我们介绍了StreamNet，这是一种自动编码器体系结构，用于分析大量白质流线的高度异质几何形状。该提出的框架利用了Wasserstein-1度量的几何形状赋值特性，以实现整个流线束的直接编码和重建。我们表明，该模型不仅可以准确捕获人群中流线的分布结构，而且还能够在真实和合成流线之间实现出色的重建性能。使用最新的ART捆绑包比较度量标准，对40个健康对照的T1加权扩散成像产生的白质流线评估了实验模型性能。

Three-dimensional geometric data offer an excellent domain for studying representation learning and generative modeling. In this paper, we look at geometric data represented as point clouds. We introduce a deep AutoEncoder (AE) network with state-of-the-art reconstruction quality and generalization ability. The learned representations outperform existing methods on 3D recognition tasks and enable shape editing via simple algebraic manipulations, such as semantic part editing, shape analogies and shape interpolation, as well as shape completion. We perform a thorough study of different generative models including GANs operating on the raw point clouds, significantly improved GANs trained in the fixed latent space of our AEs, and Gaussian Mixture Models (GMMs). To quantitatively evaluate generative models we introduce measures of sample fidelity and diversity based on matchings between sets of point clouds. Interestingly, our evaluation of generalization, fidelity and diversity reveals that GMMs trained in the latent space of our AEs yield the best results overall.

A tractogram is a virtual representation of the brain white matter. It is composed of millions of virtual fibers, encoded as 3D polylines, which approximate the white matter axonal pathways. To date, tractograms are the most accurate white matter representation and thus are used for tasks like presurgical planning and investigations of neuroplasticity, brain disorders, or brain networks. However, it is a well-known issue that a large portion of tractogram fibers is not anatomically plausible and can be considered artifacts of the tracking procedure. With Verifyber, we tackle the problem of filtering out such non-plausible fibers using a novel fully-supervised learning approach. Differently from other approaches based on signal reconstruction and/or brain topology regularization, we guide our method with the existing anatomical knowledge of the white matter. Using tractograms annotated according to anatomical principles, we train our model, Verifyber, to classify fibers as either anatomically plausible or non-plausible. The proposed Verifyber model is an original Geometric Deep Learning method that can deal with variable size fibers, while being invariant to fiber orientation. Our model considers each fiber as a graph of points, and by learning features of the edges between consecutive points via the proposed sequence Edge Convolution, it can capture the underlying anatomical properties. The output filtering results highly accurate and robust across an extensive set of experiments, and fast; with a 12GB GPU, filtering a tractogram of 1M fibers requires less than a minute. Verifyber implementation and trained models are available at https://github.com/FBK-NILab/verifyber.

随着脑成像技术和机器学习工具的出现，很多努力都致力于构建计算模型来捕获人脑中的视觉信息的编码。最具挑战性的大脑解码任务之一是通过功能磁共振成像（FMRI）测量的脑活动的感知自然图像的精确重建。在这项工作中，我们调查了来自FMRI的自然图像重建的最新学习方法。我们在架构设计，基准数据集和评估指标方面检查这些方法，并在标准化评估指标上呈现公平的性能评估。最后，我们讨论了现有研究的优势和局限，并提出了潜在的未来方向。

White matter bundle segmentation is a cornerstone of modern tractography to study the brain's structural connectivity in domains such as neurological disorders, neurosurgery, and aging. In this study, we present FIESTA (FIber gEneration and bundle Segmentation in Tractography using Autoencoders), a reliable and robust, fully automated, and easily semi-automatically calibrated pipeline based on deep autoencoders that can dissect and fully populate WM bundles. Our framework allows the transition from one anatomical bundle definition to another with marginal calibrating time. This pipeline is built upon FINTA, CINTA, and GESTA methods that demonstrated how autoencoders can be used successfully for streamline filtering, bundling, and streamline generation in tractography. Our proposed method improves bundling coverage by recovering hard-to-track bundles with generative sampling through the latent space seeding of the subject bundle and the atlas bundle. A latent space of streamlines is learned using autoencoder-based modeling combined with contrastive learning. Using an atlas of bundles in standard space (MNI), our proposed method segments new tractograms using the autoencoder latent distance between each tractogram streamline and its closest neighbor bundle in the atlas of bundles. Intra-subject bundle reliability is improved by recovering hard-to-track streamlines, using the autoencoder to generate new streamlines that increase each bundle's spatial coverage while remaining anatomically meaningful. Results show that our method is more reliable than state-of-the-art automated virtual dissection methods such as RecoBundles, RecoBundlesX, TractSeg, White Matter Analysis and XTRACT. Overall, these results show that our framework improves the practicality and usability of current state-of-the-art bundling framework

