Anatomy-guided fiber trajectory distribution estimation for cranial nerves tractography

Diffusion MRI tractography is an important tool for identifying and analyzing the intracranial course of cranial nerves (CNs). However, the complex environment of the skull base leads to ambiguous spatial correspondence between diffusion directions and fiber geometry, and existing diffusion tractography methods of CNs identification are prone to producing erroneous trajectories and missing true positive connections. To overcome the above challenge, we propose a novel CNs identification framework with anatomy-guided fiber trajectory distribution, which incorporates anatomical shape prior knowledge during the process of CNs tracing to build diffusion tensor vector fields. We introduce higher-order streamline differential equations for continuous flow field representations to directly characterize the fiber trajectory distribution of CNs from the tract-based level. The experimental results on the vivo HCP dataset and the clinical MDM dataset demonstrate that the proposed method reduces false-positive fiber production compared to competing methods and produces reconstructed CNs (i.e. CN II, CN III, CN V, and CN VII/VIII) that are judged to better correspond to the known anatomy.

MambaMIR: An Arbitrary-Masked Mamba for Joint Medical Image Reconstruction and Uncertainty Estimation

The recent Mamba model has shown remarkable adaptability for visual representation learning, including in medical imaging tasks. This study introduces MambaMIR, a Mamba-based model for medical image reconstruction, as well as its Generative Adversarial Network-based variant, MambaMIR-GAN. Our proposed MambaMIR inherits several advantages, such as linear complexity, global receptive fields, and dynamic weights, from the original Mamba model. The innovated arbitrary-mask mechanism effectively adapt Mamba to our image reconstruction task, providing randomness for subsequent Monte Carlo-based uncertainty estimation. Experiments conducted on various medical image reconstruction tasks, including fast MRI and SVCT, which cover anatomical regions such as the knee, chest, and abdomen, have demonstrated that MambaMIR and MambaMIR-GAN achieve comparable or superior reconstruction results relative to state-of-the-art methods. Additionally, the estimated uncertainty maps offer further insights into the reliability of the reconstruction quality. The code is publicly available at https://github.com/ayanglab/MambaMIR.

HAMLET: Graph Transformer Neural Operator for Partial Differential Equations

We present a novel graph transformer framework, HAMLET, designed to address the challenges in solving partial differential equations (PDEs) using neural networks. The framework uses graph transformers with modular input encoders to directly incorporate differential equation information into the solution process. This modularity enhances parameter correspondence control, making HAMLET adaptable to PDEs of arbitrary geometries and varied input formats. Notably, HAMLET scales effectively with increasing data complexity and noise, showcasing its robustness. HAMLET is not just tailored to a single type of physical simulation, but can be applied across various domains. Moreover, it boosts model resilience and performance, especially in scenarios with limited data. We demonstrate, through extensive experiments, that our framework is capable of outperforming current techniques for PDEs.

Data and Physics driven Deep Learning Models for Fast MRI Reconstruction: Fundamentals and Methodologies

Magnetic Resonance Imaging (MRI) is a pivotal clinical diagnostic tool, yet its extended scanning times often compromise patient comfort and image quality, especially in volumetric, temporal and quantitative scans. This review elucidates recent advances in MRI acceleration via data and physics-driven models, leveraging techniques from algorithm unrolling models, enhancement-based models, and plug-and-play models to emergent full spectrum of generative models. We also explore the synergistic integration of data models with physics-based insights, encompassing the advancements in multi-coil hardware accelerations like parallel imaging and simultaneous multi-slice imaging, and the optimization of sampling patterns. We then focus on domain-specific challenges and opportunities, including image redundancy exploitation, image integrity, evaluation metrics, data heterogeneity, and model generalization. This work also discusses potential solutions and future research directions, emphasizing the role of data harmonization, and federated learning for further improving the general applicability and performance of these methods in MRI reconstruction.

Multi-Agent Probabilistic Ensembles with Trajectory Sampling for Connected Autonomous Vehicles

Autonomous Vehicles (AVs) have attracted significant attention in recent years and Reinforcement Learning (RL) has shown remarkable performance in improving the autonomy of vehicles. In that regard, the widely adopted Model-Free RL (MFRL) promises to solve decision-making tasks in connected AVs (CAVs), contingent on the readiness of a significant amount of data samples for training. Nevertheless, it might be infeasible in practice and possibly lead to learning instability. In contrast, Model-Based RL (MBRL) manifests itself in sample-efficient learning, but the asymptotic performance of MBRL might lag behind the state-of-the-art MFRL algorithms. Furthermore, most studies for CAVs are limited to the decision-making of a single AV only, thus underscoring the performance due to the absence of communications. In this study, we try to address the decision-making problem of multiple CAVs with limited communications and propose a decentralized Multi-Agent Probabilistic Ensembles with Trajectory Sampling algorithm MA-PETS. In particular, in order to better capture the uncertainty of the unknown environment, MA-PETS leverages Probabilistic Ensemble (PE) neural networks to learn from communicated samples among neighboring CAVs. Afterwards, MA-PETS capably develops Trajectory Sampling (TS)-based model-predictive control for decision-making. On this basis, we derive the multi-agent group regret bound affected by the number of agents within the communication range and mathematically validate that incorporating effective information exchange among agents into the multi-agent learning scheme contributes to reducing the group regret bound in the worst case. Finally, we empirically demonstrate the superiority of MA-PETS in terms of the sample efficiency comparable to MFBL.

