A Comprehensive Survey of Graph Embedding: Problems, Techniques and Applications

Graph is an important data representation which appears in a wide diversity of real-world scenarios. Effective graph analytics provides users a deeper understanding of what is behind the data, and thus can benefit a lot of useful applications such as node classification, node recommendation, link prediction, etc. However, most graph analytics methods suffer the high computation and space cost. Graph embedding is an effective yet efficient way to solve the graph analytics problem. It converts the graph data into a low dimensional space in which the graph structural information and graph properties are maximally preserved. In this survey, we conduct a comprehensive review of the literature in graph embedding. We first introduce the formal definition of graph embedding as well as the related concepts. After that, we propose two taxonomies of graph embedding which correspond to what challenges exist in different graph embedding problem settings and how the existing work address these challenges in their solutions. Finally, we summarize the applications that graph embedding enables and suggest four promising future research directions in terms of computation efficiency, problem settings, techniques and application scenarios.Comment: A 20-page comprehensive survey of graph/network embedding for over 150+ papers till year 2018. It provides systematic categorization of problems, techniques and applications. Accepted by IEEE Transactions on Knowledge and Data Engineering (TKDE). Comments and suggestions are welcomed for continuously improving this surve

Graph Embedding Techniques, Applications, and Performance: A Survey

Graphs, such as social networks, word co-occurrence networks, and communication networks, occur naturally in various real-world applications. Analyzing them yields insight into the structure of society, language, and different patterns of communication. Many approaches have been proposed to perform the analysis. Recently, methods which use the representation of graph nodes in vector space have gained traction from the research community. In this survey, we provide a comprehensive and structured analysis of various graph embedding techniques proposed in the literature. We first introduce the embedding task and its challenges such as scalability, choice of dimensionality, and features to be preserved, and their possible solutions. We then present three categories of approaches based on factorization methods, random walks, and deep learning, with examples of representative algorithms in each category and analysis of their performance on various tasks. We evaluate these state-of-the-art methods on a few common datasets and compare their performance against one another. Our analysis concludes by suggesting some potential applications and future directions. We finally present the open-source Python library we developed, named GEM (Graph Embedding Methods, available at https://github.com/palash1992/GEM), which provides all presented algorithms within a unified interface to foster and facilitate research on the topic.Comment: Submitted to Knowledge Based Systems for revie

Deep Representation Learning for Social Network Analysis

Social network analysis is an important problem in data mining. A fundamental step for analyzing social networks is to encode network data into low-dimensional representations, i.e., network embeddings, so that the network topology structure and other attribute information can be effectively preserved. Network representation leaning facilitates further applications such as classification, link prediction, anomaly detection and clustering. In addition, techniques based on deep neural networks have attracted great interests over the past a few years. In this survey, we conduct a comprehensive review of current literature in network representation learning utilizing neural network models. First, we introduce the basic models for learning node representations in homogeneous networks. Meanwhile, we will also introduce some extensions of the base models in tackling more complex scenarios, such as analyzing attributed networks, heterogeneous networks and dynamic networks. Then, we introduce the techniques for embedding subgraphs. After that, we present the applications of network representation learning. At the end, we discuss some promising research directions for future work

Multimodal Deep Network Embedding with Integrated Structure and Attribute Information

Network embedding is the process of learning low-dimensional representations for nodes in a network, while preserving node features. Existing studies only leverage network structure information and focus on preserving structural features. However, nodes in real-world networks often have a rich set of attributes providing extra semantic information. It has been demonstrated that both structural and attribute features are important for network analysis tasks. To preserve both features, we investigate the problem of integrating structure and attribute information to perform network embedding and propose a Multimodal Deep Network Embedding (MDNE) method. MDNE captures the non-linear network structures and the complex interactions among structures and attributes, using a deep model consisting of multiple layers of non-linear functions. Since structures and attributes are two different types of information, a multimodal learning method is adopted to pre-process them and help the model to better capture the correlations between node structure and attribute information. We employ both structural proximity and attribute proximity in the loss function to preserve the respective features and the representations are obtained by minimizing the loss function. Results of extensive experiments on four real-world datasets show that the proposed method performs significantly better than baselines on a variety of tasks, which demonstrate the effectiveness and generality of our method.Comment: 15 pages, 10 figure

Scalable Graph Embeddings via Sparse Transpose Proximities

Graph embedding learns low-dimensional representations for nodes in a graph and effectively preserves the graph structure. Recently, a significant amount of progress has been made toward this emerging research area. However, there are several fundamental problems that remain open. First, existing methods fail to preserve the out-degree distributions on directed graphs. Second, many existing methods employ random walk based proximities and thus suffer from conflicting optimization goals on undirected graphs. Finally, existing factorization methods are unable to achieve scalability and non-linearity simultaneously. This paper presents an in-depth study on graph embedding techniques on both directed and undirected graphs. We analyze the fundamental reasons that lead to the distortion of out-degree distributions and to the conflicting optimization goals. We propose {\em transpose proximity}, a unified approach that solves both problems. Based on the concept of transpose proximity, we design \strap, a factorization based graph embedding algorithm that achieves scalability and non-linearity simultaneously. \strap makes use of the {\em backward push} algorithm to efficiently compute the sparse {\em Personalized PageRank (PPR)} as its transpose proximities. By imposing the sparsity constraint, we are able to apply non-linear operations to the proximity matrix and perform efficient matrix factorization to derive the embedding vectors. Finally, we present an extensive experimental study that evaluates the effectiveness of various graph embedding algorithms, and we show that \strap outperforms the state-of-the-art methods in terms of effectiveness and scalability.Comment: ACM SIGKDD201

