The behavior of the network and its stability are governed by both dynamics of individual nodes as well as their topological interconnections. Attention mechanism as an integral part of neural network models was initially designed for natural language processing (NLP), and so far, has shown excellent performance in combining dynamics of individual nodes and the coupling strengths between them within a network. Despite undoubted impact of attention mechanism, it is not yet clear why some nodes of a network get higher attention weights. To come up with more explainable solutions, we tried to look at the problem from stability perspective. Based on stability theory, negative connections in a network can create feedback loops or other complex structures by allowing information to flow in the opposite direction. These structures play a critical role in the dynamics of a complex system and can contribute to abnormal synchronization, amplification, or suppression. We hypothesized that those nodes that are involved in organizing such structures can push the entire network into instability modes and therefore need higher attention during analysis. To test this hypothesis, attention mechanism along with spectral and topological stability analyses was performed on a real-world numerical problem, i.e., a linear Multi Input Multi Output state-space model of a piezoelectric tube actuator. The findings of our study suggest that the attention should be directed toward the collective behaviour of imbalanced structures and polarity-driven structural instabilities within the network. The results demonstrated that the nodes receiving more attention cause more instability in the system. Our study provides a proof of concept to understand why perturbing some nodes of a network may cause dramatic changes in the network dynamics.

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.

图表神经网络（GNNS）在各种机器学习任务中获得了表示学习的提高。然而，应用邻域聚合的大多数现有GNN通常在图中的图表上执行不良，其中相邻的节点属于不同的类。在本文中，我们示出了在典型的异界图中，边缘可以被引导，以及是否像是处理边缘，也可以使它们过度地影响到GNN模型的性能。此外，由于异常的限制，节点对来自本地邻域之外的类似节点的消息非常有益。这些激励我们开发一个自适应地学习图表的方向性的模型，并利用潜在的长距离相关性节点之间。我们首先将图拉普拉斯概括为基于所提出的特征感知PageRank算法向数字化，该算法同时考虑节点之间的图形方向性和长距离特征相似性。然后，Digraph Laplacian定义了一个图形传播矩阵，导致一个名为{\ em diglaciangcn}的模型。基于此，我们进一步利用节点之间的通勤时间测量的节点接近度，以便在拓扑级别上保留节点的远距离相关性。具有不同级别的10个数据集的广泛实验，同意级别展示了我们在节点分类任务任务中对现有解决方案的有效性。

许多复杂网络的结构包括其拓扑顶部的边缘方向性和权重。可以无缝考虑这些属性组合的网络分析是可取的。在本文中，我们研究了两个重要的这样的网络分析技术，即中心和聚类。采用信息流基于集群的模型，该模型本身就是在计算中心的信息定理措施时构建。我们的主要捐款包括马尔可夫熵中心的广义模型，灵活地调整节点度，边缘权重和方向的重要性，具有闭合形式的渐近分析。它导致一种新颖的两级图形聚类算法。中心分析有助于推理我们对给定图形的方法的适用性，并确定探索当地社区结构的“查询”节点，从而导致群集聚类机制。熵中心计算由我们的聚类算法摊销，使其计算得高效：与使用马尔可夫熵中心为聚类的先前方法相比，我们的实验表明了多个速度的速度。我们的聚类算法自然地继承了适应边缘方向性的灵活性，以及​​边缘权重和节点度之间的不同解释和相互作用。总的来说，本文不仅具有显着的理论和概念贡献，还转化为实际相关性的文物，产生新的，有效和可扩展的中心计算和图形聚类算法，其有效通过广泛的基准测试进行了验证。

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.

Inferring missing links or detecting spurious ones based on observed graphs, known as link prediction, is a long-standing challenge in graph data analysis. With the recent advances in deep learning, graph neural networks have been used for link prediction and have achieved state-of-the-art performance. Nevertheless, existing methods developed for this purpose are typically discriminative, computing features of local subgraphs around two neighboring nodes and predicting potential links between them from the perspective of subgraph classification. In this formalism, the selection of enclosing subgraphs and heuristic structural features for subgraph classification significantly affects the performance of the methods. To overcome this limitation, this paper proposes a novel and radically different link prediction algorithm based on the network reconstruction theory, called GraphLP. Instead of sampling positive and negative links and heuristically computing the features of their enclosing subgraphs, GraphLP utilizes the feature learning ability of deep-learning models to automatically extract the structural patterns of graphs for link prediction under the assumption that real-world graphs are not locally isolated. Moreover, GraphLP explores high-order connectivity patterns to utilize the hierarchical organizational structures of graphs for link prediction. Our experimental results on all common benchmark datasets from different applications demonstrate that the proposed method consistently outperforms other state-of-the-art methods. Unlike the discriminative neural network models used for link prediction, GraphLP is generative, which provides a new paradigm for neural-network-based link prediction.

