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 the existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this article, 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 GNNs into four categories, namely, recurrent GNNs, convolutional GNNs, graph autoencoders, and spatial–temporal GNNs. We further discuss the applications of GNNs across various domains and summarize the open-source codes, benchmark data sets, and model evaluation of GNNs. Finally, we propose potential research directions in this rapidly growing field.

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A Comprehensive Survey on Graph Neural Networks

Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures (like the dependency trees of sentences and the scene graphs of images) is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are neural models that capture the dependence of graphs via message passing between the nodes of graphs. In recent years, variants of GNNs such as graph convolutional network (GCN), graph attention network (GAT), graph recurrent network (GRN) have demonstrated ground-breaking performances on many deep learning tasks. In this survey, we propose a general design pipeline for GNN models and discuss the variants of each component, systematically categorize the applications, and propose four open problems for future research.

Graph Neural Networks: A Review of Methods and Applications

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.

Deep Learning on Graphs: A Survey

Recent years have witnessed the emerging success of graph neural networks (GNNs) for modeling structured data. However, most GNNs are designed for homogeneous graphs, in which all nodes and edges belong to the same types, making it infeasible to represent heterogeneous structures. In this paper, we present the Heterogeneous Graph Transformer (HGT) architecture for modeling Web-scale heterogeneous graphs. To model heterogeneity, we design node- and edge-type dependent parameters to characterize the heterogeneous attention over each edge, empowering HGT to maintain dedicated representations for different types of nodes and edges. To handle Web-scale graph data, we design the heterogeneous mini-batch graph sampling algorithm—HGSampling—for efficient and scalable training. Extensive experiments on the Open Academic Graph of 179 million nodes and 2 billion edges show that the proposed HGT model consistently outperforms all the state-of-the-art GNN baselines by 9–21 on various downstream tasks. The dataset and source code of HGT are publicly available at https://github.com/acbull/pyHGT.

https://dl.acm.org/doi/pdf/10.1145/3366423.3380027

Heterogeneous Graph Transformer

Graph neural network, as a powerful graph representation technique based on deep learning, has shown superior performance and attracted considerable research interest. However, it has not been fully considered in graph neural network for heterogeneous graph which contains different types of nodes and links. The heterogeneity and rich semantic information bring great challenges for designing a graph neural network for heterogeneous graph. Recently, one of the most exciting advancements in deep learning is the attention mechanism, whose great potential has been well demonstrated in various areas. In this paper, we first propose a novel heterogeneous graph neural network based on the hierarchical attention, including node-level and semantic-level attentions. Specifically, the node-level attention aims to learn the importance between a node and its meta-path based neighbors, while the semantic-level attention is able to learn the importance of different meta-paths. With the learned importance from both node-level and semantic-level attention, the importance of node and meta-path can be fully considered. Then the proposed model can generate node embedding by aggregating features from meta-path based neighbors in a hierarchical manner. Extensive experimental results on three real-world heterogeneous graphs not only show the superior performance of our proposed model over the state-of-the-arts, but also demonstrate its potentially good interpretability for graph analysis.

Heterogeneous Graph Attention Network

Short text classification has been widely explored in news tagging to provide more efficient search strategies and more effective search results for information retrieval. However, most existing studies, concentrating on long text classification, deliver unsatisfactory performance on short texts due to the sparsity issue and the insufficiency of labeled data. In this article, we propose a novel heterogeneous graph neural network-based method for semi-supervised short text classification, leveraging full advantage of limited labeled data and large unlabeled data through information propagation along the graph. Specifically, we first present a flexible heterogeneous information network (HIN) framework for modeling short texts, which can integrate any type of additional information and meanwhile capture their relations to address the semantic sparsity. Then, we propose Heterogeneous Graph Attention networks (HGAT) to embed the HIN for short text classification based on a dual-level attention mechanism, including node-level and type-level attentions. To efficiently classify new coming texts that do not previously exist in the HIN, we extend our model HGAT for inductive learning, avoiding re-training the model on the evolving HIN. Extensive experiments on single-/multi-label classification demonstrates that our proposed model HGAT significantly outperforms state-of-the-art methods across the benchmark datasets under both transductive and inductive learning.

