond the challenge's initial objectives, demonstrating their real-world clinical applicability.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

Handling test-time unknown degradation is the major challenge in Blind Image Restoration (BIR), necessitating high model generalization. An effective strategy is to incorporate prior knowledge, either from human input or generative model. In this paper, we introduce Instant-reference Image Restoration (InstantIR), a novel diffusion-based BIR method which dynamically adjusts generation condition during inference. We first extract a compact representation of the input via a pre-trained vision encoder. At each generation step, this representation is used to decode current diffusion latent and instantiate it in the generative prior. The degraded image is then encoded with this reference, providing robust generation condition. We observe the variance of generative references fluctuate with degradation intensity, which we further leverage as an indicator for developing a sampling algorithm adaptive to input quality. Extensive experiments demonstrate InstantIR achieves state-of-the-art performance and offering outstanding visual quality. Through modulating generative references with textual description, InstantIR can restore extreme degradation and additionally feature creative restoration.

Object removal requires eliminating not only the target object but also its effects, such as shadows and reflections. However, diffusion-based inpainting methods often produce artifacts, hallucinate content, alter background, and struggle to remove object effects accurately. To address this challenge, we introduce a new dataset for OBject-Effect Removal, named OBER, which provides paired images with and without object effects, along with precise masks for both objects and their associated visual artifacts. The dataset comprises high-quality captured and simulated data, covering diverse object categories and complex multi-object scenes. Building on OBER, we propose a novel framework, ObjectClear, which incorporates an object-effect attention mechanism to guide the model toward the foreground removal regions by learning attention masks, effectively decoupling foreground removal from background reconstruction. Furthermore, the predicted attention map enables an attention-guided fusion strategy during inference, greatly preserving background details. Extensive experiments demonstrate that ObjectClear outperforms existing methods, achieving improved object-effect removal quality and background fidelity, especially in complex scenarios.

Although there have been significant advances in the field of image restoration recently, the system complexity of the state-of-the-art (SOTA) methods is increasing as well, which may hinder the convenient analysis and comparison of methods. In this paper, we propose a simple baseline that exceeds the SOTA methods and is computationally efficient. To further simplify the baseline, we reveal that the nonlinear activation functions, e.g. Sigmoid, ReLU, GELU, Softmax, etc. are not necessary: they could be replaced by multiplication or removed. Thus, we derive a Nonlinear Activation Free Network, namely NAFNet, from the baseline. SOTA results are achieved on various challenging benchmarks, e.g. 33.69 dB PSNR on GoPro (for image deblurring), exceeding the previous SOTA 0.38 dB with only 8.4% of its computational costs; 40.30 dB PSNR on SIDD (for image denoising), exceeding the previous SOTA 0.28 dB with less than half of its computational costs. The code and the pre-trained models are released at https://github.com/megvii-research/NAFNet.

Optimal transport (OT) theory focuses, among all maps T:R^drightarrow R^d that can morph a probability measure onto another, on those that are the ``thriftiest'', i.e. such that the averaged cost c(x, T(x)) between x and its image T(x) be as small as possible. Many computational approaches have been proposed to estimate such Monge maps when c is the ell_2^2 distance, e.g., using entropic maps [Pooladian'22], or neural networks [Makkuva'20, Korotin'20]. We propose a new model for transport maps, built on a family of translation invariant costs c(x, y):=h(x-y), where h:=1{2}|cdot|_2^2+tau and tau is a regularizer. We propose a generalization of the entropic map suitable for h, and highlight a surprising link tying it with the Bregman centroids of the divergence D_h generated by h, and the proximal operator of tau. We show that choosing a sparsity-inducing norm for tau results in maps that apply Occam's razor to transport, in the sense that the displacement vectors Delta(x):= T(x)-x they induce are sparse, with a sparsity pattern that varies depending on x. We showcase the ability of our method to estimate meaningful OT maps for high-dimensional single-cell transcription data, in the 34000-d space of gene counts for cells, without using dimensionality reduction, thus retaining the ability to interpret all displacements at the gene level.

We develop a novel theoretical framework for understating OT schemes respecting a class structure. For this purpose, we propose a convex OT program with a sum-of-norms regularization term, which provably recovers the underlying class structure under geometric assumptions. Furthermore, we derive an accelerated proximal algorithm with a closed-form projection and proximal operator scheme, thereby affording a more scalable algorithm for computing optimal transport plans. We provide a novel argument for the uniqueness of the optimum even in the absence of strong convexity. Our experiments show that the new regularizer not only results in a better preservation of the class structure in the data but also yields additional robustness to the data geometry, compared to previous regularizers.

Multimodal magnetic resonance imaging (MRI) constitutes the first line of investigation for clinicians in the care of brain tumors, providing crucial insights for surgery planning, treatment monitoring, and biomarker identification. Pre-training on large datasets have been shown to help models learn transferable representations and adapt with minimal labeled data. This behavior is especially valuable in medical imaging, where annotations are often scarce. However, applying this paradigm to multimodal medical data introduces a challenge: most existing approaches assume that all imaging modalities are available during both pre-training and fine-tuning. In practice, missing modalities often occur due to acquisition issues, specialist unavailability, or specific experimental designs on small in-house datasets. Consequently, a common approach involves training a separate model for each desired modality combination, making the process both resource-intensive and impractical for clinical use. Therefore, we introduce BM-MAE, a masked image modeling pre-training strategy tailored for multimodal MRI data. The same pre-trained model seamlessly adapts to any combination of available modalities, extracting rich representations that capture both intra- and inter-modal information. This allows fine-tuning on any subset of modalities without requiring architectural changes, while still benefiting from a model pre-trained on the full set of modalities. Extensive experiments show that the proposed pre-training strategy outperforms or remains competitive with baselines that require separate pre-training for each modality subset, while substantially surpassing training from scratch on several downstream tasks. Additionally, it can quickly and efficiently reconstruct missing modalities, highlighting its practical value. Code and trained models are available at: https://github.com/Lucas-rbnt/BM-MAE

Recent years have witnessed great progress in image restoration thanks to the advancements in modern deep neural networks e.g. Convolutional Neural Network and Transformer. However, existing restoration backbones are usually limited due to the inherent local reductive bias or quadratic computational complexity. Recently, Selective Structured State Space Model e.g., Mamba, has shown great potential for long-range dependencies modeling with linear complexity, but it is still under-explored in low-level computer vision. In this work, we introduce a simple but strong benchmark model, named MambaIR, for image restoration. In detail, we propose the Residual State Space Block as the core component, which employs convolution and channel attention to enhance the capabilities of the vanilla Mamba. In this way, our MambaIR takes advantage of local patch recurrence prior as well as channel interaction to produce restoration-specific feature representation. Extensive experiments demonstrate the superiority of our method, for example, MambaIR outperforms Transformer-based baseline SwinIR by up to 0.36dB, using similar computational cost but with a global receptive field. Code is available at https://github.com/csguoh/MambaIR.

Stochastic restoration algorithms allow to explore the space of solutions that correspond to the degraded input. In this paper we reveal additional fundamental advantages of stochastic methods over deterministic ones, which further motivate their use. First, we prove that any restoration algorithm that attains perfect perceptual quality and whose outputs are consistent with the input must be a posterior sampler, and is thus required to be stochastic. Second, we illustrate that while deterministic restoration algorithms may attain high perceptual quality, this can be achieved only by filling up the space of all possible source images using an extremely sensitive mapping, which makes them highly vulnerable to adversarial attacks. Indeed, we show that enforcing deterministic models to be robust to such attacks profoundly hinders their perceptual quality, while robustifying stochastic models hardly influences their perceptual quality, and improves their output variability. These findings provide a motivation to foster progress in stochastic restoration methods, paving the way to better recovery algorithms.

Dynamic treatment regimes (DTRs) are personalized, adaptive, multi-stage treatment plans that adapt treatment decisions both to an individual's initial features and to intermediate outcomes and features at each subsequent stage, which are affected by decisions in prior stages. Examples include personalized first- and second-line treatments of chronic conditions like diabetes, cancer, and depression, which adapt to patient response to first-line treatment, disease progression, and individual characteristics. While existing literature mostly focuses on estimating the optimal DTR from offline data such as from sequentially randomized trials, we study the problem of developing the optimal DTR in an online manner, where the interaction with each individual affect both our cumulative reward and our data collection for future learning. We term this the DTR bandit problem. We propose a novel algorithm that, by carefully balancing exploration and exploitation, is guaranteed to achieve rate-optimal regret when the transition and reward models are linear. We demonstrate our algorithm and its benefits both in synthetic experiments and in a case study of adaptive treatment of major depressive disorder using real-world data.

Video imaging is often affected by complex degradations such as blur, noise, and compression artifacts. Traditional restoration methods follow a "single-task single-model" paradigm, resulting in poor generalization and high computational cost, limiting their applicability in real-world scenarios with diverse degradation types. We propose UniFlowRestore, a general video restoration framework that models restoration as a time-continuous evolution under a prompt-guided and physics-informed vector field. A physics-aware backbone PhysicsUNet encodes degradation priors as potential energy, while PromptGenerator produces task-relevant prompts as momentum. These components define a Hamiltonian system whose vector field integrates inertial dynamics, decaying physical gradients, and prompt-based guidance. The system is optimized via a fixed-step ODE solver to achieve efficient and unified restoration across tasks. Experiments show that UniFlowRestore delivers stateof-the-art performance with strong generalization and efficiency. Quantitative results demonstrate that UniFlowRestore achieves state-of-the-art performance, attaining the highest PSNR (33.89 dB) and SSIM (0.97) on the video denoising task, while maintaining top or second-best scores across all evaluated tasks.

Magnetic Resonance Imaging can produce detailed images of the anatomy and physiology of the human body that can assist doctors in diagnosing and treating pathologies such as tumours. However, MRI suffers from very long acquisition times that make it susceptible to patient motion artifacts and limit its potential to deliver dynamic treatments. Conventional approaches such as Parallel Imaging and Compressed Sensing allow for an increase in MRI acquisition speed by reconstructing MR images from sub-sampled MRI data acquired using multiple receiver coils. Recent advancements in Deep Learning combined with Parallel Imaging and Compressed Sensing techniques have the potential to produce high-fidelity reconstructions from highly accelerated MRI data. In this work we present a novel Deep Learning-based Inverse Problem solver applied to the task of Accelerated MRI Reconstruction, called the Recurrent Variational Network (RecurrentVarNet), by exploiting the properties of Convolutional Recurrent Neural Networks and unrolled algorithms for solving Inverse Problems. The RecurrentVarNet consists of multiple recurrent blocks, each responsible for one iteration of the unrolled variational optimization scheme for solving the inverse problem of multi-coil Accelerated MRI Reconstruction. Contrary to traditional approaches, the optimization steps are performed in the observation domain (k-space) instead of the image domain. Each block of the RecurrentVarNet refines the observed k-space and comprises a data consistency term and a recurrent unit which takes as input a learned hidden state and the prediction of the previous block. Our proposed method achieves new state of the art qualitative and quantitative reconstruction results on 5-fold and 10-fold accelerated data from a public multi-coil brain dataset, outperforming previous conventional and deep learning-based approaches.

OpenAI's GPT-4o model, integrating multi-modal inputs and outputs within an autoregressive architecture, has demonstrated unprecedented performance in image generation. In this work, we investigate its potential impact on the image restoration community. We present the first systematic evaluation of GPT-4o across diverse restoration tasks. Our experiments reveal that, although restoration outputs from GPT-4o are visually appealing, they often suffer from pixel-level structural fidelity when compared to ground-truth images. Common issues are variations in image proportions, shifts in object positions and quantities, and changes in viewpoint.To address it, taking image dehazing, derainning, and low-light enhancement as representative case studies, we show that GPT-4o's outputs can serve as powerful visual priors, substantially enhancing the performance of existing dehazing networks. It offers practical guidelines and a baseline framework to facilitate the integration of GPT-4o into future image restoration pipelines. We hope the study on GPT-4o image restoration will accelerate innovation in the broader field of image generation areas. To support further research, we will release GPT-4o-restored images from over 10 widely used image restoration datasets.

We propose Pulsar, an efficient sphere-based differentiable renderer that is orders of magnitude faster than competing techniques, modular, and easy-to-use due to its tight integration with PyTorch. Differentiable rendering is the foundation for modern neural rendering approaches, since it enables end-to-end training of 3D scene representations from image observations. However, gradient-based optimization of neural mesh, voxel, or function representations suffers from multiple challenges, i.e., topological inconsistencies, high memory footprints, or slow rendering speeds. To alleviate these problems, Pulsar employs: 1) a sphere-based scene representation, 2) an efficient differentiable rendering engine, and 3) neural shading. Pulsar executes orders of magnitude faster than existing techniques and allows real-time rendering and optimization of representations with millions of spheres. Using spheres for the scene representation, unprecedented speed is obtained while avoiding topology problems. Pulsar is fully differentiable and thus enables a plethora of applications, ranging from 3D reconstruction to general neural rendering.