FI-GRL: Fast Inductive Graph Representation Learning via Projection-Cost Preservation

Graph representation learning aims at transforming graph data into meaningful low-dimensional vectors to facilitate the employment of machine learning and data mining algorithms designed for general data. Most current graph representation learning approaches are transductive, which means that they require all the nodes in the graph are known when learning graph representations and these approaches cannot naturally generalize to unseen nodes. In this paper, we present a Fast Inductive Graph Representation Learning framework (FI-GRL) to learn nodes' low-dimensional representations. Our approach can obtain accurate representations for seen nodes with provable theoretical guarantees and can easily generalize to unseen nodes. Specifically, in order to explicitly decouple nodes' relations expressed by the graph, we transform nodes into a randomized subspace spanned by a random projection matrix. This stage is guaranteed to preserve the projection-cost of the normalized random walk matrix which is highly related to the normalized cut of the graph. Then feature extraction is achieved by conducting singular value decomposition on the obtained matrix sketch. By leveraging the property of projection-cost preservation on the matrix sketch, the obtained representation result is nearly optimal. To deal with unseen nodes, we utilize folding-in technique to learn their meaningful representations. Empirically, when the amount of seen nodes are larger than that of unseen nodes, FI-GRL always achieves excellent results. Our algorithm is fast, simple to implement and theoretically guaranteed. Extensive experiments on real datasets demonstrate the superiority of our algorithm on both efficacy and efficiency over both macroscopic level (clustering) and microscopic level (structural hole detection) applications.Comment: ICDM 2018, Full Versio

Deep Learning on Graphs: A Survey

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.Comment: Accepted by Transactions on Knowledge and Data Engineering. 24 pages, 11 figure

Unsupervised Inductive Graph-Level Representation Learning via Graph-Graph Proximity

We introduce a novel approach to graph-level representation learning, which is to embed an entire graph into a vector space where the embeddings of two graphs preserve their graph-graph proximity. Our approach, UGRAPHEMB, is a general framework that provides a novel means to performing graph-level embedding in a completely unsupervised and inductive manner. The learned neural network can be considered as a function that receives any graph as input, either seen or unseen in the training set, and transforms it into an embedding. A novel graph-level embedding generation mechanism called Multi-Scale Node Attention (MSNA), is proposed. Experiments on five real graph datasets show that UGRAPHEMB achieves competitive accuracy in the tasks of graph classification, similarity ranking, and graph visualization.Comment: IJCAI 2019 camera ready version with supplementary materia

Billion-scale Network Embedding with Iterative Random Projection

Network embedding, which learns low-dimensional vector representation for nodes in the network, has attracted considerable research attention recently. However, the existing methods are incapable of handling billion-scale networks, because they are computationally expensive and, at the same time, difficult to be accelerated by distributed computing schemes. To address these problems, we propose RandNE (Iterative Random Projection Network Embedding), a novel and simple billion-scale network embedding method. Specifically, we propose a Gaussian random projection approach to map the network into a low-dimensional embedding space while preserving the high-order proximities between nodes. To reduce the time complexity, we design an iterative projection procedure to avoid the explicit calculation of the high-order proximities. Theoretical analysis shows that our method is extremely efficient, and friendly to distributed computing schemes without any communication cost in the calculation. We also design a dynamic updating procedure which can efficiently incorporate the dynamic changes of the networks without error aggregation. Extensive experimental results demonstrate the efficiency and efficacy of RandNE over state-of-the-art methods in several tasks including network reconstruction, link prediction and node classification on multiple datasets with different scales, ranging from thousands to billions of nodes and edges.Comment: Accepted by ICDM 2018. 10 pages, 8 figures, 2018 IEEE International Conference on Data Mining (ICDM

Multi-Level Network Embedding with Boosted Low-Rank Matrix Approximation

As opposed to manual feature engineering which is tedious and difficult to scale, network representation learning has attracted a surge of research interests as it automates the process of feature learning on graphs. The learned low-dimensional node vector representation is generalizable and eases the knowledge discovery process on graphs by enabling various off-the-shelf machine learning tools to be directly applied. Recent research has shown that the past decade of network embedding approaches either explicitly factorize a carefully designed matrix to obtain the low-dimensional node vector representation or are closely related to implicit matrix factorization, with the fundamental assumption that the factorized node connectivity matrix is low-rank. Nonetheless, the global low-rank assumption does not necessarily hold especially when the factorized matrix encodes complex node interactions, and the resultant single low-rank embedding matrix is insufficient to capture all the observed connectivity patterns. In this regard, we propose a novel multi-level network embedding framework BoostNE, which can learn multiple network embedding representations of different granularity from coarse to fine without imposing the prevalent global low-rank assumption. The proposed BoostNE method is also in line with the successful gradient boosting method in ensemble learning as multiple weak embeddings lead to a stronger and more effective one. We assess the effectiveness of the proposed BoostNE framework by comparing it with existing state-of-the-art network embedding methods on various datasets, and the experimental results corroborate the superiority of the proposed BoostNE network embedding framework