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Since the release of Segment Anything 2 (SAM2), the medical imaging community has been actively evaluating its performance for 3D medical image segmentation. However, different studies have employed varying evaluation pipelines, resulting in conflicting outcomes that obscure a clear understanding of SAM2's capabilities and potential applications. We shortly review existing benchmarks and point out that the SAM2 paper clearly outlines a zero-shot evaluation pipeline, which simulates user clicks iteratively for up to eight iterations. We reproduced this interactive annotation simulation on 3D CT datasets and provided the results and code~\url{https://github.com/Project-MONAI/VISTA}. Our findings reveal that directly applying SAM2 on 3D medical imaging in a zero-shot manner is far from satisfactory. It is prone to generating false positives when foreground objects disappear, and annotating more slices cannot fully offset this tendency. For smaller single-connected objects like kidney and aorta, SAM2 performs reasonably well but for most organs it is still far behind state-of-the-art 3D annotation methods. More research and innovation are needed for 3D medical imaging community to use SAM2 correctly.

Medical image segmentation is a core component of precision medicine, and 3D computed tomography (CT) is one of the most important imaging techniques. A highly accurate and clinically applicable segmentation foundation model will greatly facilitate clinicians and researchers using CT images. Although existing foundation models have attracted great interest, none are adequate for 3D CT, either because they lack accurate automatic segmentation for large cohort analysis or the ability to segment novel classes. An ideal segmentation solution should possess two features: accurate out-of-the-box performance covering major organ classes, and effective adaptation or zero-shot ability to novel structures. To achieve this goal, we introduce Versatile Imaging SegmenTation and Annotation model (VISTA3D). VISTA3D is trained systematically on 11454 volumes and provides accurate out-of-the-box segmentation for 127 common types of human anatomical structures and various lesions. Additionally, VISTA3D supports 3D interactive segmentation, allowing convenient editing of automatic results and achieving state-of-the-art annotation results on unseen classes. The novel model design and training recipe represent a promising step toward developing a versatile medical image foundation model and will serve as a valuable foundation for CT image analysis. Code and model weights are available at https://github.com/Project-MONAI/VISTA

In this paper, we give a approximation characterization, the lifting property, embedding properties and the duality of matrix weighted modulation spaces.

In 2019, B\'ona and Smith introduced the notion of \emph{strong pattern avoidance}, that is, a permutation and its square both avoid a given pattern. In this paper, we enumerate the set of permutations $\pi$ which not only strongly avoid the pattern $312$ or $231$ but also avoid the pattern $\tau$, for $\tau\in S_3$ and some $\tau\in S_4$. One of them is to give a positive answer to a conjecture of Archer and Geary.

Large machine learning models trained on diverse data have recently seen unprecedented success. Federated learning enables training on private data that may otherwise be inaccessible, such as domain-specific datasets decentralized across many clients. However, federated learning can be difficult to scale to large models when clients have limited resources. This challenge often results in a trade-off between model size and access to diverse data. To mitigate this issue and facilitate training of large models on edge devices, we introduce a simple yet effective strategy, Federated Layer-wise Learning, to simultaneously reduce per-client memory, computation, and communication costs. Clients train just a single layer each round, reducing resource costs considerably with minimal performance degradation. We also introduce Federated Depth Dropout, a complementary technique that randomly drops frozen layers during training, to further reduce resource usage. Coupling these two techniques enables us to effectively train significantly larger models on edge devices. Specifically, we reduce training memory usage by 5x or more in federated self-supervised representation learning and demonstrate that performance in downstream tasks is comparable to conventional federated self-supervised learning.

A set of permutations is called sign-balanced if the set contains the same number of even permutations as odd permutations. Let $S_n(\sigma_1, \sigma_2, \ldots, \sigma_r)$ be the set of permutations in the symmetric group $S_n$ which avoids patterns $\sigma_1, \sigma_2, \ldots, \sigma_r$. The aim of this paper is to investigate when, for certain patterns $\sigma_1, \sigma_2, \ldots, \sigma_r$, $S_n(\sigma_1, \sigma_2, \ldots, \sigma_r)$ is sign-balanced for every integer $n>1$. We prove that for any $\{\sigma_1, \sigma_2, \ldots, \sigma_r\}\subseteq S_3$, if $\{\sigma_1, \sigma_2, \ldots, \sigma_r\}$ is sign-balanced except $\{132, 213, 231, 312\}$, then $S_n(\sigma_1, \sigma_2, \ldots, \sigma_r)$ is sign-balanced for every integer $n>1$. In addition, we give some results in the case of avoiding some patterns of length $4$.