Recently, using diffusion models for zero-shot image restoration (IR) has become a new hot paradigm. This type of method only needs to use the pre-trained off-the-shelf diffusion models, without any finetuning, and can directly handle various IR tasks. The upper limit of the restoration performance depends on the pre-trained diffusion models, which are in rapid evolution. However, current methods only discuss how to deal with fixed-size images, but dealing with images of arbitrary sizes is very important for practical applications. This paper focuses on how to use those diffusion-based zero-shot IR methods to deal with any size while maintaining the excellent characteristics of zero-shot. A simple way to solve arbitrary size is to divide it into fixed-size patches and solve each patch independently. But this may yield significant artifacts since it neither considers the global semantics of all patches nor the local information of adjacent patches. Inspired by the Range-Null space Decomposition, we propose the Mask-Shift Restoration to address local incoherence and propose the Hierarchical Restoration to alleviate out-of-domain issues. Our simple, parameter-free approaches can be used not only for image restoration but also for image generation of unlimited sizes, with the potential to be a general tool for diffusion models. Code: https://github.com/wyhuai/DDNM/tree/main/hq_demo

Diffusion models, as a kind of powerful generative model, have given impressive results on image super-resolution (SR) tasks. However, due to the randomness introduced in the reverse process of diffusion models, the performances of diffusion-based SR models are fluctuating at every time of sampling, especially for samplers with few resampled steps. This inherent randomness of diffusion models results in ineffectiveness and instability, making it challenging for users to guarantee the quality of SR results. However, our work takes this randomness as an opportunity: fully analyzing and leveraging it leads to the construction of an effective plug-and-play sampling method that owns the potential to benefit a series of diffusion-based SR methods. More in detail, we propose to steadily sample high-quality SR images from pre-trained diffusion-based SR models by solving diffusion ordinary differential equations (diffusion ODEs) with optimal boundary conditions (BCs) and analyze the characteristics between the choices of BCs and their corresponding SR results. Our analysis shows the route to obtain an approximately optimal BC via an efficient exploration in the whole space. The quality of SR results sampled by the proposed method with fewer steps outperforms the quality of results sampled by current methods with randomness from the same pre-trained diffusion-based SR model, which means that our sampling method "boosts" current diffusion-based SR models without any additional training.

Recent state-of-the-art image restoration methods mostly adopt latent diffusion models with U-Net backbones, yet still facing challenges in achieving high-quality restoration due to their limited capabilities. Diffusion transformers (DiTs), like SD3, are emerging as a promising alternative because of their better quality with scalability. In this paper, we introduce DPIR (Dual Prompting Image Restoration), a novel image restoration method that effectivly extracts conditional information of low-quality images from multiple perspectives. Specifically, DPIR consits of two branches: a low-quality image conditioning branch and a dual prompting control branch. The first branch utilizes a lightweight module to incorporate image priors into the DiT with high efficiency. More importantly, we believe that in image restoration, textual description alone cannot fully capture its rich visual characteristics. Therefore, a dual prompting module is designed to provide DiT with additional visual cues, capturing both global context and local appearance. The extracted global-local visual prompts as extra conditional control, alongside textual prompts to form dual prompts, greatly enhance the quality of the restoration. Extensive experimental results demonstrate that DPIR delivers superior image restoration performance.

While diffusion-based image restoration (IR) methods have achieved remarkable success, they are still limited by the low inference speed attributed to the necessity of executing hundreds or even thousands of sampling steps. Existing acceleration sampling techniques, though seeking to expedite the process, inevitably sacrifice performance to some extent, resulting in over-blurry restored outcomes. To address this issue, this study proposes a novel and efficient diffusion model for IR that significantly reduces the required number of diffusion steps. Our method avoids the need for post-acceleration during inference, thereby avoiding the associated performance deterioration. Specifically, our proposed method establishes a Markov chain that facilitates the transitions between the high-quality and low-quality images by shifting their residuals, substantially improving the transition efficiency. A carefully formulated noise schedule is devised to flexibly control the shifting speed and the noise strength during the diffusion process. Extensive experimental evaluations demonstrate that the proposed method achieves superior or comparable performance to current state-of-the-art methods on three classical IR tasks, namely image super-resolution, image inpainting, and blind face restoration, \textbf{even only with four sampling steps}. Our code and model are publicly available at https://github.com/zsyOAOA/ResShift.

In this paper, we propose GuideSR, a novel single-step diffusion-based image super-resolution (SR) model specifically designed to enhance image fidelity. Existing diffusion-based SR approaches typically adapt pre-trained generative models to image restoration tasks by adding extra conditioning on a VAE-downsampled representation of the degraded input, which often compromises structural fidelity. GuideSR addresses this limitation by introducing a dual-branch architecture comprising: (1) a Guidance Branch that preserves high-fidelity structures from the original-resolution degraded input, and (2) a Diffusion Branch, which a pre-trained latent diffusion model to enhance perceptual quality. Unlike conventional conditioning mechanisms, our Guidance Branch features a tailored structure for image restoration tasks, combining Full Resolution Blocks (FRBs) with channel attention and an Image Guidance Network (IGN) with guided attention. By embedding detailed structural information directly into the restoration pipeline, GuideSR produces sharper and more visually consistent results. Extensive experiments on benchmark datasets demonstrate that GuideSR achieves state-of-the-art performance while maintaining the low computational cost of single-step approaches, with up to 1.39dB PSNR gain on challenging real-world datasets. Our approach consistently outperforms existing methods across various reference-based metrics including PSNR, SSIM, LPIPS, DISTS and FID, further representing a practical advancement for real-world image restoration.

Generative diffusion models can serve as a prior which ensures that solutions of image restoration systems adhere to the manifold of natural images. However, for restoring facial images, a personalized prior is necessary to accurately represent and reconstruct unique facial features of a given individual. In this paper, we propose a simple, yet effective, method for personalized restoration, called Dual-Pivot Tuning - a two-stage approach that personalize a blind restoration system while maintaining the integrity of the general prior and the distinct role of each component. Our key observation is that for optimal personalization, the generative model should be tuned around a fixed text pivot, while the guiding network should be tuned in a generic (non-personalized) manner, using the personalized generative model as a fixed ``pivot". This approach ensures that personalization does not interfere with the restoration process, resulting in a natural appearance with high fidelity to the person's identity and the attributes of the degraded image. We evaluated our approach both qualitatively and quantitatively through extensive experiments with images of widely recognized individuals, comparing it against relevant baselines. Surprisingly, we found that our personalized prior not only achieves higher fidelity to identity with respect to the person's identity, but also outperforms state-of-the-art generic priors in terms of general image quality. Project webpage: https://personalized-restoration.github.io

In optimal transport (OT), a Monge map is known as a mapping that transports a source distribution to a target distribution in the most cost-efficient way. Recently, multiple neural estimators for Monge maps have been developed and applied in diverse unpaired domain translation tasks, e.g. in single-cell biology and computer vision. However, the classic OT framework enforces mass conservation, which makes it prone to outliers and limits its applicability in real-world scenarios. The latter can be particularly harmful in OT domain translation tasks, where the relative position of a sample within a distribution is explicitly taken into account. While unbalanced OT tackles this challenge in the discrete setting, its integration into neural Monge map estimators has received limited attention. We propose a theoretically grounded method to incorporate unbalancedness into any Monge map estimator. We improve existing estimators to model cell trajectories over time and to predict cellular responses to perturbations. Moreover, our approach seamlessly integrates with the OT flow matching (OT-FM) framework. While we show that OT-FM performs competitively in image translation, we further improve performance by incorporating unbalancedness (UOT-FM), which better preserves relevant features. We hence establish UOT-FM as a principled method for unpaired image translation.

Solving the inverse problem is the key step in evaluating the capacity of a physical model to describe real phenomena. In medical image computing, it aligns with the classical theme of image-based model personalization. Traditionally, a solution to the problem is obtained by performing either sampling or variational inference based methods. Both approaches aim to identify a set of free physical model parameters that results in a simulation best matching an empirical observation. When applied to brain tumor modeling, one of the instances of image-based model personalization in medical image computing, the overarching drawback of the methods is the time complexity for finding such a set. In a clinical setting with limited time between imaging and diagnosis or even intervention, this time complexity may prove critical. As the history of quantitative science is the history of compression, we align in this paper with the historical tendency and propose a method compressing complex traditional strategies for solving an inverse problem into a simple database query task. We evaluated different ways of performing the database query task assessing the trade-off between accuracy and execution time. On the exemplary task of brain tumor growth modeling, we prove that the proposed method achieves one order speed-up compared to existing approaches for solving the inverse problem. The resulting compute time offers critical means for relying on more complex and, hence, realistic models, for integrating image preprocessing and inverse modeling even deeper, or for implementing the current model into a clinical workflow.

This paper presents a stochastic differential equation (SDE) approach for general-purpose image restoration. The key construction consists in a mean-reverting SDE that transforms a high-quality image into a degraded counterpart as a mean state with fixed Gaussian noise. Then, by simulating the corresponding reverse-time SDE, we are able to restore the origin of the low-quality image without relying on any task-specific prior knowledge. Crucially, the proposed mean-reverting SDE has a closed-form solution, allowing us to compute the ground truth time-dependent score and learn it with a neural network. Moreover, we propose a maximum likelihood objective to learn an optimal reverse trajectory that stabilizes the training and improves the restoration results. The experiments show that our proposed method achieves highly competitive performance in quantitative comparisons on image deraining, deblurring, and denoising, setting a new state-of-the-art on two deraining datasets. Finally, the general applicability of our approach is further demonstrated via qualitative results on image super-resolution, inpainting, and dehazing. Code is available at https://github.com/Algolzw/image-restoration-sde.

Effective image inversion in rectified flow models - mapping real images to editable latent representations - is crucial for practical image editing applications; however, achieving optimal balance between reconstruction fidelity and editing flexibility remains a fundamental challenge. In this work, we introduce the Optimal Transport Inversion Pipeline (OTIP), a zero-shot framework that leverages optimal transport theory to guide the inversion process in rectified flow models. Our underlying hypothesis is that incorporating transport-based guidance during the reverse diffusion process can effectively balance reconstruction accuracy and editing controllability through principled trajectory optimization. The method computes optimal transport paths between image and noise distributions while maintaining computational efficiency. Our approach achieves high-fidelity reconstruction with LPIPS scores of 0.001 and SSIM of 0.992 on face editing benchmarks, demonstrating superior preservation of fine-grained details compared to existing methods. We evaluate the framework across multiple editing tasks, observing 7.8% to 12.9% improvements in reconstruction loss over RF-Inversion on the LSUN-Bedroom and LSUN-Church datasets, respectively. For semantic face editing, our method achieves an 11.2% improvement in identity preservation and a 1.6% enhancement in perceptual quality, while maintaining computational efficiency comparable to baseline approaches. Qualitatively, our method produces visually compelling edits with superior semantic consistency and fine-grained detail preservation across diverse editing scenarios. Code is available at: https://github.com/marianlupascu/OT-Inversion

Restart techniques are common in gradient-free optimization to deal with multimodal functions. Partial warm restarts are also gaining popularity in gradient-based optimization to improve the rate of convergence in accelerated gradient schemes to deal with ill-conditioned functions. In this paper, we propose a simple warm restart technique for stochastic gradient descent to improve its anytime performance when training deep neural networks. We empirically study its performance on the CIFAR-10 and CIFAR-100 datasets, where we demonstrate new state-of-the-art results at 3.14% and 16.21%, respectively. We also demonstrate its advantages on a dataset of EEG recordings and on a downsampled version of the ImageNet dataset. Our source code is available at https://github.com/loshchil/SGDR

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

In the past five years, the use of generative and foundational AI systems has greatly improved the decoding of brain activity. Visual perception, in particular, can now be decoded from functional Magnetic Resonance Imaging (fMRI) with remarkable fidelity. This neuroimaging technique, however, suffers from a limited temporal resolution (approx0.5 Hz) and thus fundamentally constrains its real-time usage. Here, we propose an alternative approach based on magnetoencephalography (MEG), a neuroimaging device capable of measuring brain activity with high temporal resolution (approx5,000 Hz). For this, we develop an MEG decoding model trained with both contrastive and regression objectives and consisting of three modules: i) pretrained embeddings obtained from the image, ii) an MEG module trained end-to-end and iii) a pretrained image generator. Our results are threefold: Firstly, our MEG decoder shows a 7X improvement of image-retrieval over classic linear decoders. Second, late brain responses to images are best decoded with DINOv2, a recent foundational image model. Third, image retrievals and generations both suggest that high-level visual features can be decoded from MEG signals, although the same approach applied to 7T fMRI also recovers better low-level features. Overall, these results, while preliminary, provide an important step towards the decoding -- in real-time -- of the visual processes continuously unfolding within the human brain.

