Graph neural networks (GNNs) are widely used for modeling complex interactions between entities represented as vertices of a graph. Despite recent efforts to theoretically analyze the expressive power of GNNs, a formal characterization of their ability to model interactions is lacking. The current paper aims to address this gap. Formalizing strength of interactions through an established measure known as separation rank, we quantify the ability of certain GNNs to model interaction between a given subset of vertices and its complement, i.e. between sides of a given partition of input vertices. Our results reveal that the ability to model interaction is primarily determined by the partition's walk index -- a graph-theoretical characteristic that we define by the number of walks originating from the boundary of the partition. Experiments with common GNN architectures corroborate this finding. As a practical application of our theory, we design an edge sparsification algorithm named Walk Index Sparsification (WIS), which preserves the ability of a GNN to model interactions when input edges are removed. WIS is simple, computationally efficient, and markedly outperforms alternative methods in terms of induced prediction accuracy. More broadly, it showcases the potential of improving GNNs by theoretically analyzing the interactions they can model.

为了在深度学习中解释隐性正则化时，给予了矩阵和张量因子化的突出重点，这与简化的神经网络相对应。结果表明，这些模型分别表现出对低基质和张量排名的隐式趋势。当前的论文理论上绘制了更接近实际的深度学习，从理论上分析了分层张分解中的隐式正则化，该模型等同于某些深卷积神经网络。通过动态系统镜头，我们克服了与层次结构相关的挑战，并建立了对低层次张量级别的隐性正则化。这转化为相关卷积网络对区域的隐性正则化。受我们的理论的启发，我们设计了明确的正则化，阻碍了区域性，并证明了其在需要建筑变化的传统智慧的情况下，可以改善现代卷积网络在非本地任务上的性能。我们的工作突出了通过对其隐式正则化的理论分析来增强神经网络的潜力。

近年来，基于Weisfeiler-Leman算法的算法和神经架构，是一个众所周知的Graph同构问题的启发式问题，它成为具有图形和关系数据的机器学习的强大工具。在这里，我们全面概述了机器学习设置中的算法的使用，专注于监督的制度。我们讨论了理论背景，展示了如何将其用于监督的图形和节点表示学习，讨论最近的扩展，并概述算法的连接（置换 - ）方面的神经结构。此外，我们概述了当前的应用和未来方向，以刺激进一步的研究。

尽管（消息通话）图形神经网络在图形或一般关系数据上近似置换量等函数方面具有明显的局限性，但更具表现力的高阶图神经网络不会扩展到大图。他们要么在$ k $ - 订单张量子上操作，要么考虑所有$ k $ - 节点子图，这意味着在内存需求中对$ k $的指数依赖，并且不适合图形的稀疏性。通过为图同构问题引入新的启发式方法，我们设计了一类通用的，置换式的图形网络，与以前的体系结构不同，该网络在表达性和可伸缩性之间提供了细粒度的控制，并适应了图的稀疏性。这些体系结构与监督节点和图形级别的标准高阶网络以及回归体系中的标准高阶图网络相比大大减少了计算时间，同时在预测性能方面显着改善了标准图神经网络和图形内核体系结构。

Pre-publication draft of a book to be published byMorgan & Claypool publishers. Unedited version released with permission. All relevant copyrights held by the author and publisher extend to this pre-publication draft.

在处理大规模网络和关系数据时，降低图是基本的。它们可以通过在粗糙的结构中求解它们来缩小高度计算影响的尺寸。同时，图减少起着在图神经网络中合并层的作用，从结构中提取多分辨率表示。在这些情况下，还原机制保留距离关系和拓扑特性的能力似乎是基本的，以及可扩展性，使其能够应用于实际大小的问题。在本文中，我们基于最大重量$ k $独立的集合的图理论概念引入了图形粗化机制，从而提供了一种贪婪的算法，该算法允许在GPU上有效地并行实现。我们的方法是常规数据（图像，序列）中的第一个图形结构化对应物。我们证明了在路径长度上的失真界限的理论保证，以及在污垢图中保留关键拓扑特性的能力。我们利用这些概念来定义我们在图形分类任务中经验评估的图表合并机制，表明它与文献中的合并方法进行了比较。