The synergy of long-range dependencies from transformers and local representations of image content from convolutional neural networks (CNNs) has led to advanced architectures and increased performance for various medical image analysis tasks due to their complementary benefits. However, compared with CNNs, transformers require considerably more training data, due to a larger number of parameters and an absence of inductive bias. The need for increasingly large datasets continues to be problematic, particularly in the context of medical imaging, where both annotation efforts and data protection result in limited data availability. In this work, inspired by the human decision-making process of correlating new evidence with previously memorized experience, we propose a Memorizing Vision Transformer (MoViT) to alleviate the need for large-scale datasets to successfully train and deploy transformer-based architectures. MoViT leverages an external memory structure to cache history attention snapshots during the training stage. To prevent overfitting, we incorporate an innovative memory update scheme, attention temporal moving average, to update the stored external memories with the historical moving average. For inference speedup, we design a prototypical attention learning method to distill the external memory into smaller representative subsets. We evaluate our method on a public histology image dataset and an in-house MRI dataset, demonstrating that MoViT applied to varied medical image analysis tasks, can outperform vanilla transformer models across varied data regimes, especially in cases where only a small amount of annotated data is available. More importantly, MoViT can reach a competitive performance of ViT with only 3.0% of the training data.

Cerebrovascular disease is a leading cause of death globally. Prevention and early intervention are known to be the most effective forms of its management. Non-invasive imaging methods hold great promises for early stratification, but at present lack the sensitivity for personalized prognosis. Resting-state functional magnetic resonance imaging (rs-fMRI), a powerful tool previously used for mapping neural activity, is available in most hospitals. Here we show that rs-fMRI can be used to map cerebral hemodynamic function and delineate impairment. By exploiting time variations in breathing pattern during rs-fMRI, deep learning enables reproducible mapping of cerebrovascular reactivity (CVR) and bolus arrive time (BAT) of the human brain using resting-state CO2 fluctuations as a natural 'contrast media'. The deep-learning network was trained with CVR and BAT maps obtained with a reference method of CO2-inhalation MRI, which included data from young and older healthy subjects and patients with Moyamoya disease and brain tumors. We demonstrate the performance of deep-learning cerebrovascular mapping in the detection of vascular abnormalities, evaluation of revascularization effects, and vascular alterations in normal aging. In addition, cerebrovascular maps obtained with the proposed method exhibited excellent reproducibility in both healthy volunteers and stroke patients. Deep-learning resting-state vascular imaging has the potential to become a useful tool in clinical cerebrovascular imaging.

In Heterogeneous Face Recognition (HFR), the objective is to match faces across two different domains such as visible and thermal. Large domain discrepancy makes HFR a difficult problem. Recent methods attempting to fill the gap via synthesis have achieved promising results, but their performance is still limited by the scarcity of paired training data. In practice, large-scale heterogeneous face data are often inaccessible due to the high cost of acquisition and annotation process as well as privacy regulations. In this paper, we propose a new face hallucination paradigm for HFR, which not only enables data-efficient synthesis but also allows to scale up model training without breaking any privacy policy. Unlike existing methods that learn face synthesis entirely from scratch, our approach is particularly designed to take advantage of rich and diverse facial priors from visible domain for more faithful hallucination. On the other hand, large-scale training is enabled by introducing a new federated learning scheme to allow institution-wise collaborations while avoiding explicit data sharing. Extensive experiments demonstrate the advantages of our approach in tackling HFR under current data limitations. In a unified framework, our method yields the state-of-the-art hallucination results on multiple HFR datasets., Comment: CVPR2022

Cross-silo federated learning (FL) has attracted much attention in medical imaging analysis with deep learning in recent years as it can resolve the critical issues of insufficient data, data privacy, and training efficiency. However, there can be a generalization gap between the model trained from FL and the one from centralized training. This important issue comes from the non-iid data distribution of the local data in the participating clients and is well-known as client drift. In this work, we propose a novel training framework FedSM to avoid the client drift issue and successfully close the generalization gap compared with the centralized training for medical image segmentation tasks for the first time. We also propose a novel personalized FL objective formulation and a new method SoftPull to solve it in our proposed framework FedSM. We conduct rigorous theoretical analysis to guarantee its convergence for optimizing the non-convex smooth objective function. Real-world medical image segmentation experiments using deep FL validate the motivations and effectiveness of our proposed method., Comment: CVPR 2022

Federated learning (FL) is a distributed machine learning technique that enables collaborative model training while avoiding explicit data sharing. The inherent privacy-preserving property of FL algorithms makes them especially attractive to the medical field. However, in case of heterogeneous client data distributions, standard FL methods are unstable and require intensive hyperparameter tuning to achieve optimal performance. Conventional hyperparameter optimization algorithms are impractical in real-world FL applications as they involve numerous training trials, which are often not affordable with limited compute budgets. In this work, we propose an efficient reinforcement learning (RL)-based federated hyperparameter optimization algorithm, termed Auto-FedRL, in which an online RL agent can dynamically adjust hyperparameters of each client based on the current training progress. Extensive experiments are conducted to investigate different search strategies and RL agents. The effectiveness of the proposed method is validated on a heterogeneous data split of the CIFAR-10 dataset as well as two real-world medical image segmentation datasets for COVID-19 lesion segmentation in chest CT and pancreas segmentation in abdominal CT.