虽然变形式自动泊车在多个任务中成功，但是使用传统前沿的使用是限于编码输入数据的底层结构的能力。我们介绍了一个被编码的先前切片的Wasserstein AutoEncoder，其中另外的先前编码器网络学会了数据歧管的嵌入，该数据歧管保留数据的拓扑和几何属性，从而提高了潜在空间的结构。使用切片的Wassersein距离迭代培训AutoEncoder和先前编码器网络。通过沿着大学探测器的内插来遍历潜伏空间来探讨所学习歧管编码的有效性，该测量空间产生位于数据歧管上的样本，因此与欧几里德插值相比更令人逼真。为此，我们介绍一种基于图形的算法，用于探索数据歧管，并通过沿着路径的样本密度最大化，同时最小化总能量，沿着潜在空间内插入潜伏空间。我们使用3D螺旋数据来表明先前对数据不同的几何形状，与传统的自动化器不同，并通过网络算法展示嵌入式数据歧管的探索。我们将框架应用于基准图像数据集，以演示在异常生成，潜在结构和测地插值中学习数据表示的优势。

Like fingerprints, cortical folding patterns are unique to each brain even though they follow a general species-specific organization. Some folding patterns have been linked with neurodevelopmental disorders. However, due to the high inter-individual variability, the identification of rare folding patterns that could become biomarkers remains a very complex task. This paper proposes a novel unsupervised deep learning approach to identify rare folding patterns and assess the degree of deviations that can be detected. To this end, we preprocess the brain MR images to focus the learning on the folding morphology and train a beta-VAE to model the inter-individual variability of the folding. We compare the detection power of the latent space and of the reconstruction errors, using synthetic benchmarks and one actual rare configuration related to the central sulcus. Finally, we assess the generalization of our method on a developmental anomaly located in another region. Our results suggest that this method enables encoding relevant folding characteristics that can be enlightened and better interpreted based on the generative power of the beta-VAE. The latent space and the reconstruction errors bring complementary information and enable the identification of rare patterns of different nature. This method generalizes well to a different region on another dataset. Code is available at https://github.com/neurospin-projects/2022_lguillon_rare_folding_detection.

生成的对抗网络（GAN）是在众多领域成功使用的一种强大的深度学习模型。它们属于一个称为生成方法的更广泛的家族，该家族通过从真实示例中学习样本分布来生成新数据。在临床背景下，与传统的生成方法相比，GAN在捕获空间复杂，非线性和潜在微妙的疾病作用方面表现出增强的能力。这篇综述评估了有关gan在各种神经系统疾病的成像研究中的应用的现有文献，包括阿尔茨海默氏病，脑肿瘤，脑老化和多发性硬化症。我们为每个应用程序提供了各种GAN方法的直观解释，并进一步讨论了在神经影像学中利用gans的主要挑战，开放问题以及有希望的未来方向。我们旨在通过强调如何利用gan来支持临床决策，并有助于更好地理解脑部疾病的结构和功能模式，从而弥合先进的深度学习方法和神经病学研究之间的差距。

Generative adversarial networks (GANs) provide a way to learn deep representations without extensively annotated training data. They achieve this through deriving backpropagation signals through a competitive process involving a pair of networks. The representations that can be learned by GANs may be used in a variety of applications, including image synthesis, semantic image editing, style transfer, image super-resolution and classification. The aim of this review paper is to provide an overview of GANs for the signal processing community, drawing on familiar analogies and concepts where possible. In addition to identifying different methods for training and constructing GANs, we also point to remaining challenges in their theory and application.