复杂网络分析的最新进展为不同领域的应用开辟了广泛的可能性。网络分析的功能取决于节点特征。基于拓扑的节点特征是对局部和全局空间关系和节点连接结构的实现。因此，收集有关节点特征的正确信息和相邻节点的连接结构在复杂网络分析中在节点分类和链接预测中起着最突出的作用。目前的工作介绍了一种新的特征抽象方法，即基于嵌入匿名随机步行向量上的匿名随机步行，即过渡概率矩阵（TPM）。节点特征向量由从预定义半径中的一组步行中获得的过渡概率组成。过渡概率与局部连接结构直接相关，因此正确嵌入到特征向量上。在节点识别/分类中测试了建议的嵌入方法的成功，并在三个常用的现实世界网络上进行了链接预测。在现实世界网络中，具有相似连接结构的节点很常见。因此，从类似网络中获取新网络预测的信息是一种显着特征，它使所提出的算法在跨网络概括任务方面优于最先进的算法。

准确的交通状况预测为车辆环境协调和交通管制任务提供了坚实的基础。由于道路网络数据在空间分布中的复杂性以及深度学习方法的多样性，有效定义流量数据并充分捕获数据中复杂的空间非线性特征变得具有挑战性。本文将两种分层图池方法应用于流量预测任务，以减少图形信息冗余。首先，本文验证了流量预测任务中层次图池方法的有效性。分层图合并方法与其他基线在预测性能上形成鲜明对比。其次，应用了两种主流分层图池方法，节点群集池和节点下降池，用于分析流量预测中的优势和弱点。最后，对于上述图神经网络，本文比较了不同图网络输入对流量预测准确性的预测效应。分析和汇总定义图网络的有效方法。

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.

最近有一项激烈的活动在嵌入非常高维和非线性数据结构的嵌入中，其中大部分在数据科学和机器学习文献中。我们分四部分调查这项活动。在第一部分中，我们涵盖了非线性方法，例如主曲线，多维缩放，局部线性方法，ISOMAP，基于图形的方法和扩散映射，基于内核的方法和随机投影。第二部分与拓扑嵌入方法有关，特别是将拓扑特性映射到持久图和映射器算法中。具有巨大增长的另一种类型的数据集是非常高维网络数据。第三部分中考虑的任务是如何将此类数据嵌入中等维度的向量空间中，以使数据适合传统技术，例如群集和分类技术。可以说，这是算法机器学习方法与统计建模（所谓的随机块建模）之间的对比度。在论文中，我们讨论了两种方法的利弊。调查的最后一部分涉及嵌入$ \ mathbb {r}^ 2 $，即可视化中。提出了三种方法：基于第一部分，第二和第三部分中的方法，$ t $ -sne，UMAP和大节。在两个模拟数据集上进行了说明和比较。一个由嘈杂的ranunculoid曲线组成的三胞胎，另一个由随机块模型和两种类型的节点产生的复杂性的网络组成。

图形嵌入，代表数值向量的本地和全局邻域信息，是广泛的现实系统数学建模的关键部分。在嵌入算法中，事实证明，基于步行的随机算法非常成功。这些算法通过创建许多随机步行，并重新定义步骤来收集信息。创建随机步行是嵌入过程中最苛刻的部分。计算需求随着网络的规模而增加。此外，对于现实世界网络，考虑到相同基础上的所有节点，低度节点的丰度都会造成不平衡的数据问题。在这项工作中，提出了一种计算较少且节点连接性统一抽样方法。在提出的方法中，随机步行的数量与节点的程度成比例地创建。当将算法应用于大图时，所提出的算法的优点将变得更加增强。提出了使用两个网络（即Cora和Citeseer）进行比较研究。与固定数量的步行情况相比，提出的方法需要减少50％的计算工作，以达到节点分类和链接预测计算的相同精度。

Deep learning has been shown to be successful in a number of domains, ranging from acoustics, images, to natural language processing. However, applying deep learning to the ubiquitous graph data is non-trivial because of the unique characteristics of graphs. Recently, substantial research efforts have been devoted to applying deep learning methods to graphs, resulting in beneficial advances in graph analysis techniques. In this survey, we comprehensively review the different types of deep learning methods on graphs. We divide the existing methods into five categories based on their model architectures and training strategies: graph recurrent neural networks, graph convolutional networks, graph autoencoders, graph reinforcement learning, and graph adversarial methods. We then provide a comprehensive overview of these methods in a systematic manner mainly by following their development history. We also analyze the differences and compositions of different methods. Finally, we briefly outline the applications in which they have been used and discuss potential future research directions.