One major problem in deep learning-based solutions for medical imaging is the drop in performance when a model is tested on a data distribution different from the one that it is trained on. Adapting the source model to target data distribution at test-time is an efficient solution for the data-shift problem. Previous methods solve this by adapting the model to target distribution by using techniques like entropy minimization or regularization. In these methods, the models are still updated by back-propagation using an unsupervised loss on complete test data distribution. In real-world clinical settings, it makes more sense to adapt a model to a new test image on-the-fly and avoid model update during inference due to privacy concerns and lack of computing resource at deployment. To this end, we propose a new setting - On-the-Fly Adaptation which is zero-shot and episodic (i.e., the model is adapted to a single image at a time and also does not perform any back-propagation during test-time). To achieve this, we propose a new framework called Adaptive UNet where each convolutional block is equipped with an adaptive batch normalization layer to adapt the features with respect to a domain code. The domain code is generated using a pre-trained encoder trained on a large corpus of medical images. During test-time, the model takes in just the new test image and generates a domain code to adapt the features of source model according to the test data. We validate the performance on both 2D and 3D data distribution shifts where we get a better performance compared to previous test-time adaptation methods. Code is available at https://github.com/jeya-maria-jose/On-The-Fly-Adaptation, Comment: Tech Report

Magnetic Resonance (MR) image reconstruction from under-sampled acquisition promises faster scanning time. To this end, current State-of-The-Art (SoTA) approaches leverage deep neural networks and supervised training to learn a recovery model. While these approaches achieve impressive performances, the learned model can be fragile on unseen degradation, e.g. when given a different acceleration factor. These methods are also generally deterministic and provide a single solution to an ill-posed problem; as such, it can be difficult for practitioners to understand the reliability of the reconstruction. We introduce DiffuseRecon, a novel diffusion model-based MR reconstruction method. DiffuseRecon guides the generation process based on the observed signals and a pre-trained diffusion model, and does not require additional training on specific acceleration factors. DiffuseRecon is stochastic in nature and generates results from a distribution of fully-sampled MR images; as such, it allows us to explicitly visualize different potential reconstruction solutions. Lastly, DiffuseRecon proposes an accelerated, coarse-to-fine Monte-Carlo sampling scheme to approximate the most likely reconstruction candidate. The proposed DiffuseRecon achieves SoTA performances reconstructing from raw acquisition signals in fastMRI and SKM-TEA. Code will be open-sourced at www.github.com/cpeng93/DiffuseRecon.

Accelerating magnetic resonance image (MRI) reconstruction process is a challenging ill-posed inverse problem due to the excessive under-sampling operation in k-space. In this paper, we propose a recurrent transformer model, namely ReconFormer, for MRI reconstruction which can iteratively reconstruct high fertility magnetic resonance images from highly under-sampled k-space data. In particular, the proposed architecture is built upon Recurrent Pyramid Transformer Layers (RPTL), which jointly exploits intrinsic multi-scale information at every architecture unit as well as the dependencies of the deep feature correlation through recurrent states. Moreover, the proposed ReconFormer is lightweight since it employs the recurrent structure for its parameter efficiency. We validate the effectiveness of ReconFormer on multiple datasets with different magnetic resonance sequences and show that it achieves significant improvements over the state-of-the-art methods with better parameter efficiency. Implementation code will be available in https://github.com/guopengf/ReconFormer.

Deep Learning (DL) based methods for magnetic resonance (MR) image reconstruction have been shown to produce superior performance in recent years. However, these methods either only leverage under-sampled data or require a paired fully-sampled auxiliary modality to perform multi-modal reconstruction. Consequently, existing approaches neglect to explore attention mechanisms that can transfer textures from reference fully-sampled data to under-sampled data within a single modality, which limits these approaches in challenging cases. In this paper, we propose a novel Texture Transformer Module (TTM) for accelerated MRI reconstruction, in which we formulate the under-sampled data and reference data as queries and keys in a transformer. The TTM facilitates joint feature learning across under-sampled and reference data, so the feature correspondences can be discovered by attention and accurate texture features can be leveraged during reconstruction. Notably, the proposed TTM can be stacked on prior MRI reconstruction approaches to further improve their performance. Extensive experiments show that TTM can significantly improve the performance of several popular DL-based MRI reconstruction methods.