投影技术经常用于可视化高维数据，使用户能够更好地理解在2D屏幕上的多维空间的总体结构。尽管存在着许多这样的方法，相当小的工作已经逆投影的普及方法来完成 - 绘制投影点，或者更一般的过程中，投影空间回到原来的高维空间。在本文中我们提出NNInv，用近似的任何突起或映射的逆的能力的深学习技术。 NNInv学会重建上的二维投影空间从任意点高维数据，给用户在视觉分析系统所学习的高维表示的能力进行交互。我们提供NNInv的参数空间的分析，并在选择这些参数提供指导。我们通过一系列定量和定性分析的延长NNInv的有效性验证。交互式实例中插值，分级协议，梯度可视化：然后，我们把它应用到三个可视化任务，验证了该方法的效用。

在各种机器学习应用中，表示学习已被证明是一种强大的方法。然而，对于大气动力学，迄今为止尚未考虑它，这可以说是由于缺乏可用于培训的大型，标记的数据集。在这项工作中，我们表明困难是良性的，并引入了一项自我监督的学习任务，该任务定义了各种未标记的大气数据集的绝对损失。具体而言，我们在简单而复杂的任务上训练神经网络，即预测与不同但附近的大气场之间的时间距离。我们证明，对ERA5重新分析进行此任务的培训会导致内部表示，从而捕获了大气动态的内在方面。我们通过为大气状态引入数据驱动的距离度量来做到这一点。当在其他机器学习应用程序中用作损失功能时，与经典$ \ ell_2 $ -loss相比，该ATMODIST距离会改善结果。例如，对于缩小缩放，一个人获得了更高的分辨率字段，该字段比以前的方法更接近真正的统计信息，而对于缺失或遮挡数据的插值，ATMODIST距离导致的结果导致包含更真实的精细规模特征的结果。由于它来自观察数据，因此Atmodist还提供了关于大气可预测性的新观点。

与CNN的分类，分割或对象检测相比，生成网络的目标和方法根本不同。最初，它们不是作为图像分析工具，而是生成自然看起来的图像。已经提出了对抗性训练范式来稳定生成方法，并已被证明是非常成功的 - 尽管绝不是第一次尝试。本章对生成对抗网络（GAN）的动机进行了基本介绍，并通​​过抽象基本任务和工作机制并得出了早期实用方法的困难来追溯其成功的道路。将显示进行更稳定的训练方法，也将显示出不良收敛及其原因的典型迹象。尽管本章侧重于用于图像生成和图像分析的gan，但对抗性训练范式本身并非特定于图像，并且在图像分析中也概括了任务。在将GAN与最近进入场景的进一步生成建模方法进行对比之前，将闻名图像语义分割和异常检测的架构示例。这将允许对限制的上下文化观点，但也可以对gans有好处。

我们从一组稀疏的光谱时间序列中构建了一个物理参数化的概率自动编码器（PAE），以学习IA型超新星（SNE IA）的内在多样性。 PAE是一个两阶段的生成模型，由自动编码器（AE）组成，该模型在使用归一化流（NF）训练后概率地解释。我们证明，PAE学习了一个低维的潜在空间，该空间可捕获人口内存在的非线性特征范围，并且可以直接从数据直接从数据中准确地对整个波长和观察时间进行精确模拟SNE IA的光谱演化。通过引入相关性惩罚项和多阶段训练设置以及我们的物理参数化网络，我们表明可以在训练期间分离内在和外在的可变性模式，从而消除了需要进行额外标准化的其他模型。然后，我们在SNE IA的许多下游任务中使用PAE进行越来越精确的宇宙学分析，包括自动检测SN Outliers，与数据分布一致的样本的产生以及在存在噪音和不完整数据的情况下解决逆问题限制宇宙距离测量。我们发现，与以前的研究相一致的最佳固有模型参数数量似乎是三个，并表明我们可以用$ 0.091 \ pm 0.010 $ mag标准化SNE IA的测试样本，该样本对应于$ 0.074 \ pm。 0.010 $ mag如果删除了特殊的速度贡献。训练有素的模型和代码在\ href {https://github.com/georgestein/supaernova} {github.com/georgestein/supaernova}上发布

Figure 1. This paper introduces Local Deep Implicit Functions, a 3D shape representation that decomposes an input shape (mesh on left in every triplet) into a structured set of shape elements (colored ellipses on right) whose contributions to an implicit surface reconstruction (middle) are represented by latent vectors decoded by a deep network. Project video and website at ldif.cs.princeton.edu.