The integration of deep learning and neuroscience has been advancing rapidly, which has led to improvements in the analysis of brain activity and the understanding of deep learning models from a neuroscientific perspective. The reconstruction of visual experience from human brain activity is an area that has particularly benefited: the use of deep learning models trained on large amounts of natural images has greatly improved its quality, and approaches that combine the diverse information contained in visual experiences have proliferated rapidly in recent years. In this technical paper, by taking advantage of the simple and generic framework that we proposed (Takagi and Nishimoto, CVPR 2023), we examine the extent to which various additional decoding techniques affect the performance of visual experience reconstruction. Specifically, we combined our earlier work with the following three techniques: using decoded text from brain activity, nonlinear optimization for structural image reconstruction, and using decoded depth information from brain activity. We confirmed that these techniques contributed to improving accuracy over the baseline. We also discuss what researchers should consider when performing visual reconstruction using deep generative models trained on large datasets. Please check our webpage at https://sites.google.com/view/stablediffusion-with-brain/. Code is also available at https://github.com/yu-takagi/StableDiffusionReconstruction.

Medical images often contain artificial markers added by doctors, which can negatively affect the accuracy of AI-based diagnosis. To address this issue and recover the missing visual contents, inpainting techniques are highly needed. However, existing inpainting methods require manual mask input, limiting their application scenarios. In this paper, we introduce a novel blind inpainting method that automatically completes visual contents without specifying masks for target areas in an image. Our proposed model includes a mask-free reconstruction network and an object-aware discriminator. The reconstruction network consists of two branches that predict the corrupted regions with artificial markers and simultaneously recover the missing visual contents. The object-aware discriminator relies on the powerful recognition capabilities of the dense object detector to ensure that the markers of reconstructed images cannot be detected in any local regions. As a result, the reconstructed image can be close to the clean one as much as possible. Our proposed method is evaluated on different medical image datasets, covering multiple imaging modalities such as ultrasound (US), magnetic resonance imaging (MRI), and electron microscopy (EM), demonstrating that our method is effective and robust against various unknown missing region patterns.

Automatic identification of brain lesions from magnetic resonance imaging (MRI) scans of stroke survivors would be a useful aid in patient diagnosis and treatment planning. We propose a multi-modal multi-path convolutional neural network system for automating stroke lesion segmentation. Our system has nine end-to-end UNets that take as input 2-dimensional (2D) slices and examines all three planes with three different normalizations. Outputs from these nine total paths are concatenated into a 3D volume that is then passed to a 3D convolutional neural network to output a final lesion mask. We trained and tested our method on datasets from three sources: Medical College of Wisconsin (MCW), Kessler Foundation (KF), and the publicly available Anatomical Tracings of Lesions After Stroke (ATLAS) dataset. Cross-study validation results (with independent training and validation datasets) were obtained to compare with previous methods based on naive Bayes, random forests, and three recently published convolutional neural networks. Model performance was quantified in terms of the Dice coefficient. Training on the KF and MCW images and testing on the ATLAS images yielded a mean Dice coefficient of 0.54. This was reliably better than the next best previous model, UNet, at 0.47. Reversing the train and test datasets yields a mean Dice of 0.47 on KF and MCW images, whereas the next best UNet reaches 0.45. With all three datasets combined, the current system compared to previous methods also attained a reliably higher cross-validation accuracy. It also achieved high Dice values for many smaller lesions that existing methods have difficulty identifying. Overall, our system is a clear improvement over previous methods for automating stroke lesion segmentation, bringing us an important step closer to the inter-rater accuracy level of human experts.

Organ at risk (OAR) segmentation is a critical process in radiotherapy treatment planning such as head and neck tumors. Nevertheless, in clinical practice, radiation oncologists predominantly perform OAR segmentations manually on CT scans. This manual process is highly time-consuming and expensive, limiting the number of patients who can receive timely radiotherapy. Additionally, CT scans offer lower soft-tissue contrast compared to MRI. Despite MRI providing superior soft-tissue visualization, its time-consuming nature makes it infeasible for real-time treatment planning. To address these challenges, we propose a method called SegReg, which utilizes Elastic Symmetric Normalization for registering MRI to perform OAR segmentation. SegReg outperforms the CT-only baseline by 16.78% in mDSC and 18.77% in mIoU, showing that it effectively combines the geometric accuracy of CT with the superior soft-tissue contrast of MRI, making accurate automated OAR segmentation for clinical practice become possible. See project website https://steve-zeyu-zhang.github.io/SegReg

This paper introduces a versatile paradigm for integrating multi-view reflectance (optional) and normal maps acquired through photometric stereo. Our approach employs a pixel-wise joint re-parameterization of reflectance and normal, considering them as a vector of radiances rendered under simulated, varying illumination. This re-parameterization enables the seamless integration of reflectance and normal maps as input data in neural volume rendering-based 3D reconstruction while preserving a single optimization objective. In contrast, recent multi-view photometric stereo (MVPS) methods depend on multiple, potentially conflicting objectives. Despite its apparent simplicity, our proposed approach outperforms state-of-the-art approaches in MVPS benchmarks across F-score, Chamfer distance, and mean angular error metrics. Notably, it significantly improves the detailed 3D reconstruction of areas with high curvature or low visibility.

Aneurysmal subarachnoid hemorrhage (SAH) is a life-threatening neurological emergency with mortality rates exceeding 30%. Transfer learning from related hematoma types represents a potentially valuable but underexplored approach. Although Unet architectures remain the gold standard for medical image segmentation due to their effectiveness on limited datasets, Low-Rank Adaptation (LoRA) methods for parameter-efficient transfer learning have been rarely applied to convolutional neural networks in medical imaging contexts. We implemented a Unet architecture pre-trained on computed tomography scans from 124 traumatic brain injury patients across multiple institutions, then fine-tuned on 30 aneurysmal SAH patients from the University of Michigan Health System using 3-fold cross-validation. We developed a novel CP-LoRA method based on tensor CP-decomposition and introduced DoRA variants (DoRA-C, convDoRA, CP-DoRA) that decompose weight matrices into magnitude and directional components. We compared these approaches against existing LoRA methods (LoRA-C, convLoRA) and standard fine-tuning strategies across different modules on a multi-view Unet model. LoRA-based methods consistently outperformed standard Unet fine-tuning. Performance varied by hemorrhage volume, with all methods showing improved accuracy for larger volumes. CP-LoRA achieved comparable performance to existing methods while using significantly fewer parameters. Over-parameterization with higher ranks consistently yielded better performance than strictly low-rank adaptations. This study demonstrates that transfer learning between hematoma types is feasible and that LoRA-based methods significantly outperform conventional Unet fine-tuning for aneurysmal SAH segmentation.

Mini-batch optimal transport (m-OT) has been successfully used in practical applications that involve probability measures with a very high number of supports. The m-OT solves several smaller optimal transport problems and then returns the average of their costs and transportation plans. Despite its scalability advantage, the m-OT does not consider the relationship between mini-batches which leads to undesirable estimation. Moreover, the m-OT does not approximate a proper metric between probability measures since the identity property is not satisfied. To address these problems, we propose a novel mini-batch scheme for optimal transport, named Batch of Mini-batches Optimal Transport (BoMb-OT), that finds the optimal coupling between mini-batches and it can be seen as an approximation to a well-defined distance on the space of probability measures. Furthermore, we show that the m-OT is a limit of the entropic regularized version of the BoMb-OT when the regularized parameter goes to infinity. Finally, we carry out experiments on various applications including deep generative models, deep domain adaptation, approximate Bayesian computation, color transfer, and gradient flow to show that the BoMb-OT can be widely applied and performs well in various applications.

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.

Closed-loop brain stimulation refers to capturing neurophysiological measures such as electroencephalography (EEG), quickly identifying neural events of interest, and producing auditory, magnetic or electrical stimulation so as to interact with brain processes precisely. It is a promising new method for fundamental neuroscience and perhaps for clinical applications such as restoring degraded memory function; however, existing tools are expensive, cumbersome, and offer limited experimental flexibility. In this article, we propose the Portiloop, a deep learning-based, portable and low-cost closed-loop stimulation system able to target specific brain oscillations. We first document open-hardware implementations that can be constructed from commercially available components. We also provide a fast, lightweight neural network model and an exploration algorithm that automatically optimizes the model hyperparameters to the desired brain oscillation. Finally, we validate the technology on a challenging test case of real-time sleep spindle detection, with results comparable to off-line expert performance on the Massive Online Data Annotation spindle dataset (MODA; group consensus). Software and plans are available to the community as an open science initiative to encourage further development and advance closed-loop neuroscience research.

In recent times, the need for effective super-resolution (SR) techniques has surged, especially for large-scale images ranging 2K to 8K resolutions. For DNN-based SISR, decomposing images into overlapping patches is typically necessary due to computational constraints. In such patch-decomposing scheme, one can allocate computational resources differently based on each patch's difficulty to further improve efficiency while maintaining SR performance. However, this approach has a limitation: computational resources is uniformly allocated within a patch, leading to lower efficiency when the patch contain pixels with varying levels of restoration difficulty. To address the issue, we propose the Pixel-level Classifier for Single Image Super-Resolution (PCSR), a novel method designed to distribute computational resources adaptively at the pixel level. A PCSR model comprises a backbone, a pixel-level classifier, and a set of pixel-level upsamplers with varying capacities. The pixel-level classifier assigns each pixel to an appropriate upsampler based on its restoration difficulty, thereby optimizing computational resource usage. Our method allows for performance and computational cost balance during inference without re-training. Our experiments demonstrate PCSR's advantage over existing patch-distributing methods in PSNR-FLOP trade-offs across different backbone models and benchmarks. The code is available at https://github.com/3587jjh/PCSR.

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework. This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr/

3D reconstruction methods such as Neural Radiance Fields (NeRFs) excel at rendering photorealistic novel views of complex scenes. However, recovering a high-quality NeRF typically requires tens to hundreds of input images, resulting in a time-consuming capture process. We present ReconFusion to reconstruct real-world scenes using only a few photos. Our approach leverages a diffusion prior for novel view synthesis, trained on synthetic and multiview datasets, which regularizes a NeRF-based 3D reconstruction pipeline at novel camera poses beyond those captured by the set of input images. Our method synthesizes realistic geometry and texture in underconstrained regions while preserving the appearance of observed regions. We perform an extensive evaluation across various real-world datasets, including forward-facing and 360-degree scenes, demonstrating significant performance improvements over previous few-view NeRF reconstruction approaches.

We introduce a novel neural network-based algorithm to compute optimal transport (OT) plans for general cost functionals. In contrast to common Euclidean costs, i.e., ell^1 or ell^2, such functionals provide more flexibility and allow using auxiliary information, such as class labels, to construct the required transport map. Existing methods for general costs are discrete and have limitations in practice, i.e. they do not provide an out-of-sample estimation. We address the challenge of designing a continuous OT approach for general costs that generalizes to new data points in high-dimensional spaces, such as images. Additionally, we provide the theoretical error analysis for our recovered transport plans. As an application, we construct a cost functional to map data distributions while preserving the class-wise structure.

In the realm of robot-assisted minimally invasive surgery, dynamic scene reconstruction can significantly enhance downstream tasks and improve surgical outcomes. Neural Radiance Fields (NeRF)-based methods have recently risen to prominence for their exceptional ability to reconstruct scenes but are hampered by slow inference speed, prolonged training, and inconsistent depth estimation. Some previous work utilizes ground truth depth for optimization but is hard to acquire in the surgical domain. To overcome these obstacles, we present Endo-4DGS, a real-time endoscopic dynamic reconstruction approach that utilizes 3D Gaussian Splatting (GS) for 3D representation. Specifically, we propose lightweight MLPs to capture temporal dynamics with Gaussian deformation fields. To obtain a satisfactory Gaussian Initialization, we exploit a powerful depth estimation foundation model, Depth-Anything, to generate pseudo-depth maps as a geometry prior. We additionally propose confidence-guided learning to tackle the ill-pose problems in monocular depth estimation and enhance the depth-guided reconstruction with surface normal constraints and depth regularization. Our approach has been validated on two surgical datasets, where it can effectively render in real-time, compute efficiently, and reconstruct with remarkable accuracy.