最近出现了许多子图增强图神经网络（GNN），可证明增强了标准（消息通话）GNN的表达能力。但是，对这些方法之间的相互关系和weisfeiler层次结构的关系有限。此外，当前的方法要么使用给定尺寸的所有子图，要随机均匀地对其进行采样，或者使用手工制作的启发式方法，而不是学习以数据驱动的方式选择子图。在这里，我们提供了一种统一的方法来研究此类体系结构，通过引入理论框架并扩展了亚图增强GNN的已知表达结果。具体而言，我们表明，增加子图的大小总是会增加表达能力，并通过将它们与已建立的$ k \ text { - } \ Mathsf {Wl} $ hierArchy联系起来，从而更好地理解其局限性。此外，我们还使用最近通过复杂的离散概率分布进行反向传播的方法探索了学习对子图进行采样的不同方法。从经验上讲，我们研究了不同子图增强的GNN的预测性能，表明我们的数据驱动体系结构与非DATA驱动的亚图增强图形神经网络相比，在标准基准数据集上提高了对标准基准数据集的预测准确性，同时减少了计算时间。

Knowledge graphs, modeling multi-relational data, improve numerous applications such as question answering or graph logical reasoning. Many graph neural networks for such data emerged recently, often outperforming shallow architectures. However, the design of such multi-relational graph neural networks is ad-hoc, driven mainly by intuition and empirical insights. Up to now, their expressivity, their relation to each other, and their (practical) learning performance is poorly understood. Here, we initiate the study of deriving a more principled understanding of multi-relational graph neural networks. Namely, we investigate the limitations in the expressive power of the well-known Relational GCN and Compositional GCN architectures and shed some light on their practical learning performance. By aligning both architectures with a suitable version of the Weisfeiler-Leman test, we establish under which conditions both models have the same expressive power in distinguishing non-isomorphic (multi-relational) graphs or vertices with different structural roles. Further, by leveraging recent progress in designing expressive graph neural networks, we introduce the $k$-RN architecture that provably overcomes the expressiveness limitations of the above two architectures. Empirically, we confirm our theoretical findings in a vertex classification setting over small and large multi-relational graphs.

消息传递神经网络（MPNNS）是由于其简单性和可扩展性而大部分地进行图形结构数据的深度学习的领先架构。不幸的是，有人认为这些架构的表现力有限。本文提出了一种名为Comifariant Subgraph聚合网络（ESAN）的新颖框架来解决这个问题。我们的主要观察是，虽然两个图可能无法通过MPNN可区分，但它们通常包含可区分的子图。因此，我们建议将每个图形作为由某些预定义策略导出的一组子图，并使用合适的等分性架构来处理它。我们为图同构同构同构造的1立维Weisfeiler-Leman（1-WL）测试的新型变体，并在这些新的WL变体方面证明了ESAN的表达性下限。我们进一步证明，我们的方法增加了MPNNS和更具表现力的架构的表现力。此外，我们提供了理论结果，描述了设计选择诸如子图选择政策和等效性神经结构的设计方式如何影响我们的架构的表现力。要处理增加的计算成本，我们提出了一种子图采样方案，可以将其视为我们框架的随机版本。关于真实和合成数据集的一套全面的实验表明，我们的框架提高了流行的GNN架构的表现力和整体性能。

子图GNNS是最近表达的图形神经网络（GNN）的一类，它们将图形图形为子图的集合。到目前为止，可能的子图GNN体系结构的设计空间及其基本理论属性仍然在很大程度上尚未探索。在本文中，我们研究了子图方法的最突出形式，该方法采用了基于节点的子图选择策略，例如自我网络或节点标记和删除。我们解决了两个中心问题：（1）这些方法的表达能力的上限是什么？ （2）在这些子图集上传递层的模棱两可的消息家族是什么？我们回答这些问题的第一步是一种新颖的对称分析，该分析表明，建模基于节点的子图集的对称性需要比以前的作品中所采用的对称组明显小。然后，该分析用于建立子图GNN和不变图网络（IGNS）之间的联系。我们通过首先通过3-WL来界定子图方法的表达能力，然后提出一个通用子图方法的一般家族，以将所有先前基于节点的子图GNN泛化。最后，我们设计了一个新颖的子图Gnn称为Sun，从理论上讲，该子gnn统一了以前的体系结构，同时在多个基准上提供了更好的经验性能。

