网络在许多现实世界应用程序中无处不在（例如，编码信任/不信任关系的社交网络，由时间序列数据引起的相关网络）。尽管许多网络都是签名或指示的，或者两者都在图形神经网络（GNN）上缺少统一的软件包，专门为签名和定向网络设计。在本文中，我们提出了Pytorch几何签名的指示，这是一个填补此空白的软件包。在此过程中，我们还提供了简短的审查调查，以分析签名和定向网络的分析，讨论相关实验中使用的数据，提供提出的方法概述，并通过实验评估实施方法。深度学习框架包括易于使用的GNN模型，合成和现实世界数据，以及针对签名和定向网络的特定任务评估指标和损失功能。作为Pytorch几何形状的扩展库，我们提出的软件由开源版本，详细文档，连续集成，单位测试和代码覆盖范围检查维护。我们的代码可在\ url {https://github.com/sherylhyx/pytorch_geometric_signed_directed}上公开获得。

在现实世界中，签名的定向网络无处不在。但是，对于分析此类网络的方法，较少的工作提出了频谱图神经网络（GNN）方法。在这里，我们介绍了一个签名的定向拉普拉斯矩阵，我们称之为磁性签名的laplacian，作为在签名的图表上签名的laplacian的自然概括，在有向图上的磁Laplacian。然后，我们使用此矩阵来构建一种新型的光谱GNN结构，并在节点聚类和链接预测任务上进行广泛的实验。在这些实验中，我们考虑了与签名信息有关的任务，与定向信息相关的任务以及与签名和定向信息有关的任务。我们证明，我们提出的光谱GNN有效地合并了签名和定向信息，并在广泛的数据集中获得领先的性能。此外，我们提供了一种新颖的合成网络模型，我们称之为签名的定向随机块模型，以及许多基于财务时间序列中铅滞后关系的新型现实世界数据集。

图形卷积网络（GCN）及其变体是为仅包含正链的无符号图设计的。许多现有的GCN来自位于（未签名）图的信号的光谱域分析，在每个卷积层中，它们对输入特征进行低通滤波，然后进行可学习的线性转换。它们扩展到具有正面和负面链接的签名图，引发了多个问题，包括计算不规则性和模棱两可的频率解释，从而使计算有效的低通滤波器的设计具有挑战性。在本文中，我们通过签名图的光谱分析来解决这些问题，并提出了两个不同的图形神经网络，一个人仅保留低频信息，并且还保留了高频信息。我们进一步引入了磁性签名的拉普拉斯式，并使用其特征成分进行定向签名图的光谱分析。我们在签名图上测试了节点分类的方法，并链接符号预测任务并实现最先进的性能。

In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive growth of promising techniques that have been applied with success to computer science, mathematics, biology, physics and chemistry. But for any successful field to become mainstream and reliable, benchmarks must be developed to quantify progress. This led us in March 2020 to release a benchmark framework that i) comprises of a diverse collection of mathematical and real-world graphs, ii) enables fair model comparison with the same parameter budget to identify key architectures, iii) has an open-source, easy-to-use and reproducible code infrastructure, and iv) is flexible for researchers to experiment with new theoretical ideas. As of December 2022, the GitHub repository has reached 2,000 stars and 380 forks, which demonstrates the utility of the proposed open-source framework through the wide usage by the GNN community. In this paper, we present an updated version of our benchmark with a concise presentation of the aforementioned framework characteristics, an additional medium-sized molecular dataset AQSOL, similar to the popular ZINC, but with a real-world measured chemical target, and discuss how this framework can be leveraged to explore new GNN designs and insights. As a proof of value of our benchmark, we study the case of graph positional encoding (PE) in GNNs, which was introduced with this benchmark and has since spurred interest of exploring more powerful PE for Transformers and GNNs in a robust experimental setting.