Automatic and consistent meningioma segmentation in T1-weighted MRI volumes and corresponding volumetric assessment is of use for diagnosis, treatment planning, and tumor growth evaluation. In this paper, we optimized the segmentation and processing speed performances using a large number of both surgically treated meningiomas and untreated meningiomas followed at the outpatient clinic. We studied two different 3D neural network architectures: (i) a simple encoder-decoder similar to a 3D U-Net, and (ii) a lightweight multi-scale architecture (PLS-Net). In addition, we studied the impact of different training schemes. For the validation studies, we used 698 T1-weighted MR volumes from St. Olav University Hospital, Trondheim, Norway. The models were evaluated in terms of detection accuracy, segmentation accuracy and training/inference speed. While both architectures reached a similar Dice score of 70% on average, the PLS-Net was more accurate with an F1-score of up to 88%. The highest accuracy was achieved for the largest meningiomas. Speed-wise, the PLS-Net architecture tended to converge in about 50 hours while 130 hours were necessary for U-Net. Inference with PLS-Net takes less than a second on GPU and about 15 seconds on CPU. Overall, with the use of mixed precision training, it was possible to train competitive segmentation models in a relatively short amount of time using the lightweight PLS-Net architecture. In the future, the focus should be brought toward the segmentation of small meningiomas (less than 2ml) to improve clinical relevance for automatic and early diagnosis as well as speed of growth estimates.

Most existing learning-based methods for solving imaging inverse problems can be roughly divided into two classes: iterative algorithms, such as plug-and-play and diffusion methods, that leverage pretrained denoisers, and unrolled architectures that are trained end-to-end for specific imaging problems. Iterative methods in the first class are computationally costly and often provide suboptimal reconstruction performance, whereas unrolled architectures are generally specific to a single inverse problem and require expensive training. In this work, we propose a novel non-iterative, lightweight architecture that incorporates knowledge about the forward operator (acquisition physics and noise parameters) without relying on unrolling. Our model is trained to solve a wide range of inverse problems beyond denoising, including deblurring, magnetic resonance imaging, computed tomography, inpainting, and super-resolution. The proposed model can be easily adapted to unseen inverse problems or datasets with a few fine-tuning steps (up to a few images) in a self-supervised way, without ground-truth references. Throughout a series of experiments, we demonstrate state-of-the-art performance from medical imaging to low-photon imaging and microscopy.

Intravascular ultrasound (IVUS) offers a unique perspective in the treatment of vascular diseases by creating a sequence of ultrasound-slices acquired from within the vessel. However, unlike conventional hand-held ultrasound, the thin catheter only provides room for a small number of physical channels for signal transfer from a transducer-array at the tip. For continued improvement of image quality and frame rate, we present the use of deep reinforcement learning to deal with the current physical information bottleneck. Valuable inspiration has come from the field of magnetic resonance imaging (MRI), where learned acquisition schemes have brought significant acceleration in image acquisition at competing image quality. To efficiently accelerate IVUS imaging, we propose a framework that utilizes deep reinforcement learning for an optimal adaptive acquisition policy on a per-frame basis enabled by actor-critic methods and Gumbel top-K sampling.

Recent efforts on image restoration have focused on developing "all-in-one" models that can handle different degradation types and levels within single model. However, most of mainstream Transformer-based ones confronted with dilemma between model capabilities and computation burdens, since self-attention mechanism quadratically increase in computational complexity with respect to image size, and has inadequacies in capturing long-range dependencies. Most of Mamba-related ones solely scanned feature map in spatial dimension for global modeling, failing to fully utilize information in channel dimension. To address aforementioned problems, this paper has proposed to fully utilize complementary advantages from Mamba and Transformer without sacrificing computation efficiency. Specifically, the selective scanning mechanism of Mamba is employed to focus on spatial modeling, enabling capture long-range spatial dependencies under linear complexity. The self-attention mechanism of Transformer is applied to focus on channel modeling, avoiding high computation burdens that are in quadratic growth with image's spatial dimensions. Moreover, to enrich informative prompts for effective image restoration, multi-dimensional prompt learning modules are proposed to learn prompt-flows from multi-scale encoder/decoder layers, benefiting for revealing underlying characteristic of various degradations from both spatial and channel perspectives, therefore, enhancing the capabilities of "all-in-one" model to solve various restoration tasks. Extensive experiment results on several image restoration benchmark tasks such as image denoising, dehazing, and deraining, have demonstrated that the proposed method can achieve new state-of-the-art performance, compared with many popular mainstream methods. Related source codes and pre-trained parameters will be public on github https://github.com/12138-chr/MTAIR.

Subsampling is commonly used to mitigate costs associated with data acquisition, such as time or energy requirements, motivating the development of algorithms for estimating the fully-sampled signal of interest x from partially observed measurements y. In maximum-entropy sampling, one selects measurement locations that are expected to have the highest entropy, so as to minimize uncertainty about x. This approach relies on an accurate model of the posterior distribution over future measurements, given the measurements observed so far. Recently, diffusion models have been shown to produce high-quality posterior samples of high-dimensional signals using guided diffusion. In this work, we propose Active Diffusion Subsampling (ADS), a method for performing active subsampling using guided diffusion in which the model tracks a distribution of beliefs over the true state of x throughout the reverse diffusion process, progressively decreasing its uncertainty by choosing to acquire measurements with maximum expected entropy, and ultimately generating the posterior distribution p(x | y). ADS can be applied using pre-trained diffusion models for any subsampling rate, and does not require task-specific retraining - just the specification of a measurement model. Furthermore, the maximum entropy sampling policy employed by ADS is interpretable, enhancing transparency relative to existing methods using black-box policies. Experimentally, we show that ADS outperforms fixed sampling strategies, and study an application of ADS in Magnetic Resonance Imaging acceleration using the fastMRI dataset, finding that ADS performs competitively with supervised methods. Code available at https://active-diffusion-subsampling.github.io/.

The inherent generative power of denoising diffusion models makes them well-suited for image restoration tasks where the objective is to find the optimal high-quality image within the generative space that closely resembles the input image. We propose a method to adapt a pretrained diffusion model for image restoration by simply adding noise to the input image to be restored and then denoise. Our method is based on the observation that the space of a generative model needs to be constrained. We impose this constraint by finetuning the generative model with a set of anchor images that capture the characteristics of the input image. With the constrained space, we can then leverage the sampling strategy used for generation to do image restoration. We evaluate against previous methods and show superior performances on multiple real-world restoration datasets in preserving identity and image quality. We also demonstrate an important and practical application on personalized restoration, where we use a personal album as the anchor images to constrain the generative space. This approach allows us to produce results that accurately preserve high-frequency details, which previous works are unable to do. Project webpage: https://gen2res.github.io.

Most existing Image Restoration (IR) models are task-specific, which can not be generalized to different degradation operators. In this work, we propose the Denoising Diffusion Null-Space Model (DDNM), a novel zero-shot framework for arbitrary linear IR problems, including but not limited to image super-resolution, colorization, inpainting, compressed sensing, and deblurring. DDNM only needs a pre-trained off-the-shelf diffusion model as the generative prior, without any extra training or network modifications. By refining only the null-space contents during the reverse diffusion process, we can yield diverse results satisfying both data consistency and realness. We further propose an enhanced and robust version, dubbed DDNM+, to support noisy restoration and improve restoration quality for hard tasks. Our experiments on several IR tasks reveal that DDNM outperforms other state-of-the-art zero-shot IR methods. We also demonstrate that DDNM+ can solve complex real-world applications, e.g., old photo restoration.

Sampling from diffusion probabilistic models (DPMs) can be viewed as a piecewise distribution transformation, which generally requires hundreds or thousands of steps of the inverse diffusion trajectory to get a high-quality image. Recent progress in designing fast samplers for DPMs achieves a trade-off between sampling speed and sample quality by knowledge distillation or adjusting the variance schedule or the denoising equation. However, it can't be optimal in both aspects and often suffer from mode mixture in short steps. To tackle this problem, we innovatively regard inverse diffusion as an optimal transport (OT) problem between latents at different stages and propose the DPM-OT, a unified learning framework for fast DPMs with a direct expressway represented by OT map, which can generate high-quality samples within around 10 function evaluations. By calculating the semi-discrete optimal transport map between the data latents and the white noise, we obtain an expressway from the prior distribution to the data distribution, while significantly alleviating the problem of mode mixture. In addition, we give the error bound of the proposed method, which theoretically guarantees the stability of the algorithm. Extensive experiments validate the effectiveness and advantages of DPM-OT in terms of speed and quality (FID and mode mixture), thus representing an efficient solution for generative modeling. Source codes are available at https://github.com/cognaclee/DPM-OT

Image restoration involves recovering a high-quality clean image from its degraded version. Deep learning-based methods have significantly improved image restoration performance, however, they have limited generalization ability to different degradation types and levels. This restricts their real-world application since it requires training individual models for each specific degradation and knowing the input degradation type to apply the relevant model. We present a prompt-based learning approach, PromptIR, for All-In-One image restoration that can effectively restore images from various types and levels of degradation. In particular, our method uses prompts to encode degradation-specific information, which is then used to dynamically guide the restoration network. This allows our method to generalize to different degradation types and levels, while still achieving state-of-the-art results on image denoising, deraining, and dehazing. Overall, PromptIR offers a generic and efficient plugin module with few lightweight prompts that can be used to restore images of various types and levels of degradation with no prior information on the corruptions present in the image. Our code and pretrained models are available here: https://github.com/va1shn9v/PromptIR

Diffusion bridge models establish probabilistic paths between arbitrary paired distributions and exhibit great potential for universal image restoration. Most existing methods merely treat them as simple variants of stochastic interpolants, lacking a unified analytical perspective. Besides, they indiscriminately reconstruct images through global noise injection and removal, inevitably distorting undegraded regions due to imperfect reconstruction. To address these challenges, we propose the Residual Diffusion Bridge Model (RDBM). Specifically, we theoretically reformulate the stochastic differential equations of generalized diffusion bridge and derive the analytical formulas of its forward and reverse processes. Crucially, we leverage the residuals from given distributions to modulate the noise injection and removal, enabling adaptive restoration of degraded regions while preserving intact others. Moreover, we unravel the fundamental mathematical essence of existing bridge models, all of which are special cases of RDBM and empirically demonstrate the optimality of our proposed models. Extensive experiments are conducted to demonstrate the state-of-the-art performance of our method both qualitatively and quantitatively across diverse image restoration tasks. Code is publicly available at https://github.com/MiliLab/RDBM.

Diffusion model (DM) has achieved SOTA performance by modeling the image synthesis process into a sequential application of a denoising network. However, different from image synthesis, image restoration (IR) has a strong constraint to generate results in accordance with ground-truth. Thus, for IR, traditional DMs running massive iterations on a large model to estimate whole images or feature maps is inefficient. To address this issue, we propose an efficient DM for IR (DiffIR), which consists of a compact IR prior extraction network (CPEN), dynamic IR transformer (DIRformer), and denoising network. Specifically, DiffIR has two training stages: pretraining and training DM. In pretraining, we input ground-truth images into CPEN_{S1} to capture a compact IR prior representation (IPR) to guide DIRformer. In the second stage, we train the DM to directly estimate the same IRP as pretrained CPEN_{S1} only using LQ images. We observe that since the IPR is only a compact vector, DiffIR can use fewer iterations than traditional DM to obtain accurate estimations and generate more stable and realistic results. Since the iterations are few, our DiffIR can adopt a joint optimization of CPEN_{S2}, DIRformer, and denoising network, which can further reduce the estimation error influence. We conduct extensive experiments on several IR tasks and achieve SOTA performance while consuming less computational costs. Code is available at https://github.com/Zj-BinXia/DiffIR.

Availability of large and diverse medical datasets is often challenged by privacy and data sharing restrictions. For successful application of machine learning techniques for disease diagnosis, prognosis, and precision medicine, large amounts of data are necessary for model building and optimization. To help overcome such limitations in the context of brain MRI, we present NeuroSynth: a collection of generative models of normative regional volumetric features derived from structural brain imaging. NeuroSynth models are trained on real brain imaging regional volumetric measures from the iSTAGING consortium, which encompasses over 40,000 MRI scans across 13 studies, incorporating covariates such as age, sex, and race. Leveraging NeuroSynth, we produce and offer 18,000 synthetic samples spanning the adult lifespan (ages 22-90 years), alongside the model's capability to generate unlimited data. Experimental results indicate that samples generated from NeuroSynth agree with the distributions obtained from real data. Most importantly, the generated normative data significantly enhance the accuracy of downstream machine learning models on tasks such as disease classification. Data and models are available at: https://huggingface.co/spaces/rongguangw/neuro-synth.