在过去十年中，图形内核引起了很多关注，并在结构化数据上发展成为一种快速发展的学习分支。在过去的20年中，该领域发生的相当大的研究活动导致开发数十个图形内核，每个图形内核都对焦于图形的特定结构性质。图形内核已成功地成功地在广泛的域中，从社交网络到生物信息学。本调查的目标是提供图形内核的文献的统一视图。特别是，我们概述了各种图形内核。此外，我们对公共数据集的几个内核进行了实验评估，并提供了比较研究。最后，我们讨论图形内核的关键应用，并概述了一些仍有待解决的挑战。

作为建模复杂关系的强大工具，HyperGraphs从图表学习社区中获得了流行。但是，深度刻画学习中的常用框架专注于具有边缘独立的顶点权重（EIVW）的超图，而无需考虑具有具有更多建模功率的边缘依赖性顶点权重（EDVWS）的超图。为了弥补这一点，我们提出了一般的超图光谱卷积（GHSC），这是一个通用学习框架，不仅可以处理EDVW和EIVW HyperGraphs，而且更重要的是，理论上可以明确地利用现有强大的图形卷积神经网络（GCNN）明确说明，从而很大程度上可以释放。超图神经网络的设计。在此框架中，给定的无向GCNN的图形拉普拉斯被统一的HyperGraph Laplacian替换，该统一的HyperGraph Laplacian通过将我们所定义的广义超透明牌与简单的无向图等同起来，从随机的步行角度将顶点权重信息替换。来自各个领域的广泛实验，包括社交网络分析，视觉目标分类和蛋白质学习，证明了拟议框架的最新性能。

我们研究了图形表示学习的量子电路，并提出了等级的量子图电路（EQGCS），作为一类参数化量子电路，具有强大的关系感应偏压，用于学习图形结构数据。概念上，EQGCS作为量子图表表示学习的统一框架，允许我们定义几个有趣的子类，其中包含了现有的提案。就代表性权力而言，我们证明了感兴趣的子类是界限图域中的函数的普遍近似器，并提供实验证据。我们对量子图机学习方法的理论透视开启了许多方向以进行进一步的工作，可能导致具有超出古典方法的能力的模型。

Graph clustering is a fundamental problem in unsupervised learning, with numerous applications in computer science and in analysing real-world data. In many real-world applications, we find that the clusters have a significant high-level structure. This is often overlooked in the design and analysis of graph clustering algorithms which make strong simplifying assumptions about the structure of the graph. This thesis addresses the natural question of whether the structure of clusters can be learned efficiently and describes four new algorithmic results for learning such structure in graphs and hypergraphs. All of the presented theoretical results are extensively evaluated on both synthetic and real-word datasets of different domains, including image classification and segmentation, migration networks, co-authorship networks, and natural language processing. These experimental results demonstrate that the newly developed algorithms are practical, effective, and immediately applicable for learning the structure of clusters in real-world data.

Kernel matrices, as well as weighted graphs represented by them, are ubiquitous objects in machine learning, statistics and other related fields. The main drawback of using kernel methods (learning and inference using kernel matrices) is efficiency -- given $n$ input points, most kernel-based algorithms need to materialize the full $n \times n$ kernel matrix before performing any subsequent computation, thus incurring $\Omega(n^2)$ runtime. Breaking this quadratic barrier for various problems has therefore, been a subject of extensive research efforts. We break the quadratic barrier and obtain $\textit{subquadratic}$ time algorithms for several fundamental linear-algebraic and graph processing primitives, including approximating the top eigenvalue and eigenvector, spectral sparsification, solving linear systems, local clustering, low-rank approximation, arboricity estimation and counting weighted triangles. We build on the recent Kernel Density Estimation framework, which (after preprocessing in time subquadratic in $n$) can return estimates of row/column sums of the kernel matrix. In particular, we develop efficient reductions from $\textit{weighted vertex}$ and $\textit{weighted edge sampling}$ on kernel graphs, $\textit{simulating random walks}$ on kernel graphs, and $\textit{importance sampling}$ on matrices to Kernel Density Estimation and show that we can generate samples from these distributions in $\textit{sublinear}$ (in the support of the distribution) time. Our reductions are the central ingredient in each of our applications and we believe they may be of independent interest. We empirically demonstrate the efficacy of our algorithms on low-rank approximation (LRA) and spectral sparsification, where we observe a $\textbf{9x}$ decrease in the number of kernel evaluations over baselines for LRA and a $\textbf{41x}$ reduction in the graph size for spectral sparsification.

