Deep End-to-end Adaptive k-Space Sampling, Reconstruction, and Registration for Dynamic MRI

Dynamic MRI enables a range of clinical applications, including cardiac function assessment, organ motion tracking, and radiotherapy guidance. However, fully sampling the dynamic k-space data is often infeasible due to time constraints and physiological motion such as respiratory and cardiac motion. This necessitates undersampling, which degrades the quality of reconstructed images. Poor image quality not only hinders visualization but also impairs the estimation of deformation fields, crucial for registering dynamic (moving) images to a static reference image. This registration enables tasks such as motion correction, treatment planning, and quantitative analysis in applications like cardiac imaging and MR-guided radiotherapy. To overcome the challenges posed by undersampling and motion, we introduce an end-to-end deep learning (DL) framework that integrates adaptive dynamic k-space sampling, reconstruction, and registration. Our approach begins with a DL-based adaptive sampling strategy, optimizing dynamic k-space acquisition to capture the most relevant data for each specific case. This is followed by a DL-based reconstruction module that produces images optimized for accurate deformation field estimation from the undersampled moving data. Finally, a registration module estimates the deformation fields aligning the reconstructed dynamic images with a static reference. The proposed framework is independent of specific reconstruction and registration modules allowing for plug-and-play integration of these components. The entire framework is jointly trained using a combination of supervised and unsupervised loss functions, enabling end-to-end optimization for improved performance across all components. Through controlled experiments and ablation studies, we validate each component, demonstrating that each choice contributes to robust motion estimation from undersampled dynamic data.

CaPo: Cooperative Plan Optimization for Efficient Embodied Multi-Agent Cooperation

In this work, we address the cooperation problem among large language model (LLM) based embodied agents, where agents must cooperate to achieve a common goal. Previous methods often execute actions extemporaneously and incoherently, without long-term strategic and cooperative planning, leading to redundant steps, failures, and even serious repercussions in complex tasks like search-and-rescue missions where discussion and cooperative plan are crucial. To solve this issue, we propose Cooperative Plan Optimization (CaPo) to enhance the cooperation efficiency of LLM-based embodied agents. Inspired by human cooperation schemes, CaPo improves cooperation efficiency with two phases: 1) meta-plan generation, and 2) progress-adaptive meta-plan and execution. In the first phase, all agents analyze the task, discuss, and cooperatively create a meta-plan that decomposes the task into subtasks with detailed steps, ensuring a long-term strategic and coherent plan for efficient coordination. In the second phase, agents execute tasks according to the meta-plan and dynamically adjust it based on their latest progress (e.g., discovering a target object) through multi-turn discussions. This progress-based adaptation eliminates redundant actions, improving the overall cooperation efficiency of agents. Experimental results on the ThreeDworld Multi-Agent Transport and Communicative Watch-And-Help tasks demonstrate that CaPo achieves much higher task completion rate and efficiency compared with state-of-the-arts.

Deep Multi-contrast Cardiac MRI Reconstruction via vSHARP with Auxiliary Refinement Network

Cardiac MRI (CMRI) is a cornerstone imaging modality that provides in-depth insights into cardiac structure and function. Multi-contrast CMRI (MCCMRI), which acquires sequences with varying contrast weightings, significantly enhances diagnostic capabilities by capturing a wide range of cardiac tissue characteristics. However, MCCMRI is often constrained by lengthy acquisition times and susceptibility to motion artifacts. To mitigate these challenges, accelerated imaging techniques that use k-space undersampling via different sampling schemes at acceleration factors have been developed to shorten scan durations. In this context, we propose a deep learning-based reconstruction method for 2D dynamic multi-contrast, multi-scheme, and multi-acceleration MRI. Our approach integrates the state-of-the-art vSHARP model, which utilizes half-quadratic variable splitting and ADMM optimization, with a Variational Network serving as an Auxiliary Refinement Network (ARN) to better adapt to the diverse nature of MCCMRI data. Specifically, the subsampled k-space data is fed into the ARN, which produces an initial prediction for the denoising step used by vSHARP. This, along with the subsampled k-space, is then used by vSHARP to generate high-quality 2D sequence predictions. Our method outperforms traditional reconstruction techniques and other vSHARP-based models.

