Brain extraction and registration are important preprocessing steps in neuroimaging data analysis, where the goal is to extract the brain regions from MRI scans (i.e., extraction step) and align them with a target brain image (i.e., registration step). Conventional research mainly focuses on developing methods for the extraction and registration tasks separately under supervised settings. The performance of these methods highly depends on the amount of training samples and visual inspections performed by experts for error correction. However, in many medical studies, collecting voxel-level labels and conducting manual quality control in high-dimensional neuroimages (e.g., 3D MRI) are very expensive and time-consuming. Moreover, brain extraction and registration are highly related tasks in neuroimaging data and should be solved collectively. In this paper, we study the problem of unsupervised collective extraction and registration in neuroimaging data. We propose a unified end-to-end framework, called ERNet (Extraction-Registration Network), to jointly optimize the extraction and registration tasks, allowing feedback between them. Specifically, we use a pair of multi-stage extraction and registration modules to learn the extraction mask and transformation, where the extraction network improves the extraction accuracy incrementally and the registration network successively warps the extracted image until it is well-aligned with the target image. Experiment results on real-world datasets show that our proposed method can effectively improve the performance on extraction and registration tasks in neuroimaging data. Our code and data can be found at https://github.com/ERNetERNet/ERNet

Deformable image registration, i.e., the task of aligning multiple images into one coordinate system by non-linear transformation, serves as an essential preprocessing step for neuroimaging data. Recent research on deformable image registration is mainly focused on improving the registration accuracy using multi-stage alignment methods, where the source image is repeatedly deformed in stages by a same neural network until it is well-aligned with the target image. Conventional methods for multi-stage registration can often blur the source image as the pixel/voxel values are repeatedly interpolated from the image generated by the previous stage. However, maintaining image quality such as sharpness during image registration is crucial to medical data analysis. In this paper, we study the problem of anti-blur deformable image registration and propose a novel solution, called Anti-Blur Network (ABN), for multi-stage image registration. Specifically, we use a pair of short-term registration and long-term memory networks to learn the nonlinear deformations at each stage, where the short-term registration network learns how to improve the registration accuracy incrementally and the long-term memory network combines all the previous deformations to allow an interpolation to perform on the raw image directly and preserve image sharpness. Extensive experiments on both natural and medical image datasets demonstrated that ABN can accurately register images while preserving their sharpness. Our code and data can be found at https://github.com/anonymous3214/ABN

Multi-view graph clustering (MGC) methods are increasingly being studied due to the explosion of multi-view data with graph structural information. The critical point of MGC is to better utilize the view-specific and view-common information in features and graphs of multiple views. However, existing works have an inherent limitation that they are unable to concurrently utilize the consensus graph information across multiple graphs and the view-specific feature information. To address this issue, we propose Variational Graph Generator for Multi-View Graph Clustering (VGMGC). Specifically, a novel variational graph generator is proposed to extract common information among multiple graphs. This generator infers a reliable variational consensus graph based on a priori assumption over multiple graphs. Then a simple yet effective graph encoder in conjunction with the multi-view clustering objective is presented to learn the desired graph embeddings for clustering, which embeds the inferred view-common graph and view-specific graphs together with features. Finally, theoretical results illustrate the rationality of VGMGC by analyzing the uncertainty of the inferred consensus graph with information bottleneck principle. Extensive experiments demonstrate the superior performance of our VGMGC over SOTAs.

与大脑变化相关的阿尔茨海默氏病（AD）和轻度认知障碍（MCI）的评估仍然是一项艰巨的任务。最近的研究表明，多模式成像技术的组合可以更好地反映病理特征，并有助于更准确地诊断AD和MCI。在本文中，我们提出了一种新型的基于张量的多模式特征选择和回归方法，用于诊断和生物标志物对正常对照组的AD和MCI鉴定。具体而言，我们利用张量结构来利用多模式数据中固有的高级相关信息，并研究多线性回归模型中的张量级稀疏性。我们使用三种成像方式（VBM- MRI，FDG-PET和AV45-PET）具有疾病严重程度和认知评分的临床参数来分析ADNI数据的方法的实际优势。实验结果表明，我们提出的方法与疾病诊断的最新方法的优越性能以及疾病特异性区域和与模态相关的差异的鉴定。这项工作的代码可在https://github.com/junfish/bios22上公开获得。

人的大脑位于复杂的神经生物学系统的核心，神经元，电路和子系统以神秘的方式相互作用。长期以来，了解大脑的结构和功能机制一直是神经科学研究和临床障碍疗法的引人入胜的追求。将人脑作为网络的连接映射是神经科学中最普遍的范例之一。图神经网络（GNN）最近已成为建模复杂网络数据的潜在方法。另一方面，深层模型的可解释性低，从而阻止了他们在医疗保健等决策环境中的使用。为了弥合这一差距，我们提出了一个可解释的框架，以分析特定的利益区域（ROI）和突出的联系。提出的框架由两个模块组成：疾病预测的面向脑网络的主链模型和全球共享的解释发生器，该模型突出了包括疾病特异性的生物标志物，包括显着的ROI和重要连接。我们在三个现实世界中的脑疾病数据集上进行实验。结果证明了我们的框架可以获得出色的性能并确定有意义的生物标志物。这项工作的所有代码均可在https://github.com/hennyjie/ibgnn.git上获得。