Reservoir computers (RCs) provide a computationally efficient alternative to deep learning while also offering a framework for incorporating brain-inspired computational principles. By using an internal neural network with random, fixed connections-the 'reservoir'-and training only the output weights, RCs simplify the training process but remain sensitive to the choice of hyperparameters that govern activation functions and network architecture. Moreover, typical RC implementations overlook a critical aspect of neuronal dynamics: the balance between excitatory and inhibitory (E-I) signals, which is essential for robust brain function. We show that RCs characteristically perform best in balanced or slightly over-inhibited regimes, outperforming excitation-dominated ones. To reduce the need for precise hyperparameter tuning, we introduce a self-adapting mechanism that locally adjusts E/I balance to achieve target neuronal firing rates, improving performance by up to 130% in tasks like memory capacity and time series prediction compared with globally tuned RCs. Incorporating brain-inspired heterogeneity in target neuronal firing rates further reduces the need for fine-tuning hyperparameters and enables RCs to excel across linear and non-linear tasks. These results support a shift from static optimization to dynamic adaptation in reservoir design, demonstrating how brain-inspired mechanisms improve RC performance and robustness while deepening our understanding of neural computation.

Resection and whole brain radiotherapy (WBRT) are the standards of care for the treatment of patients with brain metastases (BM) but are often associated with cognitive side effects. Stereotactic radiosurgery (SRS) involves a more targeted treatment approach and has been shown to avoid the side effects associated with WBRT. However, SRS requires precise identification and delineation of BM. While many AI algorithms have been developed for this purpose, their clinical adoption has been limited due to poor model performance in the clinical setting. Major reasons for non-generalizable algorithms are the limitations in the datasets used for training the AI network. The purpose of this study was to create a large, heterogenous, annotated BM dataset for training and validation of AI models to improve generalizability. We present a BM dataset of 200 patients with pretreatment T1, T1 post-contrast, T2, and FLAIR MR images. The dataset includes contrast-enhancing and necrotic 3D segmentations on T1 post-contrast and whole tumor (including peritumoral edema) 3D segmentations on FLAIR. Our dataset contains 975 contrast-enhancing lesions, many of which are sub centimeter, along with clinical and imaging feature information. We used a streamlined approach to database-building leveraging a PACS-integrated segmentation workflow.

Diffusion models have emerged as a key pillar of foundation models in visual domains. One of their critical applications is to universally solve different downstream inverse tasks via a single diffusion prior without re-training for each task. Most inverse tasks can be formulated as inferring a posterior distribution over data (e.g., a full image) given a measurement (e.g., a masked image). This is however challenging in diffusion models since the nonlinear and iterative nature of the diffusion process renders the posterior intractable. To cope with this challenge, we propose a variational approach that by design seeks to approximate the true posterior distribution. We show that our approach naturally leads to regularization by denoising diffusion process (RED-Diff) where denoisers at different timesteps concurrently impose different structural constraints over the image. To gauge the contribution of denoisers from different timesteps, we propose a weighting mechanism based on signal-to-noise-ratio (SNR). Our approach provides a new variational perspective for solving inverse problems with diffusion models, allowing us to formulate sampling as stochastic optimization, where one can simply apply off-the-shelf solvers with lightweight iterates. Our experiments for image restoration tasks such as inpainting and superresolution demonstrate the strengths of our method compared with state-of-the-art sampling-based diffusion models.

Deep neural networks (DNNs) trained for image denoising are able to generate high-quality samples with score-based reverse diffusion algorithms. These impressive capabilities seem to imply an escape from the curse of dimensionality, but recent reports of memorization of the training set raise the question of whether these networks are learning the "true" continuous density of the data. Here, we show that two DNNs trained on non-overlapping subsets of a dataset learn nearly the same score function, and thus the same density, when the number of training images is large enough. In this regime of strong generalization, diffusion-generated images are distinct from the training set, and are of high visual quality, suggesting that the inductive biases of the DNNs are well-aligned with the data density. We analyze the learned denoising functions and show that the inductive biases give rise to a shrinkage operation in a basis adapted to the underlying image. Examination of these bases reveals oscillating harmonic structures along contours and in homogeneous regions. We demonstrate that trained denoisers are inductively biased towards these geometry-adaptive harmonic bases since they arise not only when the network is trained on photographic images, but also when it is trained on image classes supported on low-dimensional manifolds for which the harmonic basis is suboptimal. Finally, we show that when trained on regular image classes for which the optimal basis is known to be geometry-adaptive and harmonic, the denoising performance of the networks is near-optimal.

Neural Radiance Field (NeRF) has achieved superior performance for novel view synthesis by modeling the scene with a Multi-Layer Perception (MLP) and a volume rendering procedure, however, when fewer known views are given (i.e., few-shot view synthesis), the model is prone to overfit the given views. To handle this issue, previous efforts have been made towards leveraging learned priors or introducing additional regularizations. In contrast, in this paper, we for the first time provide an orthogonal method from the perspective of network structure. Given the observation that trivially reducing the number of model parameters alleviates the overfitting issue, but at the cost of missing details, we propose the multi-input MLP (mi-MLP) that incorporates the inputs (i.e., location and viewing direction) of the vanilla MLP into each layer to prevent the overfitting issue without harming detailed synthesis. To further reduce the artifacts, we propose to model colors and volume density separately and present two regularization terms. Extensive experiments on multiple datasets demonstrate that: 1) although the proposed mi-MLP is easy to implement, it is surprisingly effective as it boosts the PSNR of the baseline from 14.73 to 24.23. 2) the overall framework achieves state-of-the-art results on a wide range of benchmarks. We will release the code upon publication.

With the rapid development of diffusion models and flow-based generative models, there has been a surge of interests in solving noisy linear inverse problems, e.g., super-resolution, deblurring, denoising, colorization, etc, with generative models. However, while remarkable reconstruction performances have been achieved, their inference time is typically too slow since most of them rely on the seminal diffusion posterior sampling (DPS) framework and thus to approximate the intractable likelihood score, time-consuming gradient calculation through back-propagation is needed. To address this issue, this paper provides a fast and effective solution by proposing a simple closed-form approximation to the likelihood score. For both diffusion and flow-based models, extensive experiments are conducted on various noisy linear inverse problems such as noisy super-resolution, denoising, deblurring, and colorization. In all these tasks, our method (namely DMPS) demonstrates highly competitive or even better reconstruction performances while being significantly faster than all the baseline methods.

Beyond minimizing a single training loss, many deep learning estimation pipelines rely on an auxiliary objective to quantify and encourage desirable properties of the model (e.g. performance on another dataset, robustness, agreement with a prior). Although the simplest approach to incorporating an auxiliary loss is to sum it with the training loss as a regularizer, recent works have shown that one can improve performance by blending the gradients beyond a simple sum; this is known as gradient surgery. We cast the problem as a constrained minimization problem where the auxiliary objective is minimized among the set of minimizers of the training loss. To solve this bilevel problem, we follow a parameter update direction that combines the training loss gradient and the orthogonal projection of the auxiliary gradient to the training gradient. In a setting where gradients come from mini-batches, we explain how, using a moving average of the training loss gradients, we can carefully maintain this critical orthogonality property. We demonstrate that our method, Bloop, can lead to much better performances on NLP and vision experiments than other gradient surgery methods without EMA.

Krylov subspace, which is generated by multiplying a given vector by the matrix of a linear transformation and its successive powers, has been extensively studied in classical optimization literature to design algorithms that converge quickly for large linear inverse problems. For example, the conjugate gradient method (CG), one of the most popular Krylov subspace methods, is based on the idea of minimizing the residual error in the Krylov subspace. However, with the recent advancement of high-performance diffusion solvers for inverse problems, it is not clear how classical wisdom can be synergistically combined with modern diffusion models. In this study, we propose a novel and efficient diffusion sampling strategy that synergistically combines the diffusion sampling and Krylov subspace methods. Specifically, we prove that if the tangent space at a denoised sample by Tweedie's formula forms a Krylov subspace, then the CG initialized with the denoised data ensures the data consistency update to remain in the tangent space. This negates the need to compute the manifold-constrained gradient (MCG), leading to a more efficient diffusion sampling method. Our method is applicable regardless of the parametrization and setting (i.e., VE, VP). Notably, we achieve state-of-the-art reconstruction quality on challenging real-world medical inverse imaging problems, including multi-coil MRI reconstruction and 3D CT reconstruction. Moreover, our proposed method achieves more than 80 times faster inference time than the previous state-of-the-art method. Code is available at https://github.com/HJ-harry/DDS

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. Here we introduce BrainFM, a modality-agnostic, multi-task vision foundation model for human brain imaging. With the proposed "mild-to-severe" intra-subject generation and "real-synth" mix-up training strategy, BrainFM is resilient to the appearance of acquired images (e.g., modality, contrast, deformation, resolution, artifacts), and can be directly applied to five fundamental brain imaging tasks, including image synthesis for CT and T1w/T2w/FLAIR MRI, anatomy segmentation, scalp-to-cortical distance, bias field estimation, and registration. We evaluate the efficacy of BrainFM on eleven public datasets, and demonstrate its robustness and effectiveness across all tasks and input modalities. Code is available at https://github.com/jhuldr/BrainFM.

Denoising diffusion models (DDMs) have recently attracted increasing attention by showing impressive synthesis quality. DDMs are built on a diffusion process that pushes data to the noise distribution and the models learn to denoise. In this paper, we establish the interpretation of DDMs in terms of image restoration (IR). Integrating IR literature allows us to use an alternative objective and diverse forward processes, not confining to the diffusion process. By imposing prior knowledge on the loss function grounded on MAP-based estimation, we eliminate the need for the expensive sampling of DDMs. Also, we propose a multi-scale training, which improves the performance compared to the diffusion process, by taking advantage of the flexibility of the forward process. Experimental results demonstrate that our model improves the quality and efficiency of both training and inference. Furthermore, we show the applicability of our model to inverse problems. We believe that our framework paves the way for designing a new type of flexible general generative model.

We provide a framework for solving inverse problems with diffusion models learned from linearly corrupted data. Our method, Ambient Diffusion Posterior Sampling (A-DPS), leverages a generative model pre-trained on one type of corruption (e.g. image inpainting) to perform posterior sampling conditioned on measurements from a potentially different forward process (e.g. image blurring). We test the efficacy of our approach on standard natural image datasets (CelebA, FFHQ, and AFHQ) and we show that A-DPS can sometimes outperform models trained on clean data for several image restoration tasks in both speed and performance. We further extend the Ambient Diffusion framework to train MRI models with access only to Fourier subsampled multi-coil MRI measurements at various acceleration factors (R=2, 4, 6, 8). We again observe that models trained on highly subsampled data are better priors for solving inverse problems in the high acceleration regime than models trained on fully sampled data. We open-source our code and the trained Ambient Diffusion MRI models: https://github.com/utcsilab/ambient-diffusion-mri .

In this work, we present a computing platform named digital twin brain (DTB) that can simulate spiking neuronal networks of the whole human brain scale and more importantly, a personalized biological brain structure. In comparison to most brain simulations with a homogeneous global structure, we highlight that the sparseness, couplingness and heterogeneity in the sMRI, DTI and PET data of the brain has an essential impact on the efficiency of brain simulation, which is proved from the scaling experiments that the DTB of human brain simulation is communication-intensive and memory-access intensive computing systems rather than computation-intensive. We utilize a number of optimization techniques to balance and integrate the computation loads and communication traffics from the heterogeneous biological structure to the general GPU-based HPC and achieve leading simulation performance for the whole human brain-scaled spiking neuronal networks. On the other hand, the biological structure, equipped with a mesoscopic data assimilation, enables the DTB to investigate brain cognitive function by a reverse-engineering method, which is demonstrated by a digital experiment of visual evaluation on the DTB. Furthermore, we believe that the developing DTB will be a promising powerful platform for a large of research orients including brain-inspiredintelligence, rain disease medicine and brain-machine interface.

Extent of resection after surgery is one of the main prognostic factors for patients diagnosed with glioblastoma. To achieve this, accurate segmentation and classification of residual tumor from post-operative MR images is essential. The current standard method for estimating it is subject to high inter- and intra-rater variability, and an automated method for segmentation of residual tumor in early post-operative MRI could lead to a more accurate estimation of extent of resection. In this study, two state-of-the-art neural network architectures for pre-operative segmentation were trained for the task. The models were extensively validated on a multicenter dataset with nearly 1000 patients, from 12 hospitals in Europe and the United States. The best performance achieved was a 61\% Dice score, and the best classification performance was about 80\% balanced accuracy, with a demonstrated ability to generalize across hospitals. In addition, the segmentation performance of the best models was on par with human expert raters. The predicted segmentations can be used to accurately classify the patients into those with residual tumor, and those with gross total resection.