Space-Time Continuous PDE Forecasting using Equivariant Neural Fields

Recently, Conditional Neural Fields (NeFs) have emerged as a powerful modelling paradigm for PDEs, by learning solutions as flows in the latent space of the Conditional NeF. Although benefiting from favourable properties of NeFs such as grid-agnosticity and space-time-continuous dynamics modelling, this approach limits the ability to impose known constraints of the PDE on the solutions -- e.g. symmetries or boundary conditions -- in favour of modelling flexibility. Instead, we propose a space-time continuous NeF-based solving framework that - by preserving geometric information in the latent space - respects known symmetries of the PDE. We show that modelling solutions as flows of pointclouds over the group of interest $G$ improves generalization and data-efficiency. We validated that our framework readily generalizes to unseen spatial and temporal locations, as well as geometric transformations of the initial conditions - where other NeF-based PDE forecasting methods fail - and improve over baselines in a number of challenging geometries.

Domain Adaptation with Cauchy-Schwarz Divergence

Domain adaptation aims to use training data from one or multiple source domains to learn a hypothesis that can be generalized to a different, but related, target domain. As such, having a reliable measure for evaluating the discrepancy of both marginal and conditional distributions is crucial. We introduce Cauchy-Schwarz (CS) divergence to the problem of unsupervised domain adaptation (UDA). The CS divergence offers a theoretically tighter generalization error bound than the popular Kullback-Leibler divergence. This holds for the general case of supervised learning, including multi-class classification and regression. Furthermore, we illustrate that the CS divergence enables a simple estimator on the discrepancy of both marginal and conditional distributions between source and target domains in the representation space, without requiring any distributional assumptions. We provide multiple examples to illustrate how the CS divergence can be conveniently used in both distance metric- or adversarial training-based UDA frameworks, resulting in compelling performance.

End-to-end Adaptive Dynamic Subsampling and Reconstruction for Cardiac MRI

Accelerating dynamic MRI is essential for enhancing clinical applications, such as adaptive radiotherapy, and improving patient comfort. Traditional deep learning (DL) approaches for accelerated dynamic MRI reconstruction typically rely on predefined or random subsampling patterns, applied uniformly across all temporal phases. This standard practice overlooks the potential benefits of leveraging temporal correlations and lacks the adaptability required for case-specific subsampling optimization, which holds the potential for maximizing reconstruction quality. Addressing this gap, we present a novel end-to-end framework for adaptive dynamic MRI subsampling and reconstruction. Our pipeline integrates a DL-based adaptive sampler, generating case-specific dynamic subsampling patterns, trained end-to-end with a state-of-the-art 2D dynamic reconstruction network, namely vSHARP, which effectively reconstructs the adaptive dynamic subsampled data into a moving image. Our method is assessed using dynamic cine cardiac MRI data, comparing its performance against vSHARP models that employ common subsampling trajectories, and pipelines trained to optimize dataset-specific sampling schemes alongside vSHARP reconstruction. Our results indicate superior reconstruction quality, particularly at high accelerations.

Dynamic Prototype Adaptation with Distillation for Few-shot Point Cloud Segmentation

Few-shot point cloud segmentation seeks to generate per-point masks for previously unseen categories, using only a minimal set of annotated point clouds as reference. Existing prototype-based methods rely on support prototypes to guide the segmentation of query point clouds, but they encounter challenges when significant object variations exist between the support prototypes and query features. In this work, we present dynamic prototype adaptation (DPA), which explicitly learns task-specific prototypes for each query point cloud to tackle the object variation problem. DPA achieves the adaptation through prototype rectification, aligning vanilla prototypes from support with the query feature distribution, and prototype-to-query attention, extracting task-specific context from query point clouds. Furthermore, we introduce a prototype distillation regularization term, enabling knowledge transfer between early-stage prototypes and their deeper counterparts during adaption. By iteratively applying these adaptations, we generate task-specific prototypes for accurate mask predictions on query point clouds. Extensive experiments on two popular benchmarks show that DPA surpasses state-of-the-art methods by a significant margin, e.g., 7.43\% and 6.39\% under the 2-way 1-shot setting on S3DIS and ScanNet, respectively. Code is available at https://github.com/jliu4ai/DPA.