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。

图表是一个宇宙数据结构，广泛用于组织现实世界中的数据。像交通网络，社交和学术网络这样的各种实际网络网络可以由图表代表。近年来，目睹了在网络中代表顶点的快速发展，进入低维矢量空间，称为网络表示学习。表示学习可以促进图形数据上的新算法的设计。在本调查中，我们对网络代表学习的当前文献进行了全面审查。现有算法可以分为三组：浅埋模型，异构网络嵌入模型，图形神经网络的模型。我们为每个类别审查最先进的算法，并讨论这些算法之间的基本差异。调查的一个优点是，我们系统地研究了不同类别的算法底层的理论基础，这提供了深入的见解，以更好地了解网络表示学习领域的发展。

Graph Neural Networks (GNNs) have attracted increasing attention in recent years and have achieved excellent performance in semi-supervised node classification tasks. The success of most GNNs relies on one fundamental assumption, i.e., the original graph structure data is available. However, recent studies have shown that GNNs are vulnerable to the complex underlying structure of the graph, making it necessary to learn comprehensive and robust graph structures for downstream tasks, rather than relying only on the raw graph structure. In light of this, we seek to learn optimal graph structures for downstream tasks and propose a novel framework for semi-supervised classification. Specifically, based on the structural context information of graph and node representations, we encode the complex interactions in semantics and generate semantic graphs to preserve the global structure. Moreover, we develop a novel multi-measure attention layer to optimize the similarity rather than prescribing it a priori, so that the similarity can be adaptively evaluated by integrating measures. These graphs are fused and optimized together with GNN towards semi-supervised classification objective. Extensive experiments and ablation studies on six real-world datasets clearly demonstrate the effectiveness of our proposed model and the contribution of each component.

时间图代表实体之间的动态关系，并发生在许多现实生活中的应用中，例如社交网络，电子商务，通信，道路网络，生物系统等。他们需要根据其生成建模和表示学习的研究超出与静态图有关的研究。在这项调查中，我们全面回顾了近期针对处理时间图提出的神经时间依赖图表的学习和生成建模方法。最后，我们确定了现有方法的弱点，并讨论了我们最近发表的论文提格的研究建议[24]。

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.

马尔可夫链是一类概率模型，在定量科学中已广泛应用。这部分是由于它们的多功能性，但是可以通过分析探测的便利性使其更加复杂。本教程为马尔可夫连锁店提供了深入的介绍，并探索了它们与图形和随机步行的联系。我们利用从线性代数和图形论的工具来描述不同类型的马尔可夫链的过渡矩阵，特别着眼于探索与这些矩阵相对应的特征值和特征向量的属性。提出的结果与机器学习和数据挖掘中的许多方法有关，我们在各个阶段描述了这些方法。本文并没有本身就成为一项新颖的学术研究，而是提出了一些已知结果的集合以及一些新概念。此外，该教程的重点是向读者提供直觉，而不是正式的理解，并且仅假定对线性代数和概率理论的概念的基本曝光。因此，来自各种学科的学生和研究人员可以访问它。

图形神经网络（GNNS）依赖于图形结构来定义聚合策略，其中每个节点通过与邻居的信息组合来更新其表示。已知GNN的限制是，随着层数的增加，信息被平滑，压扁并且节点嵌入式变得无法区分，对性能产生负面影响。因此，实用的GNN模型雇用了几层，只能在每个节点周围的有限邻域利用图形结构。不可避免地，实际的GNN不会根据图的全局结构捕获信息。虽然有几种研究GNNS的局限性和表达性，但是关于图形结构数据的实际应用的问题需要全局结构知识，仍然没有答案。在这项工作中，我们通过向几个GNN模型提供全球信息并观察其对下游性能的影响来认证解决这个问题。我们的研究结果表明，全球信息实际上可以为共同的图形相关任务提供显着的好处。我们进一步确定了一项新的正规化策略，导致所有考虑的任务的平均准确性提高超过5％。

时间序列分析中产生的最重要的问题之一是分叉或变化点检测。也就是说，给定时间序列的集合在不同的参数上，何时基础动力系统的结构发生了变化？对于此任务，我们转向拓扑数据分析（TDA）的领域，该领域编码有关数据形状和结构的信息。近年来，利用TDA的工具用于信号处理任务（称为拓扑信号处理（TSP）（TSP））的想法在很大程度上通过标准管道获得了很多关注，该标准管道计算出Takens嵌入产生的点云的持久同源性。但是，此过程受到计算时间的限制，因为在这种情况下生成的简单复合物很大，但也有很多冗余数据。因此，我们求助于编码吸引子结构的最新方法，该方法构建了代表有关何时在状态空间区域之间动态系统传递的信息的序数分区网络（OPN）。结果是一个加权图，其结构编码有关基础吸引子的信息。我们以前的工作开始寻找以TDA适合的方式包装OPN信息的方法。但是，这项工作仅使用网络结构，而没有采取任何行动来编码其他加权信息。在本文中，我们采取下一步：构建管道来分析使用TDA的加权OPN，并表明该框架为系统中的噪声或扰动提供了更大的弹性，并提高了动态状态检测的准确性。