Solving a linear system Ax=b is a fundamental scientific computing primitive for which numerous solvers and preconditioners have been developed. These come with parameters whose optimal values depend on the system being solved and are often impossible or too expensive to identify; thus in practice sub-optimal heuristics are used. We consider the common setting in which many related linear systems need to be solved, e.g. during a single numerical simulation. In this scenario, can we sequentially choose parameters that attain a near-optimal overall number of iterations, without extra matrix computations? We answer in the affirmative for Successive Over-Relaxation (SOR), a standard solver whose parameter omega has a strong impact on its runtime. For this method, we prove that a bandit online learning algorithm--using only the number of iterations as feedback--can select parameters for a sequence of instances such that the overall cost approaches that of the best fixed omega as the sequence length increases. Furthermore, when given additional structural information, we show that a contextual bandit method asymptotically achieves the performance of the instance-optimal policy, which selects the best omega for each instance. Our work provides the first learning-theoretic treatment of high-precision linear system solvers and the first end-to-end guarantees for data-driven scientific computing, demonstrating theoretically the potential to speed up numerical methods using well-understood learning algorithms.

Current deep learning-based approaches to lesion segmentation in neuroimaging often depend on high-resolution images and extensive annotated data, limiting clinical applicability. This paper introduces a novel synthetic data framework tailored for stroke lesion segmentation, expanding the SynthSeg methodology to incorporate lesion-specific augmentations that simulate diverse pathological features. Using a modified nnUNet architecture, our approach trains models with label maps from healthy and stroke datasets, facilitating segmentation across both normal and pathological tissue without reliance on specific sequence-based training. Evaluation across in-domain and out-of-domain (OOD) datasets reveals that our method matches state-of-the-art performance within the training domain and significantly outperforms existing methods on OOD data. By minimizing dependence on large annotated datasets and allowing for cross-sequence applicability, our framework holds potential to improve clinical neuroimaging workflows, particularly in stroke pathology. PyTorch training code and weights are publicly available at https://github.com/liamchalcroft/SynthStroke, along with an SPM toolbox featuring a plug-and-play model at https://github.com/liamchalcroft/SynthStrokeSPM.

In this paper, we present Uformer, an effective and efficient Transformer-based architecture for image restoration, in which we build a hierarchical encoder-decoder network using the Transformer block. In Uformer, there are two core designs. First, we introduce a novel locally-enhanced window (LeWin) Transformer block, which performs nonoverlapping window-based self-attention instead of global self-attention. It significantly reduces the computational complexity on high resolution feature map while capturing local context. Second, we propose a learnable multi-scale restoration modulator in the form of a multi-scale spatial bias to adjust features in multiple layers of the Uformer decoder. Our modulator demonstrates superior capability for restoring details for various image restoration tasks while introducing marginal extra parameters and computational cost. Powered by these two designs, Uformer enjoys a high capability for capturing both local and global dependencies for image restoration. To evaluate our approach, extensive experiments are conducted on several image restoration tasks, including image denoising, motion deblurring, defocus deblurring and deraining. Without bells and whistles, our Uformer achieves superior or comparable performance compared with the state-of-the-art algorithms. The code and models are available at https://github.com/ZhendongWang6/Uformer.

Multimodal MRI provides critical complementary information for accurate brain tumor segmentation. However, conventional methods struggle when certain modalities are missing due to issues such as image quality, protocol inconsistencies, patient allergies, or financial constraints. To address this, we propose a robust single-modality parallel processing framework that achieves high segmentation accuracy even with incomplete modalities. Leveraging Holder divergence and mutual information, our model maintains modality-specific features while dynamically adjusting network parameters based on the available inputs. By using these divergence- and information-based loss functions, the framework effectively quantifies discrepancies between predictions and ground-truth labels, resulting in consistently accurate segmentation. Extensive evaluations on the BraTS 2018 and BraTS 2020 datasets demonstrate superior performance over existing methods in handling missing modalities.

Diffusion Probabilistic Models (DPMs) have recently been employed for image deblurring, formulated as an image-conditioned generation process that maps Gaussian noise to the high-quality image, conditioned on the blurry input. Image-conditioned DPMs (icDPMs) have shown more realistic results than regression-based methods when trained on pairwise in-domain data. However, their robustness in restoring images is unclear when presented with out-of-domain images as they do not impose specific degradation models or intermediate constraints. To this end, we introduce a simple yet effective multiscale structure guidance as an implicit bias that informs the icDPM about the coarse structure of the sharp image at the intermediate layers. This guided formulation leads to a significant improvement of the deblurring results, particularly on unseen domain. The guidance is extracted from the latent space of a regression network trained to predict the clean-sharp target at multiple lower resolutions, thus maintaining the most salient sharp structures. With both the blurry input and multiscale guidance, the icDPM model can better understand the blur and recover the clean image. We evaluate a single-dataset trained model on diverse datasets and demonstrate more robust deblurring results with fewer artifacts on unseen data. Our method outperforms existing baselines, achieving state-of-the-art perceptual quality while keeping competitive distortion metrics.

Pre-trained text-to-image diffusion models are increasingly applied to real-world image super-resolution (Real-ISR) task. Given the iterative refinement nature of diffusion models, most existing approaches are computationally expensive. While methods such as SinSR and OSEDiff have emerged to condense inference steps via distillation, their performance in image restoration or details recovery is not satisfied. To address this, we propose TSD-SR, a novel distillation framework specifically designed for real-world image super-resolution, aiming to construct an efficient and effective one-step model. We first introduce the Target Score Distillation, which leverages the priors of diffusion models and real image references to achieve more realistic image restoration. Secondly, we propose a Distribution-Aware Sampling Module to make detail-oriented gradients more readily accessible, addressing the challenge of recovering fine details. Extensive experiments demonstrate that our TSD-SR has superior restoration results (most of the metrics perform the best) and the fastest inference speed (e.g. 40 times faster than SeeSR) compared to the past Real-ISR approaches based on pre-trained diffusion priors.

The diffusion MRI Neurite Exchange Imaging model offers a promising framework for probing gray matter microstructure by estimating parameters such as compartment sizes, diffusivities, and inter-compartmental water exchange time. However, existing protocols require long scan times. This study proposes a reduced acquisition scheme for the Connectome 2.0 scanner that preserves model accuracy while substantially shortening scan duration. We developed a data-driven framework using explainable artificial intelligence with a guided recursive feature elimination strategy to identify an optimal 8-feature subset from a 15-feature protocol. The performance of this optimized protocol was validated in vivo and benchmarked against the full acquisition and alternative reduction strategies. Parameter accuracy, preservation of anatomical contrast, and test-retest reproducibility were assessed. The reduced protocol yielded parameter estimates and cortical maps comparable to the full protocol, with low estimation errors in synthetic data and minimal impact on test-retest variability. Compared to theory-driven and heuristic reduction schemes, the optimized protocol demonstrated superior robustness, reducing the deviation in water exchange time estimates by over two-fold. In conclusion, this hybrid optimization framework enables viable imaging of neurite exchange in 14 minutes without loss of parameter fidelity. This approach supports the broader application of exchange-sensitive diffusion magnetic resonance imaging in neuroscience and clinical research, and offers a generalizable method for designing efficient acquisition protocols in biophysical parameter mapping.

Universal image restoration (UIR) aims to recover images degraded by unknown mixtures while preserving semantics -- conditions under which discriminative restorers and UNet-based diffusion priors often oversmooth, hallucinate, or drift. We present LucidFlux, a caption-free UIR framework that adapts a large diffusion transformer (Flux.1) without image captions. LucidFlux introduces a lightweight dual-branch conditioner that injects signals from the degraded input and a lightly restored proxy to respectively anchor geometry and suppress artifacts. Then, a timestep- and layer-adaptive modulation schedule is designed to route these cues across the backbone's hierarchy, in order to yield coarse-to-fine and context-aware updates that protect the global structure while recovering texture. After that, to avoid the latency and instability of text prompts or MLLM captions, we enforce caption-free semantic alignment via SigLIP features extracted from the proxy. A scalable curation pipeline further filters large-scale data for structure-rich supervision. Across synthetic and in-the-wild benchmarks, LucidFlux consistently outperforms strong open-source and commercial baselines, and ablation studies verify the necessity of each component. LucidFlux shows that, for large DiTs, when, where, and what to condition on -- rather than adding parameters or relying on text prompts -- is the governing lever for robust and caption-free universal image restoration in the wild.

Blind all-in-one image restoration models aim to recover a high-quality image from an input degraded with unknown distortions. However, these models require all the possible degradation types to be defined during the training stage while showing limited generalization to unseen degradations, which limits their practical application in complex cases. In this paper, we propose a simple but effective adaptive blind all-in-one restoration (ABAIR) model, which can address multiple degradations, generalizes well to unseen degradations, and efficiently incorporate new degradations by training a small fraction of parameters. First, we train our baseline model on a large dataset of natural images with multiple synthetic degradations, augmented with a segmentation head to estimate per-pixel degradation types, resulting in a powerful backbone able to generalize to a wide range of degradations. Second, we adapt our baseline model to varying image restoration tasks using independent low-rank adapters. Third, we learn to adaptively combine adapters to versatile images via a flexible and lightweight degradation estimator. Our model is both powerful in handling specific distortions and flexible in adapting to complex tasks, it not only outperforms the state-of-the-art by a large margin on five- and three-task IR setups, but also shows improved generalization to unseen degradations and also composite distortions.

Recently, diffusion-based blind super-resolution (SR) methods have shown great ability to generate high-resolution images with abundant high-frequency detail, but the detail is often achieved at the expense of fidelity. Meanwhile, another line of research focusing on rectifying the reverse process of diffusion models (i.e., diffusion guidance), has demonstrated the power to generate high-fidelity results for non-blind SR. However, these methods rely on known degradation kernels, making them difficult to apply to blind SR. To address these issues, we present DADiff in this paper. DADiff incorporates degradation-aware models into the diffusion guidance framework, eliminating the need to know degradation kernels. Additionally, we propose two novel techniques: input perturbation and guidance scalar, to further improve our performance. Extensive experimental results show that our proposed method has superior performance over state-of-the-art methods on blind SR benchmarks.

Image restoration problems are typically ill-posed in the sense that each degraded image can be restored in infinitely many valid ways. To accommodate this, many works generate a diverse set of outputs by attempting to randomly sample from the posterior distribution of natural images given the degraded input. Here we argue that this strategy is commonly of limited practical value because of the heavy tail of the posterior distribution. Consider for example inpainting a missing region of the sky in an image. Since there is a high probability that the missing region contains no object but clouds, any set of samples from the posterior would be entirely dominated by (practically identical) completions of sky. However, arguably, presenting users with only one clear sky completion, along with several alternative solutions such as airships, birds, and balloons, would better outline the set of possibilities. In this paper, we initiate the study of meaningfully diverse image restoration. We explore several post-processing approaches that can be combined with any diverse image restoration method to yield semantically meaningful diversity. Moreover, we propose a practical approach for allowing diffusion based image restoration methods to generate meaningfully diverse outputs, while incurring only negligent computational overhead. We conduct extensive user studies to analyze the proposed techniques, and find the strategy of reducing similarity between outputs to be significantly favorable over posterior sampling. Code and examples are available at https://noa-cohen.github.io/MeaningfulDiversityInIR.

The recent emergence of new algorithms for permuting models into functionally equivalent regions of the solution space has shed some light on the complexity of error surfaces, and some promising properties like mode connectivity. However, finding the right permutation is challenging, and current optimization techniques are not differentiable, which makes it difficult to integrate into a gradient-based optimization, and often leads to sub-optimal solutions. In this paper, we propose a Sinkhorn re-basin network with the ability to obtain the transportation plan that better suits a given objective. Unlike the current state-of-art, our method is differentiable and, therefore, easy to adapt to any task within the deep learning domain. Furthermore, we show the advantage of our re-basin method by proposing a new cost function that allows performing incremental learning by exploiting the linear mode connectivity property. The benefit of our method is compared against similar approaches from the literature, under several conditions for both optimal transport finding and linear mode connectivity. The effectiveness of our continual learning method based on re-basin is also shown for several common benchmark datasets, providing experimental results that are competitive with state-of-art results from the literature.

Biophysical modeling, particularly involving partial differential equations (PDEs), offers significant potential for tailoring disease treatment protocols to individual patients. However, the inverse problem-solving aspect of these models presents a substantial challenge, either due to the high computational requirements of model-based approaches or the limited robustness of deep learning (DL) methods. We propose a novel framework that leverages the unique strengths of both approaches in a synergistic manner. Our method incorporates a DL ensemble for initial parameter estimation, facilitating efficient downstream evolutionary sampling initialized with this DL-based prior. We showcase the effectiveness of integrating a rapid deep-learning algorithm with a high-precision evolution strategy in estimating brain tumor cell concentrations from magnetic resonance images. The DL-Prior plays a pivotal role, significantly constraining the effective sampling-parameter space. This reduction results in a fivefold convergence acceleration and a Dice-score of 95%

In applications of diffusion models, controllable generation is of practical significance, but is also challenging. Current methods for controllable generation primarily focus on modifying the score function of diffusion models, while Mean Reverting (MR) Diffusion directly modifies the structure of the stochastic differential equation (SDE), making the incorporation of image conditions simpler and more natural. However, current training-free fast samplers are not directly applicable to MR Diffusion. And thus MR Diffusion requires hundreds of NFEs (number of function evaluations) to obtain high-quality samples. In this paper, we propose a new algorithm named MRS (MR Sampler) to reduce the sampling NFEs of MR Diffusion. We solve the reverse-time SDE and the probability flow ordinary differential equation (PF-ODE) associated with MR Diffusion, and derive semi-analytical solutions. The solutions consist of an analytical function and an integral parameterized by a neural network. Based on this solution, we can generate high-quality samples in fewer steps. Our approach does not require training and supports all mainstream parameterizations, including noise prediction, data prediction and velocity prediction. Extensive experiments demonstrate that MR Sampler maintains high sampling quality with a speedup of 10 to 20 times across ten different image restoration tasks. Our algorithm accelerates the sampling procedure of MR Diffusion, making it more practical in controllable generation.