HGAT: Heterogeneous Graph Attention Networks for Semi-supervised Short Text Classification

Short text classification has found rich and critical applications in news and tweet tagging to help users find relevant information. Due to lack of labeled training data in many practical use cases, there is a pressing need for studying semi-supervised short text classification. Most existing studies focus on long texts and achieve unsatisfactory performance on short texts due to the sparsity and limited labeled data. In this paper, we propose a novel heterogeneous graph neural network based method for semi-supervised short text classification, leveraging full advantage of few labeled data and large unlabeled data through information propagation along the graph. In particular, we first present a flexible HIN (heterogeneous information network) framework for modeling the short texts, which can integrate any type of additional information as well as capture their relations to address the semantic sparsity. Then, we propose Heterogeneous Graph ATtention networks (HGAT) to embed the HIN for short text classification based on a dual-level attention mechanism, including node-level and type-level attentions. The attention mechanism can learn the importance of different neighboring nodes as well as the importance of different node (information) types to a current node. Extensive experimental results have demonstrated that our proposed model outperforms state-of-the-art methods across six benchmark datasets significantly.

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Heterogeneous Graph Attention Networks for Semi-supervised Short Text Classification

Graph Neural Networks (GNNs) have received considerable attention on graph-structured data learning for a wide variety of tasks. The well-designed propagation mechanism which has been demonstrated effective is the most fundamental part of GNNs. Although most of GNNs basically follow a message passing manner, litter effort has been made to discover and analyze their essential relations. In this paper, we establish a surprising connection between different propagation mechanisms with a unified optimization problem, showing that despite the proliferation of various GNNs, in fact, their proposed propagation mechanisms are the optimal solution optimizing a feature fitting function over a wide class of graph kernels with a graph regularization term. Our proposed unified optimization framework, summarizing the commonalities between several of the most representative GNNs, not only provides a macroscopic view on surveying the relations between different GNNs, but also further opens up new opportunities for flexibly designing new GNNs. With the proposed framework, we discover that existing works usually utilize naive graph convolutional kernels for feature fitting function, and we further develop two novel objective functions considering adjustable graph kernels showing low-pass or high-pass filtering capabilities respectively. Moreover, we provide the convergence proofs and expressive power comparisons for the proposed models. Extensive experiments on benchmark datasets clearly show that the proposed GNNs not only outperform the state-of-the-art methods but also have good ability to alleviate over-smoothing, and further verify the feasibility for designing GNNs with our unified optimization framework.

Interpreting and Unifying Graph Neural Networks with An Optimization Framework

Graph neural network (GNN), as a powerful graph representation technique based on deep learning, has shown superior performance and attracted considerable research interest. Recently, some works attempt to generalize GNN to heterogeneous graph which contains different types of nodes and links. Heterogeneous graph neural networks (HeteGNNs) usually follow two steps: aggregate neighbors via single meta-path and then aggregate rich semantics via multiple meta-paths. However, we discover an important semantic confusion phenomenon in HeteGNNs, i.e., with the growth of model depth, the learned node embeddings become indistinguishable, leading to the performance degradation of HeteGNNs. We explain semantic confusion by theoretically deriving that HeteGNNs and multiple meta-paths based random walk are essentially equivalent. Following the theoretical analysis, we propose a novel Heterogeneous graph Propagation Network (HPN) to alleviate the semantic confusion. Specically, the semantic propagation mechanism of HPN absorbes nodes local semantic with a proper weight during aggregating process, which makes HPN capture the characteristics of each node and learn distinguishable node embedding with deeper HeteGNN architecture. Then, the semantic fusion mechanism is designed to learn the importance of meta-path and fuse them judiciously. Extensive experimental results on three datasets show the superior performance of the proposed HPN over the state-of-the-arts.

Houye Ji

Papers

Heterogeneous Graph Attention Network

HGAT: Heterogeneous Graph Attention Networks for Semi-supervised Short Text Classification

Heterogeneous Graph Attention Networks for Semi-supervised Short Text Classification

Interpreting and Unifying Graph Neural Networks with An Optimization Framework

Heterogeneous Graph Propagation Network