High-Resolution Reference Image Assisted Volumetric Super-Resolution of Cardiac Diffusion Weighted Imaging

Diffusion Tensor Cardiac Magnetic Resonance (DT-CMR) is the only in vivo method to non-invasively examine the microstructure of the human heart. Current research in DT-CMR aims to improve the understanding of how the cardiac microstructure relates to the macroscopic function of the healthy heart as well as how microstructural dysfunction contributes to disease. To get the final DT-CMR metrics, we need to acquire diffusion weighted images of at least 6 directions. However, due to DWI's low signal-to-noise ratio, the standard voxel size is quite big on the scale for microstructures. In this study, we explored the potential of deep-learning-based methods in improving the image quality volumetrically (x4 in all dimensions). This study proposed a novel framework to enable volumetric super-resolution, with an additional model input of high-resolution b0 DWI. We demonstrated that the additional input could offer higher super-resolved image quality. Going beyond, the model is also able to super-resolve DWIs of unseen b-values, proving the model framework's generalizability for cardiac DWI superresolution. In conclusion, we would then recommend giving the model a high-resolution reference image as an additional input to the low-resolution image for training and inference to guide all super-resolution frameworks for parametric imaging where a reference image is available.

Beyond U: Making Diffusion Models Faster & Lighter

Diffusion models are a family of generative models that yield record-breaking performance in tasks such as image synthesis, video generation, and molecule design. Despite their capabilities, their efficiency, especially in the reverse denoising process, remains a challenge due to slow convergence rates and high computational costs. In this work, we introduce an approach that leverages continuous dynamical systems to design a novel denoising network for diffusion models that is more parameter-efficient, exhibits faster convergence, and demonstrates increased noise robustness. Experimenting with denoising probabilistic diffusion models, our framework operates with approximately a quarter of the parameters and 30% of the Floating Point Operations (FLOPs) compared to standard U-Nets in Denoising Diffusion Probabilistic Models (DDPMs). Furthermore, our model is up to 70% faster in inference than the baseline models when measured in equal conditions while converging to better quality solutions.

Style Transfer and Self-Supervised Learning Powered Myocardium Infarction Super-Resolution Segmentation

This study proposes a pipeline that incorporates a novel style transfer model and a simultaneous super-resolution and segmentation model. The proposed pipeline aims to enhance diffusion tensor imaging (DTI) images by translating them into the late gadolinium enhancement (LGE) domain, which offers a larger amount of data with high-resolution and distinct highlighting of myocardium infarction (MI) areas. Subsequently, the segmentation task is performed on the LGE style image. An end-to-end super-resolution segmentation model is introduced to generate high-resolution mask from low-resolution LGE style DTI image. Further, to enhance the performance of the model, a multi-task self-supervised learning strategy is employed to pre-train the super-resolution segmentation model, allowing it to acquire more representative knowledge and improve its segmentation performance after fine-tuning. https: github.com/wlc2424762917/Med_Img

Efficient Post-processing of Diffusion Tensor Cardiac Magnetic Imaging Using Texture-conserving Deformable Registration

Diffusion tensor based cardiac magnetic resonance (DT-CMR) is a method capable of providing non-invasive measurements of myocardial microstructure. Image registration is essential to correct image shifts due to intra and inter breath-hold motion. Registration is challenging in DT-CMR due to the low signal-to-noise and various contrasts induced by the diffusion encoding in the myocardial and surrounding organs. Traditional deformable registration destroys the texture information while rigid registration inefficiently discards frames with local deformation. In this study, we explored the possibility of deep learning-based deformable registration on DT- CMR. Based on the noise suppression using low-rank features and diffusion encoding suppression using variational auto encoder-decoder, a B-spline based registration network extracted the displacement fields and maintained the texture features of DT-CMR. In this way, our method improved the efficiency of frame utilization, manual cropping, and computational speed.

Is attention all you need in medical image analysis? A review

Medical imaging is a key component in clinical diagnosis, treatment planning and clinical trial design, accounting for almost 90% of all healthcare data. CNNs achieved performance gains in medical image analysis (MIA) over the last years. CNNs can efficiently model local pixel interactions and be trained on small-scale MI data. The main disadvantage of typical CNN models is that they ignore global pixel relationships within images, which limits their generalisation ability to understand out-of-distribution data with different 'global' information. The recent progress of Artificial Intelligence gave rise to Transformers, which can learn global relationships from data. However, full Transformer models need to be trained on large-scale data and involve tremendous computational complexity. Attention and Transformer compartments (Transf/Attention) which can well maintain properties for modelling global relationships, have been proposed as lighter alternatives of full Transformers. Recently, there is an increasing trend to co-pollinate complementary local-global properties from CNN and Transf/Attention architectures, which led to a new era of hybrid models. The past years have witnessed substantial growth in hybrid CNN-Transf/Attention models across diverse MIA problems. In this systematic review, we survey existing hybrid CNN-Transf/Attention models, review and unravel key architectural designs, analyse breakthroughs, and evaluate current and future opportunities as well as challenges. We also introduced a comprehensive analysis framework on generalisation opportunities of scientific and clinical impact, based on which new data-driven domain generalisation and adaptation methods can be stimulated.