Equivariant Multiscale Learned Invertible Reconstruction for Cone Beam CT

Cone Beam CT (CBCT) is an essential imaging modality nowadays, but the image quality of CBCT still lags behind the high quality standards established by the conventional Computed Tomography. We propose LIRE+, a learned iterative scheme for fast and memory-efficient CBCT reconstruction, which is a substantially faster and more parameter-efficient alternative to the recently proposed LIRE method. LIRE+ is a rotationally-equivariant multiscale learned invertible primal-dual iterative scheme for CBCT reconstruction. Memory usage is optimized by relying on simple reversible residual networks in primal/dual cells and patch-wise computations inside the cells during forward and backward passes, while increased inference speed is achieved by making the primal-dual scheme multiscale so that the reconstruction process starts at low resolution and with low resolution primal/dual latent vectors. A LIRE+ model was trained and validated on a set of 260 + 22 thorax CT scans and tested using a set of 142 thorax CT scans with additional evaluation with and without finetuning on an out-of-distribution set of 79 Head and Neck (HN) CT scans. Our method surpasses classical and deep learning baselines, including LIRE, on the thorax test set. For a similar inference time and with only 37 % of the parameter budget, LIRE+ achieves a +0.2 dB PSNR improvement over LIRE, while being able to match the performance of LIRE in 45 % less inference time and with 28 % of the parameter budget. Rotational equivariance ensures robustness of LIRE+ to patient orientation, while LIRE and other deep learning baselines suffer from substantial performance degradation when patient orientation is unusual. On the HN dataset in the absence of finetuning, LIRE+ is generally comparable to LIRE in performance apart from a few outlier cases, whereas after identical finetuning LIRE+ demonstates a +1.02 dB PSNR improvement over LIRE.

How to Train Neural Field Representations: A Comprehensive Study and Benchmark

Neural fields (NeFs) have recently emerged as a versatile method for modeling signals of various modalities, including images, shapes, and scenes. Subsequently, a number of works have explored the use of NeFs as representations for downstream tasks, e.g. classifying an image based on the parameters of a NeF that has been fit to it. However, the impact of the NeF hyperparameters on their quality as downstream representation is scarcely understood and remains largely unexplored. This is in part caused by the large amount of time required to fit datasets of neural fields. In this work, we propose $\verb|fit-a-nef|$, a JAX-based library that leverages parallelization to enable fast optimization of large-scale NeF datasets, resulting in a significant speed-up. With this library, we perform a comprehensive study that investigates the effects of different hyperparameters -- including initialization, network architecture, and optimization strategies -- on fitting NeFs for downstream tasks. Our study provides valuable insights on how to train NeFs and offers guidance for optimizing their effectiveness in downstream applications. Finally, based on the proposed library and our analysis, we propose Neural Field Arena, a benchmark consisting of neural field variants of popular vision datasets, including MNIST, CIFAR, variants of ImageNet, and ShapeNetv2. Our library and the Neural Field Arena will be open-sourced to introduce standardized benchmarking and promote further research on neural fields.

JSSL: Joint Supervised and Self-supervised Learning for MRI Reconstruction

Magnetic Resonance Imaging represents an important diagnostic modality; however, its inherently slow acquisition process poses challenges in obtaining fully sampled k-space data under motion in clinical scenarios such as abdominal, cardiac, and prostate imaging. In the absence of fully sampled acquisitions, which can serve as ground truth data, training deep learning algorithms in a supervised manner to predict the underlying ground truth image becomes an impossible task. To address this limitation, self-supervised methods have emerged as a viable alternative, leveraging available subsampled k-space data to train deep learning networks for MRI reconstruction. Nevertheless, these self-supervised approaches often fall short when compared to supervised methodologies. In this paper, we introduce JSSL (Joint Supervised and Self-supervised Learning), a novel training approach for deep learning-based MRI reconstruction algorithms aimed at enhancing reconstruction quality in scenarios where target dataset(s) containing fully sampled k-space measurements are unavailable. Our proposed method operates by simultaneously training a model in a self-supervised learning setting, using subsampled data from the target dataset(s), and in a supervised learning manner, utilizing data from other datasets, referred to as proxy datasets, where fully sampled k-space data is accessible. To demonstrate the efficacy of JSSL, we utilized subsampled prostate parallel MRI measurements as the target dataset, while employing fully sampled brain and knee k-space acquisitions as proxy datasets. Our results showcase a substantial improvement over conventional self-supervised training methods, thereby underscoring the effectiveness of our joint approach. We provide a theoretical motivation for JSSL and establish a practical "rule-of-thumb" for selecting the most appropriate training approach for deep MRI reconstruction.