Motor impairments, frequently caused by neurological incidents like strokes or traumatic brain injuries, present substantial obstacles in rehabilitation therapy. This research aims to elevate the field by optimizing motor imagery classification algorithms within Brain-Computer Interfaces (BCIs). By improving the efficiency of BCIs, we offer a novel approach that holds significant promise for enhancing motor rehabilitation outcomes. Utilizing unsupervised techniques for dimensionality reduction, namely Uniform Manifold Approximation and Projection (UMAP) coupled with K-Nearest Neighbors (KNN), we evaluate the necessity of employing supervised methods such as Long Short-Term Memory (LSTM) and Convolutional Neural Networks (CNNs) for classification tasks. Importantly, participants who exhibited high KNN scores following UMAP dimensionality reduction also achieved high accuracy in supervised deep learning (DL) models. Due to individualized model requirements and massive neural training data, dimensionality reduction becomes an effective preprocessing step that minimizes the need for extensive data labeling and supervised deep learning techniques. This approach has significant implications not only for targeted therapies in motor dysfunction but also for addressing regulatory, safety, and reliability concerns in the rapidly evolving BCI field.

Plug-and-play Image Restoration (IR) has been widely recognized as a flexible and interpretable method for solving various inverse problems by utilizing any off-the-shelf denoiser as the implicit image prior. However, most existing methods focus on discriminative Gaussian denoisers. Although diffusion models have shown impressive performance for high-quality image synthesis, their potential to serve as a generative denoiser prior to the plug-and-play IR methods remains to be further explored. While several other attempts have been made to adopt diffusion models for image restoration, they either fail to achieve satisfactory results or typically require an unacceptable number of Neural Function Evaluations (NFEs) during inference. This paper proposes DiffPIR, which integrates the traditional plug-and-play method into the diffusion sampling framework. Compared to plug-and-play IR methods that rely on discriminative Gaussian denoisers, DiffPIR is expected to inherit the generative ability of diffusion models. Experimental results on three representative IR tasks, including super-resolution, image deblurring, and inpainting, demonstrate that DiffPIR achieves state-of-the-art performance on both the FFHQ and ImageNet datasets in terms of reconstruction faithfulness and perceptual quality with no more than 100 NFEs. The source code is available at {https://github.com/yuanzhi-zhu/DiffPIR}

Safety fine-tuning algorithms are commonly used to fine-tune language models to reduce harmful outputs, but the exact internal mechanisms of how those models achieve this remain unclear. In studying direct preference optimisation (DPO) for toxicity reduction, current explanations claim that DPO works by dampening the most toxic MLP neurons to learn an offset to avert toxic regions in the residual stream. However, by ablating the most toxic neurons and applying activation patching, we find this explanation incomplete. By projecting neuron activation changes onto a toxicity probe, we find that only 31.8\% of toxicity reduction comes from dampened toxic neurons. Instead, DPO reduces toxicity by accumulating effects across multiple neuron groups, both reducing writing in the toxic direction and promoting anti-toxicity in the residual stream. Moreover, DPO gives noisy adjustments to neuron activations, with many neurons actually increasing toxicity. This indicates that DPO is a balancing process between opposing neuron effects to achieve toxicity reduction.

DreamFusion has recently demonstrated the utility of a pre-trained text-to-image diffusion model to optimize Neural Radiance Fields (NeRF), achieving remarkable text-to-3D synthesis results. However, the method has two inherent limitations: (a) extremely slow optimization of NeRF and (b) low-resolution image space supervision on NeRF, leading to low-quality 3D models with a long processing time. In this paper, we address these limitations by utilizing a two-stage optimization framework. First, we obtain a coarse model using a low-resolution diffusion prior and accelerate with a sparse 3D hash grid structure. Using the coarse representation as the initialization, we further optimize a textured 3D mesh model with an efficient differentiable renderer interacting with a high-resolution latent diffusion model. Our method, dubbed Magic3D, can create high quality 3D mesh models in 40 minutes, which is 2x faster than DreamFusion (reportedly taking 1.5 hours on average), while also achieving higher resolution. User studies show 61.7% raters to prefer our approach over DreamFusion. Together with the image-conditioned generation capabilities, we provide users with new ways to control 3D synthesis, opening up new avenues to various creative applications.

Image restoration is a low-level vision task which is to restore degraded images to noise-free images. With the success of deep neural networks, the convolutional neural networks surpass the traditional restoration methods and become the mainstream in the computer vision area. To advance the performanceof denoising algorithms, we propose a blind real image denoising network (SRMNet) by employing a hierarchical architecture improved from U-Net. Specifically, we use a selective kernel with residual block on the hierarchical structure called M-Net to enrich the multi-scale semantic information. Furthermore, our SRMNet has competitive performance results on two synthetic and two real-world noisy datasets in terms of quantitative metrics and visual quality. The source code and pretrained model are available at https://github.com/TentativeGitHub/SRMNet.

The Evidence Lower Bound (ELBO) is a quantity that plays a key role in variational inference. It can also be used as a criterion in model selection. However, though extremely popular in practice in the variational Bayes community, there has never been a general theoretic justification for selecting based on the ELBO. In this paper, we show that the ELBO maximization strategy has strong theoretical guarantees, and is robust to model misspecification while most works rely on the assumption that one model is correctly specified. We illustrate our theoretical results by an application to the selection of the number of principal components in probabilistic PCA.

Fairness in image restoration tasks is the desire to treat different sub-groups of images equally well. Existing definitions of fairness in image restoration are highly restrictive. They consider a reconstruction to be a correct outcome for a group (e.g., women) only if it falls within the group's set of ground truth images (e.g., natural images of women); otherwise, it is considered entirely incorrect. Consequently, such definitions are prone to controversy, as errors in image restoration can manifest in various ways. In this work we offer an alternative approach towards fairness in image restoration, by considering the Group Perceptual Index (GPI), which we define as the statistical distance between the distribution of the group's ground truth images and the distribution of their reconstructions. We assess the fairness of an algorithm by comparing the GPI of different groups, and say that it achieves perfect Perceptual Fairness (PF) if the GPIs of all groups are identical. We motivate and theoretically study our new notion of fairness, draw its connection to previous ones, and demonstrate its utility on state-of-the-art face image super-resolution algorithms.

Quantitative susceptibility maps from magnetic resonance images can provide both prognostic and diagnostic information in multiple sclerosis, a neurodegenerative disease characterized by the formation of lesions in white matter brain tissue. In particular, susceptibility maps provide adequate contrast to distinguish between "rim" lesions, surrounded by deposited paramagnetic iron, and "non-rim" lesion types. These paramagnetic rim lesions (PRLs) are an emerging biomarker in multiple sclerosis. Much effort has been devoted to both detection and segmentation of such lesions to monitor longitudinal change. As paramagnetic rim lesions are rare, addressing this problem requires confronting the class imbalance between rim and non-rim lesions. We produce synthetic quantitative susceptibility maps of paramagnetic rim lesions and show that inclusion of such synthetic data improves classifier performance and provide a multi-channel extension to generate accompanying contrasts and probabilistic segmentation maps. We exploit the projection capability of our trained generative network to demonstrate a novel denoising approach that allows us to train on ambiguous rim cases and substantially increase the minority class. We show that both synthetic lesion synthesis and our proposed rim lesion label denoising method best approximate the unseen rim lesion distribution and improve detection in a clinically interpretable manner. We release our code and generated data at https://github.com/agr78/PRLx-GAN upon publication.

Multi-task image restoration has gained significant interest due to its inherent versatility and efficiency compared to its single-task counterpart. Despite its potential, performance degradation is observed with an increase in the number of tasks, primarily attributed to the distinct nature of each restoration task. Addressing this challenge, we introduce \textbf{DINO-IR}, a novel multi-task image restoration approach leveraging robust features extracted from DINOv2. Our empirical analysis shows that while shallow features of DINOv2 capture rich low-level image characteristics, the deep features ensure a robust semantic representation insensitive to degradations while preserving high-frequency contour details. Building on these features, we devise specialized components, including multi-layer semantic fusion module, DINO-Restore adaption and fusion module, and DINO perception contrastive loss, to integrate DINOv2 features into the restoration paradigm. Equipped with the aforementioned components, our DINO-IR performs favorably against existing multi-task image restoration approaches in various tasks by a large margin, indicating the superiority and necessity of reinforcing the robust features for multi-task image restoration.

Underwater image restoration algorithms seek to restore the color, contrast, and appearance of a scene that is imaged underwater. They are a critical tool in applications ranging from marine ecology and aquaculture to underwater construction and archaeology. While existing pixel-domain diffusion-based image restoration approaches are effective at restoring simple scenes with limited depth variation, they are computationally intensive and often generate unrealistic artifacts when applied to scenes with complex geometry and significant depth variation. In this work we overcome these limitations by combining a novel network architecture (SLURPP) with an accurate synthetic data generation pipeline. SLURPP combines pretrained latent diffusion models -- which encode strong priors on the geometry and depth of scenes -- with an explicit scene decomposition -- which allows one to model and account for the effects of light attenuation and backscattering. To train SLURPP we design a physics-based underwater image synthesis pipeline that applies varied and realistic underwater degradation effects to existing terrestrial image datasets. This approach enables the generation of diverse training data with dense medium/degradation annotations. We evaluate our method extensively on both synthetic and real-world benchmarks and demonstrate state-of-the-art performance. Notably, SLURPP is over 200X faster than existing diffusion-based methods while offering ~ 3 dB improvement in PSNR on synthetic benchmarks. It also offers compelling qualitative improvements on real-world data. Project website https://tianfwang.github.io/slurpp/.

Brain simulation builds dynamical models to mimic the structure and functions of the brain, while brain-inspired computing (BIC) develops intelligent systems by learning from the structure and functions of the brain. The two fields are intertwined and should share a common programming framework to facilitate each other's development. However, none of the existing software in the fields can achieve this goal, because traditional brain simulators lack differentiability for training, while existing deep learning (DL) frameworks fail to capture the biophysical realism and complexity of brain dynamics. In this paper, we introduce BrainPy, a differentiable brain simulator developed using JAX and XLA, with the aim of bridging the gap between brain simulation and BIC. BrainPy expands upon the functionalities of JAX, a powerful AI framework, by introducing complete capabilities for flexible, efficient, and scalable brain simulation. It offers a range of sparse and event-driven operators for efficient and scalable brain simulation, an abstraction for managing the intricacies of synaptic computations, a modular and flexible interface for constructing multi-scale brain models, and an object-oriented just-in-time compilation approach to handle the memory-intensive nature of brain dynamics. We showcase the efficiency and scalability of BrainPy on benchmark tasks, highlight its differentiable simulation for biologically plausible spiking models, and discuss its potential to support research at the intersection of brain simulation and BIC.

Conventional Computed Tomography (CT) methods require large numbers of noise-free projections for accurate density reconstructions, limiting their applicability to the more complex class of Cone Beam Geometry CT (CBCT) reconstruction. Recently, deep learning methods have been proposed to overcome these limitations, with methods based on neural fields (NF) showing strong performance, by approximating the reconstructed density through a continuous-in-space coordinate based neural network. Our focus is on improving such methods, however, unlike previous work, which requires training an NF from scratch for each new set of projections, we instead propose to leverage anatomical consistencies over different scans by training a single conditional NF on a dataset of projections. We propose a novel conditioning method where local modulations are modeled per patient as a field over the input domain through a Neural Modulation Field (NMF). The resulting Conditional Cone Beam Neural Tomography (CondCBNT) shows improved performance for both high and low numbers of available projections on noise-free and noisy data.