病理学家拥有丰富的词汇，他们可以描述细胞形态的所有细微差别。在他们的世界中，图像和单词都有自然的配对。最近的进步表明，现在可以对机器学习模型进行培训，以学习高质量的图像功能并将其表示为离散信息。这使得自然语言（也是离散的语言）可以与成像旁边共同建模，从而描述了成像内容。在这里，我们介绍了将离散建模技术应用于非黑色素瘤皮肤癌的问题结构域，特别是eme骨内癌（IEC）的组织学图像。通过实施IEC图像的高分辨率（256x256）图像的VQ-GAN模型，我们训练了序列到序列变压器，以使用病理学家术语来生成自然语言描述。结合使用连续生成方法获得的交互式概念矢量的概念，我们展示了一个额外的解释性角度。结果是为高度表达的机器学习系统而努力的一种有希望的方法，不仅可以用作预测/分类工具，而且还意味着要进一步了解我们对疾病的科学理解。

Brain decoding is a field of computational neuroscience that uses measurable brain activity to infer mental states or internal representations of perceptual inputs. Therefore, we propose a novel approach to brain decoding that also relies on semantic and contextual similarity. We employ an fMRI dataset of natural image vision and create a deep learning decoding pipeline inspired by the existence of both bottom-up and top-down processes in human vision. We train a linear brain-to-feature model to map fMRI activity features to visual stimuli features, assuming that the brain projects visual information onto a space that is homeomorphic to the latent space represented by the last convolutional layer of a pretrained convolutional neural network, which typically collects a variety of semantic features that summarize and highlight similarities and differences between concepts. These features are then categorized in the latent space using a nearest-neighbor strategy, and the results are used to condition a generative latent diffusion model to create novel images. From fMRI data only, we produce reconstructions of visual stimuli that match the original content very well on a semantic level, surpassing the state of the art in previous literature. We evaluate our work and obtain good results using a quantitative semantic metric (the Wu-Palmer similarity metric over the WordNet lexicon, which had an average value of 0.57) and perform a human evaluation experiment that resulted in correct evaluation, according to the multiplicity of human criteria in evaluating image similarity, in over 80% of the test set.

反事实可以以人类的可解释方式解释神经网络的分类决策。我们提出了一种简单但有效的方法来产生这种反事实。更具体地说，我们执行合适的差异坐标转换，然后在这些坐标中执行梯度上升，以查找反事实，这些反事实是由置信度良好的指定目标类别分类的。我们提出了两种方法来利用生成模型来构建完全或大约差异的合适坐标系。我们使用Riemannian差异几何形状分析了生成过程，并使用各种定性和定量测量方法验证了生成的反事实质量。

Our method completes a partial 3D scan using a 3D Encoder-Predictor network that leverages semantic features from a 3D classification network. The predictions are correlated with a shape database, which we use in a multi-resolution 3D shape synthesis step. We obtain completed high-resolution meshes that are inferred from partial, low-resolution input scans.

Pixel-aligned Implicit function (PIFu): We present pixel-aligned implicit function (PIFu), which allows recovery of high-resolution 3D textured surfaces of clothed humans from a single input image (top row). Our approach can digitize intricate variations in clothing, such as wrinkled skirts and high-heels, including complex hairstyles. The shape and textures can be fully recovered including largely unseen regions such as the back of the subject. PIFu can also be naturally extended to multi-view input images (bottom row).

白质纤维聚类（WMFC）是白质细胞的重要策略，可以对健康和疾病中的白质连接进行定量分析。 WMFC通常以无监督的方式进行，而无需标记地面真相数据。尽管广泛使用的WMFC方法使用经典的机器学习技术显示出良好的性能，但深度学习的最新进展揭示了朝着快速有效的WMFC方向发展。在这项工作中，我们为WMFC，深纤维聚类（DFC）提出了一个新颖的深度学习框架，该框架解决了无监督的聚类问题，作为具有特定领域的借口任务，以预测成对的光纤距离。这使纤维表示能够在WMFC中学习已知的挑战，即聚类的敏感性对沿纤维的点排序的敏感性。我们设计了一种新颖的网络体系结构，该网络体系结构代表输入纤维作为点云，并允许从灰质拟合中纳入其他输入信息来源。因此，DFC利用有关白质纤维几何形状和灰质解剖结构的组合信息来改善纤维簇的解剖相干性。此外，DFC通过拒绝簇分配概率低的纤维来以自然方式进行异常去除。我们评估了三个独立获取的队列的DFC，包括来自220名性别，年龄（年轻和老年人）的220名个人的数据，以及不同的健康状况（健康对照和多种神经精神疾病）。我们将DFC与几种最先进的WMFC算法进行比较。实验结果表明，DFC在集群紧凑，泛化能力，解剖相干性和计算效率方面的表现出色。