Deep learning has achieved promising progress in many fields such as computer vision and natural language processing. The data in these tasks are usually represented in the Euclidean domain. However, many learning tasks require dealing with non-Euclidean graph data that contains rich relational information between elements, such as modeling physical systems, learning molecular fingerprints, predicting protein interface, etc. Graph neural networks (GNNs) are deep learning-based methods that operate on graph domains. Due to its convincing performance and high interpretability, GNN has recently been a widely applied graph analysis method.

The book provides a comprehensive introduction to the basic concepts, models, and applications of graph neural networks. It starts with the basics of mathematics and neural networks. In the first chapters, it gives an introduction to the basic concepts of GNNs, which aims to provide a general overview for readers. Then it introduces different variants of GNNs: graph convolutional networks, graph recurrent networks, graph attention networks, graph residual networks, and several general frameworks. These variants tend to generalize different deep learning techniques into graphs, such as convolutional neural network, recurrent neural network, attention mechanism, and skip connections. Further, the book introduces different applications of GNNs in structural scenarios (physics, chemistry, knowledge graph), non-structural scenarios (image, text) and other scenarios (generative models, combinatorial optimization). Finally, the book lists relevant datasets, open source platforms, and implementations of GNNs.

This book is organized as follows. After an overview in Chapter 1, we introduce some basic knowledge of math and graph theory in Chapter 2. We show the basics of neural networks in Chapter 3 and then give a brief introduction to the vanilla GNN in Chapter 4. Four types of models are introduced in Chapters 5, 6, 7, and 8, respectively. Other variants for different graph types and advanced training methods are introduced in Chapters 9 and 10. Then we propose several general GNN frameworks in Chapter 11. Applications of GNN in structural scenarios, nonstructural scenarios, and other scenarios are presented in Chapters 12, 13, and 14. And finally, we provide some open resources in Chapter 15 and conclude the book in Chapter 16.

Zhiyuan Liu and Jie Zhou

March 2020

Acknowledgments

We would like to thank those who contributed and gave advice in individual chapters:

Chapter 1: Ganqu Cui, Zhengyan Zhang

Chapter 2: Yushi Bai

Chapter 3: Yushi Bai

Chapter 4: Zhengyan Zhang

Chapter 9: Zhengyan Zhang, Ganqu Cui, Shengding Hu

Chapter 10: Ganqu Cui

Chapter 12: Ganqu Cui

Chapter 13: Ganqu Cui, Zhengyan Zhang

Chapter 14: Ganqu Cui, Zhengyan Zhang

Chapter 15: Yushi Bai, Shengding Hu

We would also thank those who provide feedback on the content of the book: Cheng Yang, Ruidong Wu, Chang Shu, Yufeng Du, and Jiayou Zhang.

Finally, we would like to thank all the editors, reviewers, and staff who helped with the publication of the book. Without you, this book would not have been possible.

Zhiyuan Liu and Jie Zhou

March 2020

CHAPTER 1

Introduction

Graphs are a kind of data structure which models a set of objects (nodes) and their relationships (edges). Recently, researches of analyzing graphs with machine learning have received more and more attention because of the great expressive power of graphs, i.e., graphs can be used as denotation of a large number of systems across various areas including social science (social networks) [Hamilton et al., 2017b, Kipf and Welling, 2017], natural science (physical systems [Battaglia et al., 2016, Sanchez et al., 2018] and protein-protein interaction networks [Fout et al., 2017]), knowledge graphs [Hamaguchi et al., 2017] and many other research areas [Khalil et al., 2017]. As a unique non-Euclidean data structure for machine learning, graph draws attention on analyses that focus on node classification, link prediction, and clustering. Graph neural networks (GNNs) are deep learning-based methods that operate on graph domain. Due to its convincing performance and high interpretability, GNN has been a widely applied graph analysis method recently. In the following paragraphs, we will illustrate the fundamental motivations of GNNs.

1.1 MOTIVATIONS

1.1.1 CONVOLUTIONAL NEURAL NETWORKS

Firstly, GNNs are motivated by convolutional neural networks (CNNs) LeCun et al. [1998]. CNNs is capable of extracting and composing multi-scale localized spatial features for features of high representation power, which have result in breakthroughs in almost all machine learning areas and the revolution of deep learning. As we go deeper into CNNs and graphs, we find the keys of CNNs: local connection, shared weights, and the use of multi-layer [LeCun et al., 2015]. These are also of great importance in solving problems of graph domain, because (1) graphs are the most typical locally connected structure, (2) shared weights reduce the computational cost compared with traditional spectral graph theory [Chung and Graham, 1997], (3) multi-layer structure is the key to deal with hierarchical patterns, which captures the features of various sizes. However, CNNs can only operate on regular Euclidean data like images (2D grid) and text (1D sequence), which can also be regarded as instances of graphs. Therefore, it is straightforward to think of finding the generalization of CNNs to graphs. As shown in Скачать книгу