Image restoration is a long-standing low-level vision problem that aims to restore high-quality images from low-quality images (e.g., downscaled, noisy and compressed images). While state-of-the-art image restoration methods are based on convolutional neural networks, few attempts have been made with Transformers which show impressive performance on high-level vision tasks. In this paper, we propose a strong baseline model SwinIR for image restoration based on the Swin Transformer. SwinIR consists of three parts: shallow feature extraction, deep feature extraction and high-quality image reconstruction. In particular, the deep feature extraction module is composed of several residual Swin Transformer blocks (RSTB), each of which has several Swin Transformer layers together with a residual connection. We conduct experiments on three representative tasks: image super-resolution (including classical, lightweight and real-world image super-resolution), image denoising (including grayscale and color image denoising) and JPEG compression artifact reduction. Experimental results demonstrate that SwinIR outperforms state-of-the-art methods on different tasks by up to 0.14\sim0.45dB, while the total number of parameters can be reduced by up to 67%.

Functional magnetic resonance imaging (fMRI) is an indispensable tool in modern neuroscience, providing a non-invasive window into whole-brain dynamics at millimeter-scale spatial resolution. However, fMRI is constrained by issues such as high operation costs and immobility. With the rapid advancements in cross-modality synthesis and brain decoding, the use of deep neural networks has emerged as a promising solution for inferring whole-brain, high-resolution fMRI features directly from electroencephalography (EEG), a more widely accessible and portable neuroimaging modality. Nonetheless, the complex projection from neural activity to fMRI hemodynamic responses and the spatial ambiguity of EEG pose substantial challenges both in modeling and interpretability. Relatively few studies to date have developed approaches for EEG-fMRI translation, and although they have made significant strides, the inference of fMRI signals in a given study has been limited to a small set of brain areas and to a single condition (i.e., either resting-state or a specific task). The capability to predict fMRI signals in other brain areas, as well as to generalize across conditions, remain critical gaps in the field. To tackle these challenges, we introduce a novel and generalizable framework: NeuroBOLT, i.e., Neuro-to-BOLD Transformer, which leverages multi-dimensional representation learning from temporal, spatial, and spectral domains to translate raw EEG data to the corresponding fMRI activity signals across the brain. Our experiments demonstrate that NeuroBOLT effectively reconstructs unseen resting-state fMRI signals from primary sensory, high-level cognitive areas, and deep subcortical brain regions, achieving state-of-the-art accuracy with the potential to generalize across varying conditions and sites, which significantly advances the integration of these two modalities.

Cerebrovascular disease often requires multiple imaging modalities for accurate diagnosis, treatment, and monitoring. Computed Tomography Angiography (CTA) and Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) are two common non-invasive angiography techniques, each with distinct strengths in accessibility, safety, and diagnostic accuracy. While CTA is more widely used in acute stroke due to its faster acquisition times and higher diagnostic accuracy, TOF-MRA is preferred for its safety, as it avoids radiation exposure and contrast agent-related health risks. Despite the predominant role of CTA in clinical workflows, there is a scarcity of open-source CTA data, limiting the research and development of AI models for tasks such as large vessel occlusion detection and aneurysm segmentation. This study explores diffusion-based image-to-image translation models to generate synthetic CTA images from TOF-MRA input. We demonstrate the modality conversion from TOF-MRA to CTA and show that diffusion models outperform a traditional U-Net-based approach. Our work compares different state-of-the-art diffusion architectures and samplers, offering recommendations for optimal model performance in this cross-modality translation task.

Despite the ever-increasing interest in applying deep learning (DL) models to medical imaging, the typical scarcity and imbalance of medical datasets can severely impact the performance of DL models. The generation of synthetic data that might be freely shared without compromising patient privacy is a well-known technique for addressing these difficulties. Inpainting algorithms are a subset of DL generative models that can alter one or more regions of an input image while matching its surrounding context and, in certain cases, non-imaging input conditions. Although the majority of inpainting techniques for medical imaging data use generative adversarial networks (GANs), the performance of these algorithms is frequently suboptimal due to their limited output variety, a problem that is already well-known for GANs. Denoising diffusion probabilistic models (DDPMs) are a recently introduced family of generative networks that can generate results of comparable quality to GANs, but with diverse outputs. In this paper, we describe a DDPM to execute multiple inpainting tasks on 2D axial slices of brain MRI with various sequences, and present proof-of-concept examples of its performance in a variety of evaluation scenarios. Our model and a public online interface to try our tool are available at: https://github.com/Mayo-Radiology-Informatics-Lab/MBTI

The landscape of computational building blocks of efficient image restoration architectures is dominated by a combination of convolutional processing and various attention mechanisms. However, convolutional filters, while efficient, are inherently local and therefore struggle with modeling long-range dependencies in images. In contrast, attention excels at capturing global interactions between arbitrary image regions, but suffers from a quadratic cost in image dimension. In this work, we propose Serpent, an efficient architecture for high-resolution image restoration that combines recent advances in state space models (SSMs) with multi-scale signal processing in its core computational block. SSMs, originally introduced for sequence modeling, can maintain a global receptive field with a favorable linear scaling in input size. We propose a novel hierarchical architecture inspired by traditional signal processing principles, that converts the input image into a collection of sequences and processes them in a multi-scale fashion. Our experimental results demonstrate that Serpent can achieve reconstruction quality on par with state-of-the-art techniques, while requiring orders of magnitude less compute (up to 150 fold reduction in FLOPS) and a factor of up to 5times less GPU memory while maintaining a compact model size. The efficiency gains achieved by Serpent are especially notable at high image resolutions.

Segmentation of blood vessels in murine cerebral 3D OCTA images is foundational for in vivo quantitative analysis of the effects of neurovascular disorders, such as stroke or Alzheimer's, on the vascular network. However, to accurately segment blood vessels with state-of-the-art deep learning methods, a vast amount of voxel-level annotations is required. Since cerebral 3D OCTA images are typically plagued by artifacts and generally have a low signal-to-noise ratio, acquiring manual annotations poses an especially cumbersome and time-consuming task. To alleviate the need for manual annotations, we propose utilizing synthetic data to supervise segmentation algorithms. To this end, we extract patches from vessel graphs and transform them into synthetic cerebral 3D OCTA images paired with their matching ground truth labels by simulating the most dominant 3D OCTA artifacts. In extensive experiments, we demonstrate that our approach achieves competitive results, enabling annotation-free blood vessel segmentation in cerebral 3D OCTA images.

Existing image restoration methods mostly leverage the posterior distribution of natural images. However, they often assume known degradation and also require supervised training, which restricts their adaptation to complex real applications. In this work, we propose the Generative Diffusion Prior (GDP) to effectively model the posterior distributions in an unsupervised sampling manner. GDP utilizes a pre-train denoising diffusion generative model (DDPM) for solving linear inverse, non-linear, or blind problems. Specifically, GDP systematically explores a protocol of conditional guidance, which is verified more practical than the commonly used guidance way. Furthermore, GDP is strength at optimizing the parameters of degradation model during the denoising process, achieving blind image restoration. Besides, we devise hierarchical guidance and patch-based methods, enabling the GDP to generate images of arbitrary resolutions. Experimentally, we demonstrate GDP's versatility on several image datasets for linear problems, such as super-resolution, deblurring, inpainting, and colorization, as well as non-linear and blind issues, such as low-light enhancement and HDR image recovery. GDP outperforms the current leading unsupervised methods on the diverse benchmarks in reconstruction quality and perceptual quality. Moreover, GDP also generalizes well for natural images or synthesized images with arbitrary sizes from various tasks out of the distribution of the ImageNet training set.

Dynamic imaging addresses the recovery of a time-varying 2D or 3D object at each time instant using its undersampled measurements. In particular, in the case of dynamic tomography, only a single projection at a single view angle may be available at a time, making the problem severely ill-posed. In this work, we propose an approach, RED-PSM, which combines for the first time two powerful techniques to address this challenging imaging problem. The first, are partially separable models, which have been used to efficiently introduce a low-rank prior for the spatio-temporal object. The second is the recent Regularization by Denoising (RED), which provides a flexible framework to exploit the impressive performance of state-of-the-art image denoising algorithms, for various inverse problems. We propose a partially separable objective with RED and a computationally efficient and scalable optimization scheme with variable splitting and ADMM. Theoretical analysis proves the convergence of our objective to a value corresponding to a stationary point satisfying the first-order optimality conditions. Convergence is accelerated by a particular projection-domain-based initialization. We demonstrate the performance and computational improvements of our proposed RED-PSM with a learned image denoiser by comparing it to a recent deep-prior-based method known as TD-DIP. Although the main focus is on dynamic tomography, we also show the performance advantages of RED-PSM in a cardiac dynamic MRI setting.

Bayesian optimization (BO) has established itself as a leading strategy for efficiently optimizing expensive-to-evaluate functions. Existing BO methods mostly rely on Gaussian process (GP) surrogate models and are not applicable to (doubly-stochastic) Gaussian Cox processes, where the observation process is modulated by a latent intensity function modeled as a GP. In this paper, we propose a novel maximum a posteriori inference of Gaussian Cox processes. It leverages the Laplace approximation and change of kernel technique to transform the problem into a new reproducing kernel Hilbert space, where it becomes more tractable computationally. It enables us to obtain both a functional posterior of the latent intensity function and the covariance of the posterior, thus extending existing works that often focus on specific link functions or estimating the posterior mean. Using the result, we propose a BO framework based on the Gaussian Cox process model and further develop a Nystr\"om approximation for efficient computation. Extensive evaluations on various synthetic and real-world datasets demonstrate significant improvement over state-of-the-art inference solutions for Gaussian Cox processes, as well as effective BO with a wide range of acquisition functions designed through the underlying Gaussian Cox process model.

We study the use of amortized optimization to predict optimal transport (OT) maps from the input measures, which we call Meta OT. This helps repeatedly solve similar OT problems between different measures by leveraging the knowledge and information present from past problems to rapidly predict and solve new problems. Otherwise, standard methods ignore the knowledge of the past solutions and suboptimally re-solve each problem from scratch. We instantiate Meta OT models in discrete and continuous settings between grayscale images, spherical data, classification labels, and color palettes and use them to improve the computational time of standard OT solvers. Our source code is available at http://github.com/facebookresearch/meta-ot

Recorrupted-to-Recorrupted (R2R) has emerged as a methodology for training deep networks for image restoration in a self-supervised manner from noisy measurement data alone, demonstrating equivalence in expectation to the supervised squared loss in the case of Gaussian noise. However, its effectiveness with non-Gaussian noise remains unexplored. In this paper, we propose Generalized R2R (GR2R), extending the R2R framework to handle a broader class of noise distribution as additive noise like log-Rayleigh and address the natural exponential family including Poisson and Gamma noise distributions, which play a key role in many applications including low-photon imaging and synthetic aperture radar. We show that the GR2R loss is an unbiased estimator of the supervised loss and that the popular Stein's unbiased risk estimator can be seen as a special case. A series of experiments with Gaussian, Poisson, and Gamma noise validate GR2R's performance, showing its effectiveness compared to other self-supervised methods.

Diffusion models have recently achieved success in solving Bayesian inverse problems with learned data priors. Current methods build on top of the diffusion sampling process, where each denoising step makes small modifications to samples from the previous step. However, this process struggles to correct errors from earlier sampling steps, leading to worse performance in complicated nonlinear inverse problems, such as phase retrieval. To address this challenge, we propose a new method called Decoupled Annealing Posterior Sampling (DAPS) that relies on a novel noise annealing process. Specifically, we decouple consecutive steps in a diffusion sampling trajectory, allowing them to vary considerably from one another while ensuring their time-marginals anneal to the true posterior as we reduce noise levels. This approach enables the exploration of a larger solution space, improving the success rate for accurate reconstructions. We demonstrate that DAPS significantly improves sample quality and stability across multiple image restoration tasks, particularly in complicated nonlinear inverse problems. For example, we achieve a PSNR of 30.72dB on the FFHQ 256 dataset for phase retrieval, which is an improvement of 9.12dB compared to existing methods.

We present a flow-based approach to the optimal transport (OT) problem between two continuous distributions pi_0,pi_1 on R^d, of minimizing a transport cost E[c(X_1-X_0)] in the set of couplings (X_0,X_1) whose marginal distributions on X_0,X_1 equals pi_0,pi_1, respectively, where c is a cost function. Our method iteratively constructs a sequence of neural ordinary differentiable equations (ODE), each learned by solving a simple unconstrained regression problem, which monotonically reduce the transport cost while automatically preserving the marginal constraints. This yields a monotonic interior approach that traverses inside the set of valid couplings to decrease the transport cost, which distinguishes itself from most existing approaches that enforce the coupling constraints from the outside. The main idea of the method draws from rectified flow, a recent approach that simultaneously decreases the whole family of transport costs induced by convex functions c (and is hence multi-objective in nature), but is not tailored to minimize a specific transport cost. Our method is a single-object variant of rectified flow that guarantees to solve the OT problem for a fixed, user-specified convex cost function c.