图形神经网络（GNNS）是关于图形机器学习问题的深度学习架构。最近已经表明，GNN的富有效力可以精确地由组合Weisfeiler-Leman算法和有限可变计数逻辑来表征。该对应关系甚至导致了对应于更高维度的WL算法的新的高阶GNN。本文的目的是解释GNN的这些描述性特征。

Although theoretical properties such as expressive power and over-smoothing of graph neural networks (GNN) have been extensively studied recently, its convergence property is a relatively new direction. In this paper, we investigate the convergence of one powerful GNN, Invariant Graph Network (IGN) over graphs sampled from graphons. We first prove the stability of linear layers for general $k$-IGN (of order $k$) based on a novel interpretation of linear equivariant layers. Building upon this result, we prove the convergence of $k$-IGN under the model of \citet{ruiz2020graphon}, where we access the edge weight but the convergence error is measured for graphon inputs. Under the more natural (and more challenging) setting of \citet{keriven2020convergence} where one can only access 0-1 adjacency matrix sampled according to edge probability, we first show a negative result that the convergence of any IGN is not possible. We then obtain the convergence of a subset of IGNs, denoted as IGN-small, after the edge probability estimation. We show that IGN-small still contains function class rich enough that can approximate spectral GNNs arbitrarily well. Lastly, we perform experiments on various graphon models to verify our statements.

Graph classification is an important area in both modern research and industry. Multiple applications, especially in chemistry and novel drug discovery, encourage rapid development of machine learning models in this area. To keep up with the pace of new research, proper experimental design, fair evaluation, and independent benchmarks are essential. Design of strong baselines is an indispensable element of such works. In this thesis, we explore multiple approaches to graph classification. We focus on Graph Neural Networks (GNNs), which emerged as a de facto standard deep learning technique for graph representation learning. Classical approaches, such as graph descriptors and molecular fingerprints, are also addressed. We design fair evaluation experimental protocol and choose proper datasets collection. This allows us to perform numerous experiments and rigorously analyze modern approaches. We arrive to many conclusions, which shed new light on performance and quality of novel algorithms. We investigate application of Jumping Knowledge GNN architecture to graph classification, which proves to be an efficient tool for improving base graph neural network architectures. Multiple improvements to baseline models are also proposed and experimentally verified, which constitutes an important contribution to the field of fair model comparison.

图形神经网络（GNNS）具有有限的表现力量，无法正确代表许多图形类。虽然更具表现力的图表表示学习（GRL）替代方案可以区分其中一些类，但它们明显难以实现，可能不会很好地扩展，并且尚未显示在现实世界任务中优于经过良好调整的GNN。因此，设计简单，可扩展和表现力的GRL架构，也实现了现实世界的改进仍然是一个开放的挑战。在这项工作中，我们展示了图形重建的程度 - 从其子图重建图形 - 可以减轻GRL架构目前面临的理论和实际问题。首先，我们利用图形重建来构建两个新的表达图表表示。其次，我们展示了图形重建如何提升任何GNN架构的表现力，同时是一个（可证明的）强大的归纳偏见，用于侵略性的侵略性。凭经验，我们展示了重建如何提高GNN的表现力 - 同时保持其与顶点的排列的不变性 - 通过解决原始GNN的七个图形属性任务而无法解决。此外，我们展示了如何在九世界基准数据集中提升最先进的GNN性能。

在处理表格数据时，基于回归和决策树的模型是一个流行的选择，因为与其他模型类别相比，它们在此类任务上提供了高精度及其易于应用。但是，在图形结构数据方面，当前的树学习算法不提供管理数据结构的工具，而不是依靠功能工程。在这项工作中，我们解决了上述差距，并引入了图形树（GTA），这是一个新的基于树的学习算法，旨在在图形上操作。 GTA既利用图形结构又利用了顶点的特征，并采用了一种注意机制，该机制允许决策专注于图形的子结构。我们分析了GTA模型，并表明它们比平原决策树更具表现力。我们还在多个图和节点预测基准上证明了GTA的好处。在这些实验中，GTA始终优于其他基于树的模型，并且通常优于其他类型的图形学习算法，例如图形神经网络（GNNS）和图核。最后，我们还为GTA提供了一种解释性机制，并证明它可以提供直观的解释。