图表表示学习是一种快速增长的领域，其中一个主要目标是在低维空间中产生有意义的图形表示。已经成功地应用了学习的嵌入式来执行各种预测任务，例如链路预测，节点分类，群集和可视化。图表社区的集体努力提供了数百种方法，但在所有评估指标下没有单一方法擅长，例如预测准确性，运行时间，可扩展性等。该调查旨在通过考虑算法来评估嵌入方法的所有主要类别的图表变体，参数选择，可伸缩性，硬件和软件平台，下游ML任务和多样化数据集。我们使用包含手动特征工程，矩阵分解，浅神经网络和深图卷积网络的分类法组织了图形嵌入技术。我们使用广泛使用的基准图表评估了节点分类，链路预测，群集和可视化任务的这些类别算法。我们在Pytorch几何和DGL库上设计了我们的实验，并在不同的多核CPU和GPU平台上运行实验。我们严格地审查了各种性能指标下嵌入方法的性能，并总结了结果。因此，本文可以作为比较指南，以帮助用户选择最适合其任务的方法。

This paper introduces SigMaNet, a generalized Graph Convolutional Network (GCN) capable of handling both undirected and directed graphs with weights not restricted in sign nor magnitude. The cornerstone of SigMaNet is the Sign-Magnetic Laplacian ($L^{\sigma}$), a new Laplacian matrix that we introduce ex novo in this work. $L^{\sigma}$ allows us to bridge a gap in the current literature by extending the theory of spectral GCNs to (directed) graphs with both positive and negative weights. $L^{\sigma}$ exhibits several desirable properties not enjoyed by other Laplacian matrices on which several state-of-the-art architectures are based, among which encoding the edge direction and weight in a clear and natural way that is not negatively affected by the weight magnitude. $L^{\sigma}$ is also completely parameter-free, which is not the case of other Laplacian operators such as, e.g., the Magnetic Laplacian. The versatility and the performance of our proposed approach is amply demonstrated via computational experiments. Indeed, our results show that, for at least a metric, SigMaNet achieves the best performance in 15 out of 21 cases and either the first- or second-best performance in 21 cases out of 21, even when compared to architectures that are either more complex or that, due to being designed for a narrower class of graphs, should -- but do not -- achieve a better performance.

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

Clustering is a fundamental problem in network analysis that finds closely connected groups of nodes and separates them from other nodes in the graph, while link prediction is to predict whether two nodes in a network are likely to have a link. The definition of both naturally determines that clustering must play a positive role in obtaining accurate link prediction tasks. Yet researchers have long ignored or used inappropriate ways to undermine this positive relationship. In this article, We construct a simple but efficient clustering-driven link prediction framework(ClusterLP), with the goal of directly exploiting the cluster structures to obtain connections between nodes as accurately as possible in both undirected graphs and directed graphs. Specifically, we propose that it is easier to establish links between nodes with similar representation vectors and cluster tendencies in undirected graphs, while nodes in a directed graphs can more easily point to nodes similar to their representation vectors and have greater influence in their own cluster. We customized the implementation of ClusterLP for undirected and directed graphs, respectively, and the experimental results using multiple real-world networks on the link prediction task showed that our models is highly competitive with existing baseline models. The code implementation of ClusterLP and baselines we use are available at https://github.com/ZINUX1998/ClusterLP.

Graphs are ubiquitous in nature and can therefore serve as models for many practical but also theoretical problems. For this purpose, they can be defined as many different types which suitably reflect the individual contexts of the represented problem. To address cutting-edge problems based on graph data, the research field of Graph Neural Networks (GNNs) has emerged. Despite the field's youth and the speed at which new models are developed, many recent surveys have been published to keep track of them. Nevertheless, it has not yet been gathered which GNN can process what kind of graph types. In this survey, we give a detailed overview of already existing GNNs and, unlike previous surveys, categorize them according to their ability to handle different graph types and properties. We consider GNNs operating on static and dynamic graphs of different structural constitutions, with or without node or edge attributes. Moreover, we distinguish between GNN models for discrete-time or continuous-time dynamic graphs and group the models according to their architecture. We find that there are still graph types that are not or only rarely covered by existing GNN models. We point out where models are missing and give potential reasons for their absence.