大脑网络将大脑区域之间的复杂连接性描述为图形结构，这为研究脑连接素提供了强大的手段。近年来，图形神经网络已成为使用结构化数据的普遍学习范式。但是，由于数据获取的成本相对较高，大多数大脑网络数据集的样本量受到限制，这阻碍了足够的培训中的深度学习模型。受元学习的启发，该论文以有限的培训示例快速学习新概念，研究了在跨数据库中分析脑连接组的数据有效培训策略。具体而言，我们建议在大型样本大小的数据集上进行元训练模型，并将知识转移到小数据集中。此外，我们还探索了两种面向脑网络的设计，包括Atlas转换和自适应任务重新启动。与其他训练前策略相比，我们的基于元学习的方法实现了更高和稳定的性能，这证明了我们提出的解决方案的有效性。该框架还能够以数据驱动的方式获得有关数据集和疾病之间相似之处的新见解。

Mapping the connectome of the human brain using structural or functional connectivity has become one of the most pervasive paradigms for neuroimaging analysis. Recently, Graph Neural Networks (GNNs) motivated from geometric deep learning have attracted broad interest due to their established power for modeling complex networked data. Despite their superior performance in many fields, there has not yet been a systematic study of how to design effective GNNs for brain network analysis. To bridge this gap, we present BrainGB, a benchmark for brain network analysis with GNNs. BrainGB standardizes the process by (1) summarizing brain network construction pipelines for both functional and structural neuroimaging modalities and (2) modularizing the implementation of GNN designs. We conduct extensive experiments on datasets across cohorts and modalities and recommend a set of general recipes for effective GNN designs on brain networks. To support open and reproducible research on GNN-based brain network analysis, we host the BrainGB website at https://braingb.us with models, tutorials, examples, as well as an out-of-box Python package. We hope that this work will provide useful empirical evidence and offer insights for future research in this novel and promising direction.

本文介绍了一种基于图形的Concionome分析的基于图形的内核学习方法。具体地，我们演示了如何利用图表表示内的自然可用结构来编码内核中的先验知识。我们首先提出了一种矩阵分解，以直接从连接数据的自然对称图表表示中提取结构特征。然后，我们使用它们来导出一个结构悬停的图形内核将被馈送到支持向量机中。拟议的方法具有临床思考的优势。对挑战性HIV疾病分类的定量评估（DTI和FMRI衍生的连接数据）和情感识别（EEG导出的连接数据）任务证明了我们提出的方法对现有技术的卓越性能。结果表明，在情感监管任务期间，相关的EEG结合信息主要在Alpha带中编码。

Designing experiments often requires balancing between learning about the true treatment effects and earning from allocating more samples to the superior treatment. While optimal algorithms for the Multi-Armed Bandit Problem (MABP) provide allocation policies that optimally balance learning and earning, they tend to be computationally expensive. The Gittins Index (GI) is a solution to the MABP that can simultaneously attain optimality and computationally efficiency goals, and it has been recently used in experiments with Bernoulli and Gaussian rewards. For the first time, we present a modification of the GI rule that can be used in experiments with exponentially-distributed rewards. We report its performance in simulated 2- armed and 3-armed experiments. Compared to traditional non-adaptive designs, our novel GI modified design shows operating characteristics comparable in learning (e.g. statistical power) but substantially better in earning (e.g. direct benefits). This illustrates the potential that designs using a GI approach to allocate participants have to improve participant benefits, increase efficiencies, and reduce experimental costs in adaptive multi-armed experiments with exponential rewards.

Transformer has achieved impressive successes for various computer vision tasks. However, most of existing studies require to pretrain the Transformer backbone on a large-scale labeled dataset (e.g., ImageNet) for achieving satisfactory performance, which is usually unavailable for medical images. Additionally, due to the gap between medical and natural images, the improvement generated by the ImageNet pretrained weights significantly degrades while transferring the weights to medical image processing tasks. In this paper, we propose Bootstrap Own Latent of Transformer (BOLT), a self-supervised learning approach specifically for medical image classification with the Transformer backbone. Our BOLT consists of two networks, namely online and target branches, for self-supervised representation learning. Concretely, the online network is trained to predict the target network representation of the same patch embedding tokens with a different perturbation. To maximally excavate the impact of Transformer from limited medical data, we propose an auxiliary difficulty ranking task. The Transformer is enforced to identify which branch (i.e., online/target) is processing the more difficult perturbed tokens. Overall, the Transformer endeavours itself to distill the transformation-invariant features from the perturbed tokens to simultaneously achieve difficulty measurement and maintain the consistency of self-supervised representations. The proposed BOLT is evaluated on three medical image processing tasks, i.e., skin lesion classification, knee fatigue fracture grading and diabetic retinopathy grading. The experimental results validate the superiority of our BOLT for medical image classification, compared to ImageNet pretrained weights and state-of-the-art self-supervised learning approaches.