We present the OPEN GRAPH BENCHMARK (OGB), a diverse set of challenging and realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine learning (ML) research. OGB datasets are large-scale, encompass multiple important graph ML tasks, and cover a diverse range of domains, ranging from social and information networks to biological networks, molecular graphs, source code ASTs, and knowledge graphs. For each dataset, we provide a unified evaluation protocol using meaningful application-specific data splits and evaluation metrics. In addition to building the datasets, we also perform extensive benchmark experiments for each dataset. Our experiments suggest that OGB datasets present significant challenges of scalability to large-scale graphs and out-of-distribution generalization under realistic data splits, indicating fruitful opportunities for future research. Finally, OGB provides an automated end-to-end graph ML pipeline that simplifies and standardizes the process of graph data loading, experimental setup, and model evaluation. OGB will be regularly updated and welcomes inputs from the community. OGB datasets as well as data loaders, evaluation scripts, baseline code, and leaderboards are publicly available at https://ogb.stanford.edu.

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.

Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs-a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DIFFPOOL, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DIFFPOOL learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DIFFPOOL yields an average improvement of 5-10% accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark data sets.

图神经网络（GNN）在节点分类任务上取得了巨大成功。尽管对开发和评估GNN具有广泛的兴趣，但它们已经通过有限的基准数据集进行了评估。结果，现有的GNN评估缺乏来自图的各种特征的细粒分析。在此激励的情况下，我们对合成图生成器进行了广泛的实验，该实验可以生成具有控制特征以进行细粒分析的图形。我们的实证研究阐明了带有节点类标签的真实图形标签的四个主要特征的GNN的优势和劣势，即1）类规模分布（平衡与失衡），2）等级之间的边缘连接比例（均质VS之间）异性词），3）属性值（偏见与随机），4）图形大小（小与大）。此外，为了促进对GNN的未来研究，我们公开发布了我们的代码库，该代码库允许用户用各种图表评估各种GNN。我们希望这项工作为未来的研究提供有趣的见解。

根据数据的性质，有几种类型的图形。定向图具有链接的方向，签名的图具有链接类型，例如正和负面。签名的定向图是两者兼有的最复杂和信息的。签名有向图的图形卷积尚未得到太多。尽管已经提供了许多图形卷积研究，但大多数是为无方向或未签名设计的。在本文中，我们研究了一个用于签名的有向图的光谱图卷积网络。我们提出了一个新型的复杂居式邻接矩阵，该矩阵通过复数字编码图形信息。复数数字代表通过阶段和大小的链路方向，符号和连通性。然后，我们定义了带有Hermitian基质的磁性laplacian，并证明其阳性半限体性质。最后，我们介绍了签名的有向图卷积网络（SD-GCN）。据我们所知，这是带有符号的图形的第一频谱卷积。此外，与专为特定图形类型设计的现有卷积不同，该模型具有可应用于任何图的通用性，包括无方向性，指示或签名。用四个现实世界图评估了所提出的模型的性能。在链接标志预测的任务中，它的表现优于所有其他最新图形卷积。

Graph Neural Networks (GNNs) have become increasingly important in recent years due to their state-of-the-art performance on many important downstream applications. Existing GNNs have mostly focused on learning a single node representation, despite that a node often exhibits polysemous behavior in different contexts. In this work, we develop a persona-based graph neural network framework called PersonaSAGE that learns multiple persona-based embeddings for each node in the graph. Such disentangled representations are more interpretable and useful than a single embedding. Furthermore, PersonaSAGE learns the appropriate set of persona embeddings for each node in the graph, and every node can have a different number of assigned persona embeddings. The framework is flexible enough and the general design helps in the wide applicability of the learned embeddings to suit the domain. We utilize publicly available benchmark datasets to evaluate our approach and against a variety of baselines. The experiments demonstrate the effectiveness of PersonaSAGE for a variety of important tasks including link prediction where we achieve an average gain of 15% while remaining competitive for node classification. Finally, we also demonstrate the utility of PersonaSAGE with a case study for personalized recommendation of different entity types in a data management platform.

图形神经网络（GNN）已在许多图分析任务（例如节点分类和链接预测）上实现了最新结果。然而，事实证明，图形群集等图形上的重要无监督问题对GNN的进步具有更大的抵抗力。图群集的总体目标与GNN中的节点合并相同 - 这是否意味着GNN池方法在聚类图上做得很好？令人惊讶的是，答案是没有的 - 当前的GNN合并方法通常无法恢复群集结构，而在简单的基线（例如应用于学习的表示形式上的K-均值）良好工作的情况下。我们通过仔细设计一组实验来进一步研究，以研究图形结构和属性数据中的不同信噪比情景。为了解决这些方法在聚类中的性能不佳，我们引入了深层模块化网络（DMON），这是一种受群集质量模块化量度启发的无监督池方法，并显示了它如何解决现实世界图的挑战性聚类结构的恢复。同样，在现实世界中，我们表明DMON产生的高质量簇与地面真相标签密切相关，从而实现了最先进的结果，比不同指标的其他合并方法提高了40％以上。

图表神经网络（GNNS）最近在人工智能（AI）领域的普及，这是由于它们作为输入数据相对非结构化数据类型的独特能力。尽管GNN架构的一些元素在概念上类似于传统神经网络（以及神经网络变体）的操作中，但是其他元件代表了传统深度学习技术的偏离。本教程通过整理和呈现有关GNN最常见和性能变种的动机，概念，数学和应用的细节，将GNN的权力和新颖性暴露给AI从业者。重要的是，我们简明扼要地向实际示例提出了本教程，从而为GNN的主题提供了实用和可访问的教程。

图表可以模拟实体之间的复杂交互，它在许多重要的应用程序中自然出现。这些应用程序通常可以投入到标准图形学习任务中，其中关键步骤是学习低维图表示。图形神经网络（GNN）目前是嵌入方法中最受欢迎的模型。然而，邻域聚合范例中的标准GNN患有区分\ EMPH {高阶}图形结构的有限辨别力，而不是\ EMPH {低位}结构。为了捕获高阶结构，研究人员求助于主题和开发的基于主题的GNN。然而，现有的基于主基的GNN仍然仍然遭受较少的辨别力的高阶结构。为了克服上述局限性，我们提出了一个新颖的框架，以更好地捕获高阶结构的新框架，铰接于我们所提出的主题冗余最小化操作员和注射主题组合的新颖框架。首先，MGNN生成一组节点表示W.R.T.每个主题。下一阶段是我们在图案中提出的冗余最小化，该主题在彼此相互比较并蒸馏出每个主题的特征。最后，MGNN通过组合来自不同图案的多个表示来执行节点表示的更新。特别地，为了增强鉴别的功率，MGNN利用重新注射功能来组合表示的函数w.r.t.不同的主题。我们进一步表明，我们的拟议体系结构增加了GNN的表现力，具有理论分析。我们展示了MGNN在节点分类和图形分类任务上的七个公共基准上表现出最先进的方法。

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）通过考虑其内在的几何形状来扩展神经网络的成功到图形结构化数据。尽管根据图表学习基准的集合，已经对开发具有卓越性能的GNN模型进行了广泛的研究，但目前尚不清楚其探测给定模型的哪些方面。例如，他们在多大程度上测试模型利用图形结构与节点特征的能力？在这里，我们开发了一种原则性的方法来根据$ \ textit {敏感性配置文件} $进行基准测试数据集，该方法基于由于图形扰动的集合而导致的GNN性能变化了多少。我们的数据驱动分析提供了对GNN利用哪些基准测试数据特性的更深入的了解。因此，我们的分类法可以帮助选择和开发适当的图基准测试，并更好地评估未来的GNN方法。最后，我们在$ \ texttt {gtaxogym} $软件包中的方法和实现可扩展到多个图形预测任务类型和未来数据集。